Your message dated Fri, 15 May 2020 10:18:48 +0000
with message-id <e1jzxqw-0003uj...@fasolo.debian.org>
and subject line Bug#959587: fixed in python-biopython 1.76+dfsg-2
has caused the Debian Bug report #959587,
regarding python-biopython: FTBFS: AssertionError: False is not true
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.)
--
959587: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=959587
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: python-biopython
Version: 1.76+dfsg-1
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200501 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> mkdir -p Tests_avoid
> for avoid in PAML_tools EmbossPhylipNew MSAProbs_tool NACCESS_tool
> PopGen_GenePop PopGen_GenePop_EasyController XXmotif_tool PDB_ResidueDepth
> mmtf mmtf_online BioSQL_MySQLdb BioSQL_psycopg2 \
> ; do \
> mv Tests/test_${avoid}.py Tests_avoid ; \
> done
> # For the doc package we need a clean testsuite without all the remaining
> files. So keep a clean copy here
> mkdir -p debian/tmp_tests
> cp -a Tests debian/tmp_tests
> # remove duplicated file
> rm -f debian/tmp_tests/Tests/Quality/example.fastq.gz
> # We also keep the tests we need to avoid for later inspection
> cp -a Tests_avoid debian/tmp_tests
> # in the Debian package dialign it is not needed to set DIALIGN2_DIR but the
> test is verifying this dir
> # to run the EMBOSS test test_Emboss also requires to have the environment
> variable EMBOSS_ROOT set
> LC_ALL=C.UTF-8 dh_auto_test -- --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'
> pybuild --test -i python{version} -p 3.8 --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"
> I: pybuild base:217: set -e; \
> mkdir -p
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/home; \
> mkdir -p
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc/examples; \
> cp -a Doc/Tutorial.tex
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \
> cp -a Doc/Tutorial
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \
> cp -a Doc/examples
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \
> cp -a Tests
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build; \
> cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests; \
> env DIALIGN2_DIR=/usr/share/dialign
> EMBOSS_ROOT=/usr/lib/emboss
> HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/home python3.8 run_tests.py
> --offline
> x_order_2: colinear!
> x_order_2: colinear!
> test_Ace ... ok
> test_Affy ... ok
> test_AlignIO ... ok
> test_AlignIO_ClustalIO ... ok
> test_AlignIO_EmbossIO ... ok
> test_AlignIO_FastaIO ... ok
> test_AlignIO_MauveIO ... ok
> test_AlignIO_PhylipIO ... ok
> test_AlignIO_convert ... ok
> test_AlignInfo ... ok
> test_Application ... ok
> test_BWA_tool ... ok
> test_BioSQL_MySQLdb_online ... skipping. internet not available
> test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file
> biosql.ini missing (see biosql.ini.sample)
> test_BioSQL_mysql_connector_online ... skipping. internet not available
> test_BioSQL_psycopg2_online ... skipping. internet not available
> test_BioSQL_sqlite3 ... ok
> test_BioSQL_sqlite3_online ... skipping. internet not available
> test_Blast_Record ... 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_ColorSpiral ... ok
> test_Compass ... ok
> test_Consensus ... ok
> test_Crystal ... ok
> test_DSSP_tool ... ok
> test_Dialign_tool ... ok
> test_EMBL_unittest ... ok
> test_Emboss ... ok
> test_EmbossPrimer ... ok
> test_Entrez ... ok
> test_Entrez_online ... skipping. internet not available
> test_Entrez_parser ... ok
> test_Enzyme ... ok
> test_ExPASy ... skipping. internet not available
> test_FSSP ... ok
> test_Fasttree_tool ... ok
> test_File ... ok
> test_GenBank ... 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_LogisticRegression ... ok
> test_MafIO_index ... ok
> test_Mafft_tool ... ok
> test_MarkovModel ... ok
> test_Medline ... ok
> test_Muscle_tool ... ok
> test_NCBITextParser ... ok
> test_NCBIXML ... ok
> test_NCBI_BLAST_tools ...
