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Bug#966928: python-biopython: FTBFS: AssertionError: 0.018551002172574885 != 0.0194 within 4 places (0.00084899782742511518 difference)

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  Bug#966928: python-biopython: FTBFS: AssertionError: 0.018551002172574885 != 0.0194 within 4 places (0.00084899782742511518 difference) Lucas Nussbaum <lucas@debian.org> - 2020-08-03 11:10 +0200
    Bug#966928: python-biopython: FTBFS: AssertionError: 0.018551002172574885 != 0.0194 within 4 places (0.00084899782742511518 difference) Étienne Mollier <etienne.mollier@mailoo.org> - 2020-08-03 23:20 +0200
      Bug#966928: python-biopython: FTBFS: AssertionError: 0.018551002172574885 != 0.0194 within 4 places (0.00084899782742511518 difference) Andreas Tille <andreas@an3as.eu> - 2020-08-05 12:20 +0200

#1020310 — Bug#966928: python-biopython: FTBFS: AssertionError: 0.018551002172574885 != 0.0194 within 4 places (0.00084899782742511518 difference)

Source: python-biopython
Version: 1.77+dfsg-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200802 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
> 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_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 ... Warn: Can't find .pfb for face 'Times-Roman'
> ok
> test_GraphicsBitmaps ... skipping. Check the fonts needed by ReportLab if you want bitmaps from Bio.Graphics
> Can't setFont(Times-Roman) missing the T1 files?
> Originally <class 'TypeError'>: makeT1Font() argument 2 must be str, not None
> test_GraphicsChromosome ... ok
> test_GraphicsDistribution ... ok
> test_GraphicsGeneral ... ok
> test_HMMCasino ... ok
> test_HMMGeneral ... 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 ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_MarkovModel.py:370: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
>   training_outputs = array([[0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3], [
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_MarkovModel.py:372: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
>   training_states = array([[0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3], [
> 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:481: 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(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:481: 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(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:481: 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(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:481: 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(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:481: 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(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:481: 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(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:481: 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(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:481: 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(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:481: 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(
> ok
> test_NCBI_qblast ... ok
> 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_internal_coords ... ok
> test_PDB_parse_pdb_header ... ok
> test_PDB_vectors ... ok
> test_PQR ... 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:304: 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_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:2713: 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(
> /usr/lib/python3/dist-packages/scipy/optimize/_numdiff.py:519: RuntimeWarning: invalid value encountered in true_divide
>   J_transposed[i] = df / dx
> FAIL
> test_geo ... ok
> test_kNN ... ok
> test_lowess ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Bio/Statistics/__init__.py:11: BiopythonDeprecationWarning: Bio.Statistics has been deprecated, and we intend to remove it in a future release of Biopython.
>   warnings.warn(
> 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
> 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.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 docstring test ... ok
> Bio.PDB.AbstractPropertyMap 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.PICIO 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.SCADIO 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.ic_data docstring test ... ok
> Bio.PDB.ic_rebuild docstring test ... ok
> Bio.PDB.internal_coords docstring test ... ok
> Bio.PDB.kdtrees docstring test ... ok
> Bio.PDB.mmcifio docstring test ... ok
> Bio.PDB.mmtf docstring test ... ok
> Bio.PDB.mmtf.DefaultParser docstring test ... ok
> Bio.PDB.mmtf.mmtfio docstring test ... ok
> 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.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._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._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
> 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_dn_ds (test_codonalign.Test_dn_ds)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_codonalign.py", line 250, in test_dn_ds
>     self.assertAlmostEqual(dN, 0.0194, places=4)
> AssertionError: 0.018551002172574885 != 0.0194 within 4 places (0.00084899782742511518 difference)
> 
> ----------------------------------------------------------------------
> Ran 515 tests in 246.240 seconds
> 
> FAILED (failures = 1)
> Skipping any tests requiring internet access
> Python version: 3.8.5 (default, Jul 20 2020, 18:32:44) 
> [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:84: override_dh_auto_test] Error 25

The full build log is available from:
   http://qa-logs.debian.net/2020/08/02/python-biopython_1.77+dfsg-2_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.

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#1020444

[Multipart message — attachments visible in raw view] — view raw

Control: tags -1 fixed-upstream

Good day,

Looking to upstream issue tracker, the problem has been hit as
well and seems triggered by the update past Scipy 1.5.0.  Here
are the details of the issue, and the