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398:
> UserWarning: NCBI BLAST+ blastn and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing:
> -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
> warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please "
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398:
> UserWarning: NCBI BLAST+ blastp and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing:
> -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
> warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please "
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398:
> UserWarning: NCBI BLAST+ blastx and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing:
> -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
> warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please "
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398:
> 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:
> -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
> warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please "
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398:
> UserWarning: NCBI BLAST+ makeblastdb and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing: -blastdb_version)
> warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please "
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398:
> 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:
> -ipglist,-negative_ipglist,-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
> warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please "
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398:
> UserWarning: NCBI BLAST+ rpsblast and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing: -sorthits,-sorthsps,-subject_besthit)
> warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please "
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398:
> UserWarning: NCBI BLAST+ rpstblastn and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing: -sorthits,-sorthsps)
> warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please "
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398:
> UserWarning: NCBI BLAST+ tblastn and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing:
> -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
> warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please "
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:398:
> UserWarning: NCBI BLAST+ tblastx and Biopython out sync. Please update
> Biopython, or report this issue if you are already using the latest version.
> (Extra args: ; Missing:
> -negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
> warnings.warn("NCBI BLAST+ %s and Biopython out sync. Please "
> FAIL
> test_NCBI_qblast ... skipping. internet not available
> test_NMR ... ok
> test_NaiveBayes ... ok
> test_Nexus ... ok
> test_PAML_baseml ... ok
> test_PAML_codeml ... ok
> test_PAML_yn00 ... ok
> test_PDB ... ok
> test_PDBList ... skipping. internet not available
> test_PDB_Dice ... ok
> test_PDB_FragmentMapper ... ok
> test_PDB_KDTree ... ok
> test_PDB_MMCIF2Dict ... ok
> test_PDB_MMCIFParser ... ok
> test_PDB_Polypetide ... ok
> test_PDB_StructureAlignment ...
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/PDB/StructureBuilder.py:89:
> PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298.
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/PDB/StructureBuilder.py:89:
> PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344.
> warnings.warn(
> ok
> test_PDB_Superimposer ... ok
> test_PDB_parse_pdb_header ... ok
> test_PDB_vectors ... ok
> test_Pathway ... ok
> test_Phd ... ok
> test_Phylo ... ok
> test_PhyloXML ... ok
> test_Phylo_CDAO ... ok
> test_Phylo_NeXML ... ok
> test_Phylo_matplotlib ... ok
> test_Phylo_networkx ... ok
> test_PopGen_GenePop_nodepend ... ok
> test_Prank_tool ... ok
> test_Probcons_tool ... ok
> test_ProtParam ... ok
> test_QCPSuperimposer ... ok
> test_RCSBFormats ... 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_hhsuite2_text ... 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_interproscan_xml ... ok
> test_SearchIO_legacy ... ok
> test_SearchIO_model ... ok
> test_SearchIO_write ... ok
> test_SeqFeature ... ok
> test_SeqIO ... ok
> test_SeqIO_AbiIO ... ok
> test_SeqIO_FastaIO ... ok
> test_SeqIO_Gck ... ok
> test_SeqIO_Insdc ...
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/GenBank/Scanner.py:303:
> BiopythonParserWarning: Non-standard feature line wrapping (didn't break on
> comma)?
> warnings.warn(
> ok
> test_SeqIO_NibIO ... ok
> test_SeqIO_PdbIO ... ok
> test_SeqIO_QualityIO ... ok
> test_SeqIO_SeqXML ... ok
> test_SeqIO_SnapGene ... ok
> test_SeqIO_Xdna ... 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_GOA ... ok
> test_Uniprot ... ok
> test_Wise ... ok
> test_align ... ok
> test_align_substitution_matrices ... ok
> test_bgzf ... ok
> test_cellosaurus ... ok
> test_codonalign ...
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/Seq.py:2828:
> BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP
> and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be
> translated as amino acid.
> warnings.warn(
> ok
> test_geo ... ok
> test_kNN ... ok
> test_lowess ...
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/Statistics/__init__.py:14:
> BiopythonDeprecationWarning: Bio.Statistics has been deprecated, and we
> intend to remove it in a future release of Biopython.
> warnings.warn("Bio.Statistics has been deprecated, and we intend to remove
> it "
> ok
> test_motifs ... ok
> test_motifs_online ... skipping. internet not available
> test_pairwise2 ... ok
> test_pairwise2_no_C ... ok
> test_pairwise_aligner ... ok
> test_phenotype ... ok
> test_phenotype_fit ... ok
> test_phyml_tool ... ok
> test_prodoc ... ok
> test_prosite1 ... ok
> test_prosite2 ... ok
> test_psw ... ok
> test_raxml_tool ... ok
> test_samtools_tool ... ok
> test_seq ... ok
> test_translate ... ok
> test_trie ... ok
> Bio docstring test ... ok
> Bio.Affy docstring test ... ok
> Bio.Affy.CelFile docstring test ... ok
> Bio.Align docstring test ... ok
> Bio.Align.AlignInfo docstring test ... ok
> Bio.Align.Applications docstring test ... ok
> Bio.Align.Applications._ClustalOmega docstring test ... ok
> Bio.Align.Applications._Clustalw docstring test ... ok
> Bio.Align.Applications._Dialign 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._Prank docstring test ... ok
> Bio.Align.Applications._Probcons docstring test ... ok
> Bio.Align.Applications._TCoffee docstring test ... ok
> Bio.Align._aligners docstring test ... ok
> Bio.Align.substitution_matrices docstring test ... ok
> Bio.AlignIO docstring test ... ok
> Bio.AlignIO.ClustalIO docstring test ... ok
> Bio.AlignIO.EmbossIO docstring test ... ok
> Bio.AlignIO.FastaIO docstring test ... ok
> Bio.AlignIO.Interfaces docstring test ... ok
> Bio.AlignIO.MafIO docstring test ... ok
> Bio.AlignIO.MauveIO docstring test ... ok
> Bio.AlignIO.MsfIO docstring test ... ok
> Bio.AlignIO.NexusIO docstring test ... ok
> Bio.AlignIO.PhylipIO docstring test ... ok
> Bio.AlignIO.StockholmIO docstring test ... ok
> Bio.Alphabet docstring test ... ok
> Bio.Alphabet.IUPAC docstring test ... ok
> Bio.Alphabet.Reduced docstring test ... ok
> Bio.Application docstring test ... ok
> Bio.Blast docstring test ... ok
> Bio.Blast.Applications docstring test ... ok
> Bio.Blast.NCBIWWW docstring test ... ok
> Bio.Blast.NCBIXML docstring test ... ok
> Bio.Blast.ParseBlastTable docstring test ... ok
> Bio.Blast.Record docstring test ... ok
> Bio.CAPS docstring test ... ok
> Bio.Cluster docstring test ... ok
> Bio.Cluster._cluster docstring test ... ok
> Bio.Compass docstring test ... ok
> Bio.Crystal docstring test ... ok
> Bio.Data docstring test ... ok
> Bio.Data.CodonTable docstring test ... ok
> Bio.Data.IUPACData docstring test ... ok
> Bio.Data.SCOPData docstring test ... ok
> Bio.Emboss docstring test ... ok
> Bio.Emboss.Applications docstring test ... ok
> Bio.Emboss.Primer3 docstring test ... ok
> Bio.Emboss.PrimerSearch docstring test ... ok
> Bio.Entrez.Parser docstring test ... ok
> Bio.ExPASy.Enzyme docstring test ... ok
> Bio.ExPASy.Prodoc docstring test ... ok
> Bio.ExPASy.Prosite docstring test ... ok
> Bio.ExPASy.ScanProsite docstring test ... ok
> Bio.ExPASy.cellosaurus docstring test ... ok
> Bio.FSSP docstring test ... ok
> Bio.FSSP.FSSPTools docstring test ... ok
> Bio.FSSP.fssp_rec docstring test ... ok
> Bio.File docstring test ... ok
> Bio.GenBank docstring test ... ok
> Bio.GenBank.Record docstring test ... ok
> Bio.GenBank.Scanner docstring test ... ok
> Bio.GenBank.utils docstring test ... ok
> Bio.Geo docstring test ... ok
> Bio.Geo.Record docstring test ... ok
> Bio.Graphics docstring test ... ok
> Bio.Graphics.BasicChromosome docstring test ... ok
> Bio.Graphics.ColorSpiral docstring test ... ok
> Bio.Graphics.Comparative docstring test ... ok
> Bio.Graphics.DisplayRepresentation docstring test ... ok
> Bio.Graphics.Distribution docstring test ... ok
> Bio.Graphics.GenomeDiagram docstring test ... ok
> Bio.Graphics.GenomeDiagram._AbstractDrawer docstring test ... ok
> Bio.Graphics.GenomeDiagram._CircularDrawer docstring test ... ok
> Bio.Graphics.GenomeDiagram._Colors docstring test ... ok
> Bio.Graphics.GenomeDiagram._CrossLink docstring test ... ok
> Bio.Graphics.GenomeDiagram._Diagram docstring test ... ok
> Bio.Graphics.GenomeDiagram._Feature docstring test ... ok
> Bio.Graphics.GenomeDiagram._FeatureSet docstring test ... ok
> Bio.Graphics.GenomeDiagram._Graph docstring test ... ok
> Bio.Graphics.GenomeDiagram._GraphSet docstring test ... ok
> Bio.Graphics.GenomeDiagram._LinearDrawer docstring test ... ok
> Bio.Graphics.GenomeDiagram._Track docstring test ... ok
> Bio.Graphics.KGML_vis docstring test ... ok
> Bio.HMM docstring test ... ok
> Bio.HMM.DynamicProgramming docstring test ... ok
> Bio.HMM.MarkovModel docstring test ... ok
> Bio.HMM.Trainer docstring test ... ok
> Bio.HMM.Utilities docstring test ... ok
> Bio.Index docstring test ... ok
> Bio.KDTree docstring test ... ok
> Bio.KDTree.KDTree docstring test ... ok
> Bio.KDTree._CKDTree docstring test ... ok
> Bio.KEGG docstring test ... ok
> Bio.KEGG.Compound docstring test ... ok
> Bio.KEGG.Enzyme docstring test ... ok
> Bio.KEGG.Gene docstring test ... ok
> Bio.KEGG.KGML docstring test ... ok
> Bio.KEGG.KGML.KGML_parser docstring test ... ok
> Bio.KEGG.KGML.KGML_pathway docstring test ... ok
> Bio.KEGG.Map docstring test ... ok
> Bio.KEGG.REST docstring test ... ok
> Bio.LogisticRegression docstring test ... ok
> Bio.MarkovModel docstring test ... ok
> Bio.MaxEntropy docstring test ... ok
> Bio.Medline docstring test ... ok
> Bio.NMR docstring test ... ok
> Bio.NMR.NOEtools docstring test ... ok
> Bio.NMR.xpktools docstring test ... ok
> Bio.NaiveBayes docstring test ... ok
> Bio.Nexus docstring test ... ok
> Bio.Nexus.Nexus docstring test ... ok
> Bio.Nexus.Nodes docstring test ... ok
> Bio.Nexus.StandardData docstring test ... ok
> Bio.Nexus.Trees docstring test ... ok
> Bio.Nexus.cnexus docstring test ... ok
> Bio.PDB.Atom docstring test ... ok
> Bio.PDB.Chain docstring test ... ok
> Bio.PDB.DSSP docstring test ... ok
> Bio.PDB.Dice docstring test ... ok
> Bio.PDB.Entity docstring test ... ok
> Bio.PDB.FragmentMapper docstring test ... ok
> Bio.PDB.HSExposure docstring test ... ok
> Bio.PDB.MMCIF2Dict docstring test ... ok
> Bio.PDB.MMCIFParser docstring test ... ok
> Bio.PDB.Model docstring test ... ok
> Bio.PDB.NACCESS docstring test ... ok
> Bio.PDB.NeighborSearch docstring test ... ok
> Bio.PDB.PDBExceptions docstring test ... ok
> Bio.PDB.PDBIO docstring test ... ok
> Bio.PDB.PDBList docstring test ... ok
> Bio.PDB.PDBParser docstring test ... ok
> Bio.PDB.PSEA docstring test ... ok
> Bio.PDB.Polypeptide docstring test ... ok
> Bio.PDB.QCPSuperimposer docstring test ... ok
> Bio.PDB.QCPSuperimposer.qcprotmodule docstring test ... ok
> Bio.PDB.Residue docstring test ... ok
> Bio.PDB.ResidueDepth docstring test ... ok
> Bio.PDB.Selection docstring test ... ok
> Bio.PDB.Structure docstring test ... ok
> Bio.PDB.StructureAlignment docstring test ... ok
> Bio.PDB.StructureBuilder docstring test ... ok
> Bio.PDB.Superimposer docstring test ... ok
> Bio.PDB.kdtrees docstring test ... ok
> Bio.PDB.mmcifio docstring test ... ok
> Bio.PDB.mmtf docstring test ... skipped, missing Python dependency
> Bio.PDB.mmtf.DefaultParser docstring test ... skipped, missing Python
> dependency
> Bio.PDB.mmtf.mmtfio docstring test ... skipped, missing Python dependency
> Bio.PDB.parse_pdb_header docstring test ... ok
> Bio.PDB.vectors docstring test ... ok
> Bio.Pathway docstring test ... ok
> Bio.Pathway.Rep docstring test ... ok
> Bio.Pathway.Rep.Graph docstring test ... ok
> Bio.Pathway.Rep.MultiGraph docstring test ... ok
> Bio.Phylo docstring test ... ok
> Bio.Phylo.Applications docstring test ... ok
> Bio.Phylo.Applications._Fasttree docstring test ... ok
> Bio.Phylo.Applications._Phyml docstring test ... ok
> Bio.Phylo.Applications._Raxml docstring test ... ok
> Bio.Phylo.BaseTree docstring test ... ok
> Bio.Phylo.CDAO docstring test ... ok
> Bio.Phylo.CDAOIO docstring test ... ok
> Bio.Phylo.Consensus docstring test ... ok
> Bio.Phylo.NeXML docstring test ... ok
> Bio.Phylo.NeXMLIO docstring test ... ok
> Bio.Phylo.Newick docstring test ... ok
> Bio.Phylo.NewickIO docstring test ... ok
> Bio.Phylo.NexusIO docstring test ... ok
> Bio.Phylo.PAML docstring test ... ok
> Bio.Phylo.PAML._paml docstring test ... ok
> Bio.Phylo.PAML._parse_baseml docstring test ... ok
> Bio.Phylo.PAML._parse_codeml docstring test ... ok
> Bio.Phylo.PAML._parse_yn00 docstring test ... ok
> Bio.Phylo.PAML.baseml docstring test ... ok
> Bio.Phylo.PAML.chi2 docstring test ... ok
> Bio.Phylo.PAML.codeml docstring test ... ok
> Bio.Phylo.PAML.yn00 docstring test ... ok
> Bio.Phylo.PhyloXML docstring test ... ok
> Bio.Phylo.PhyloXMLIO docstring test ... ok
> Bio.Phylo.TreeConstruction docstring test ... ok
> Bio.Phylo._cdao_owl docstring test ... ok
> Bio.Phylo._io docstring test ... ok
> Bio.Phylo._utils docstring test ... ok
> Bio.PopGen docstring test ... ok
> Bio.PopGen.GenePop docstring test ... ok
> Bio.PopGen.GenePop.Controller docstring test ... ok
> Bio.PopGen.GenePop.EasyController docstring test ... ok
> Bio.PopGen.GenePop.FileParser docstring test ... ok
> Bio.PopGen.GenePop.LargeFileParser docstring test ... ok
> Bio.PopGen.GenePop.Utils docstring test ... ok
> Bio.Restriction docstring test ... ok
> Bio.Restriction.PrintFormat docstring test ... ok
> Bio.Restriction.Restriction docstring test ... ok
> Bio.Restriction.Restriction_Dictionary docstring test ... ok
> Bio.SCOP docstring test ... ok
> Bio.SCOP.Cla docstring test ... ok
> Bio.SCOP.Des docstring test ... ok
> Bio.SCOP.Dom docstring test ... ok
> Bio.SCOP.Hie docstring test ... ok
> Bio.SCOP.Raf docstring test ... ok
> Bio.SCOP.Residues docstring test ... ok
> Bio.SVDSuperimposer docstring test ... ok
> Bio.SearchIO docstring test ... ok
> Bio.SearchIO.BlastIO docstring test ... ok
> Bio.SearchIO.BlastIO.blast_tab docstring test ... ok
> Bio.SearchIO.BlastIO.blast_text docstring test ... ok
> Bio.SearchIO.BlastIO.blast_xml docstring test ... ok
> Bio.SearchIO.BlatIO docstring test ... ok
> Bio.SearchIO.ExonerateIO docstring test ... ok
> Bio.SearchIO.ExonerateIO._base docstring test ... ok
> Bio.SearchIO.ExonerateIO.exonerate_cigar docstring test ... ok
> Bio.SearchIO.ExonerateIO.exonerate_text docstring test ... ok
> Bio.SearchIO.ExonerateIO.exonerate_vulgar docstring test ... ok
> Bio.SearchIO.FastaIO docstring test ... ok
> Bio.SearchIO.HHsuiteIO docstring test ... ok
> Bio.SearchIO.HHsuiteIO.hhsuite2_text docstring test ... ok
> Bio.SearchIO.HmmerIO docstring test ... ok
> Bio.SearchIO.HmmerIO._base docstring test ... ok
> Bio.SearchIO.HmmerIO.hmmer2_text docstring test ... ok
> Bio.SearchIO.HmmerIO.hmmer3_domtab docstring test ... ok
> Bio.SearchIO.HmmerIO.hmmer3_tab docstring test ... ok
> Bio.SearchIO.HmmerIO.hmmer3_text docstring test ... ok
> Bio.SearchIO.InterproscanIO docstring test ... ok
> Bio.SearchIO.InterproscanIO.interproscan_xml docstring test ... ok
> Bio.SearchIO._index docstring test ... ok
> Bio.SearchIO._legacy docstring test ... ok
> Bio.SearchIO._legacy.NCBIStandalone docstring test ... ok
> Bio.SearchIO._legacy.ParserSupport docstring test ... ok
> Bio.SearchIO._model docstring test ... ok
> Bio.SearchIO._model._base docstring test ... ok
> Bio.SearchIO._model.hit docstring test ... ok
> Bio.SearchIO._model.hsp docstring test ... ok
> Bio.SearchIO._model.query docstring test ... ok
> Bio.SearchIO._utils docstring test ... ok
> Bio.Seq docstring test ... ok
> Bio.SeqFeature docstring test ... ok
> Bio.SeqIO docstring test ... ok
> Bio.SeqIO.AbiIO docstring test ... ok
> Bio.SeqIO.AceIO docstring test ... ok
> Bio.SeqIO.FastaIO docstring test ... ok
> Bio.SeqIO.GckIO docstring test ... ok
> Bio.SeqIO.IgIO docstring test ... ok
> Bio.SeqIO.InsdcIO docstring test ... ok
> Bio.SeqIO.Interfaces docstring test ... ok
> Bio.SeqIO.NibIO docstring test ... ok
> Bio.SeqIO.PdbIO docstring test ... ok
> Bio.SeqIO.PhdIO docstring test ... ok
> Bio.SeqIO.PirIO docstring test ... ok
> Bio.SeqIO.QualityIO docstring test ... ok
> Bio.SeqIO.SeqXmlIO docstring test ... ok
> Bio.SeqIO.SffIO docstring test ... ok
> Bio.SeqIO.SnapGeneIO docstring test ... ok
> Bio.SeqIO.SwissIO docstring test ... ok
> Bio.SeqIO.TabIO docstring test ... ok
> Bio.SeqIO.UniprotIO docstring test ... ok
> Bio.SeqIO.XdnaIO docstring test ... ok
> Bio.SeqIO._convert docstring test ... ok
> Bio.SeqIO._index docstring test ... ok
> Bio.SeqRecord docstring test ... ok
> Bio.SeqUtils docstring test ... ok
> Bio.SeqUtils.CheckSum docstring test ... ok
> Bio.SeqUtils.CodonUsage docstring test ... ok
> Bio.SeqUtils.CodonUsageIndices docstring test ... ok
> Bio.SeqUtils.IsoelectricPoint docstring test ... ok
> Bio.SeqUtils.MeltingTemp docstring test ... ok
> Bio.SeqUtils.ProtParam docstring test ... ok
> Bio.SeqUtils.ProtParamData docstring test ... ok
> Bio.SeqUtils.lcc docstring test ... ok
> Bio.Sequencing docstring test ... ok
> Bio.Sequencing.Ace docstring test ... ok
> Bio.Sequencing.Applications 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.Sequencing.Phd docstring test ... ok
> Bio.Statistics docstring test ... ok
> Bio.Statistics.lowess docstring test ... ok
> Bio.SubsMat docstring test ... ok
> Bio.SubsMat.FreqTable docstring test ... ok
> Bio.SubsMat.MatrixInfo docstring test ... ok
> Bio.SwissProt docstring test ... ok
> Bio.SwissProt.KeyWList docstring test ... ok
> Bio.UniGene docstring test ... ok
> Bio.UniProt docstring test ... ok
> Bio.UniProt.GOA docstring test ... ok
> Bio.Wise docstring test ... ok
> Bio.Wise.dnal docstring test ... ok
> Bio.Wise.psw docstring test ... ok
> Bio._py3k docstring test ... ok
> Bio._utils docstring test ... ok
> Bio.bgzf docstring test ... ok
> Bio.codonalign docstring test ... ok
> Bio.codonalign.chisq docstring test ... ok
> Bio.codonalign.codonalignment docstring test ... ok
> Bio.codonalign.codonalphabet docstring test ... ok
> Bio.codonalign.codonseq docstring test ... ok
> Bio.cpairwise2 docstring test ... ok
> Bio.kNN docstring test ... ok
> Bio.motifs docstring test ... ok
> Bio.motifs._pwm docstring test ... ok
> Bio.motifs.alignace docstring test ... ok
> Bio.motifs.applications docstring test ... ok
> Bio.motifs.applications._xxmotif docstring test ... ok
> Bio.motifs.clusterbuster docstring test ... ok
> Bio.motifs.jaspar docstring test ... ok
> Bio.motifs.jaspar.db docstring test ... ok
> Bio.motifs.mast docstring test ... ok
> Bio.motifs.matrix docstring test ... ok
> Bio.motifs.meme docstring test ... ok
> Bio.motifs.minimal docstring test ... ok
> Bio.motifs.pfm docstring test ... ok
> Bio.motifs.thresholds docstring test ... ok
> Bio.motifs.transfac docstring test ... ok
> Bio.motifs.xms docstring test ... ok
> Bio.pairwise2 docstring test ... ok
> Bio.phenotype docstring test ... ok
> Bio.phenotype.phen_micro docstring test ... ok
> Bio.phenotype.pm_fitting docstring test ... ok
> Bio.trie docstring test ... ok
> Bio.triefind docstring test ... ok
> BioSQL docstring test ... ok
> BioSQL.BioSeq docstring test ... ok
> BioSQL.BioSeqDatabase docstring test ... ok
> BioSQL.DBUtils docstring test ... ok
> BioSQL.Loader docstring test ... ok
> ======================================================================
> FAIL: test_fasta_db_nucl (test_NCBI_BLAST_tools.BlastDB)
> Test makeblastdb wrapper with nucleotide database.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py",
> line 248, in test_fasta_db_nucl
> self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nsd"))
> AssertionError: False is not true
>
> ======================================================================
> FAIL: test_fasta_db_prot (test_NCBI_BLAST_tools.BlastDB)
> Test makeblastdb wrapper with protein database.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py",
> line 213, in test_fasta_db_prot
> self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.psd"))
> AssertionError: False is not true
>
> ----------------------------------------------------------------------
> Ran 519 tests in 222.972 seconds
>
> FAILED (failures = 1)
> Skipping any tests requiring internet access
> Python version: 3.8.3rc1 (default, Apr 30 2020, 07:33:30)
> [GCC 9.3.0]
> Operating system: posix linux
> E: pybuild pybuild:352: test: plugin custom failed with: exit code=1: set -e;
> \
> mkdir -p
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/home; \
> mkdir -p
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc/examples; \
> cp -a Doc/Tutorial.tex
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \
> cp -a Doc/Tutorial
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \
> cp -a Doc/examples
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Doc; \
> cp -a Tests
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build; \
> cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests; \
> env DIALIGN2_DIR=/usr/share/dialign
> EMBOSS_ROOT=/usr/lib/emboss
> HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/home python3.8 run_tests.py
> --offline
> dh_auto_test: error: pybuild --test -i python{version} -p 3.8 --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" returned exit code 13
> make[1]: *** [debian/rules:83: override_dh_auto_test] Error 25
The full build log is available from:
http://qa-logs.debian.net/2020/05/01/python-biopython_1.76+dfsg-1_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.76+dfsg-2
Done: =?utf-8?q?Dylan_A=C3=AFssi?= <dai...@debian.org>
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 959...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Dylan Aïssi <dai...@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: Fri, 15 May 2020 11:40:33 +0200
Source: python-biopython
Architecture: source
Version: 1.76+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Dylan Aïssi <dai...@debian.org>
Closes: 959587
Changes:
python-biopython (1.76+dfsg-2) unstable; urgency=medium
.
* Team upload.
.
[ Michael R. Crusoe ]
* debian/control: mark the -doc package as Multi-Arch: foreign
.
[ Dylan Aïssi ]
* Add upstream patch to fix tests with new NCBI BLAST DB v5 (Closes: #959587)
.
[ Andreas Tille ]
* Standards-Version: 4.5.0 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
* Refer to specific version of license GPL-2+.
Checksums-Sha1:
5343c6e845f978589b1906043b9ac34d8d6a922a 2820 python-biopython_1.76+dfsg-2.dsc
81368b67e8cd89611f1b0f7afe9842ab9c730084 15072
python-biopython_1.76+dfsg-2.debian.tar.xz
1ffe29b127036f0d4bffcaf6a8e119e0b6f0d168 13353
python-biopython_1.76+dfsg-2_amd64.buildinfo
Checksums-Sha256:
c307d070bd2385e13c27b588598793abca595173b6dd9a179cdce600517a592c 2820
python-biopython_1.76+dfsg-2.dsc
d484c0c08437181c289ac7be87401bc9b3cfda8c62125d659f71a24ab65d1e05 15072
python-biopython_1.76+dfsg-2.debian.tar.xz
5c1f4e61c94285533946dc2422ef8dde00328f51c4cc9b3bca62c9c4ea8270f5 13353
python-biopython_1.76+dfsg-2_amd64.buildinfo
Files:
dd76f0da302ac0c212682a0abe67d343 2820 python optional
python-biopython_1.76+dfsg-2.dsc
cd1ee3264bae9c123e14fcdaa342d545 15072 python optional
python-biopython_1.76+dfsg-2.debian.tar.xz
95f2637079dade9dc6a4a9505a3baa30 13353 python optional
python-biopython_1.76+dfsg-2_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----
iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl6+aewRHHRpbGxlQGRl
Ymlhbi5vcmcACgkQV4oElNHGRtEg9w//eixeJ6U0Zo5k38dyBvHMYQ3/N2TD9icy
Tz8uxCLxmpP/bnHXZZMdi2egr+0UMbe4Nv6zXxlD71KXe10tNZlGaGtqPOmP6rZb
u92evZHRKXSUd+Pgh4arSO0gRMdJR5GEqZ7IM9BVKdMUr3AL5PD6NEw/2nK++t+B
R10WqUWZdD6WxXIxAI5e/oFxKBokmQW98ZB2KHMAD/3XCRx7kMHsI9AeVEX0+Dnb
n1rzLpquZ4L+c2YJI91fNrP0GYVqbynyhUM7Ti7yhTodeVhm8e6P9/PTxVta0c3b
z6OjW7VdvHplvb5JGhHcvw7bapYOgMkvxiBT7gUOe6GnlAnb5atXXDAXdUY/Lbc7
Po8iHbqaC0oDu9rXta5KXROVl5bjr3Rs8Jd+F/isxrmUFxIdqanvRT1uStyJBX6Z
QB6JujTcdQlcBdzN79Lw6RmjRNgZiko/bTrLnpYAqwmy17X8G7LKW/T5QDjMVCF2
Wb8Ad93dHt6UzBost8dKU4E6BUz5nPfcgZiQZT/xY6yI2ZolKmCCKvzCBeiPdcXQ
NChTHuuA7tPUV75ps3vIHC8Flxy47C1HgAT2f8jwPyyTSdaPsBTB6qxX79OzLW6N
YEraHOiQckeVJRxaaA0QWFYTLcFEZp863mq88+wJdX67gjSSMR+WmBidGpi6NcMx
xkAwG+sxPnA=
=489u
-----END PGP SIGNATURE-----
--- End Message ---
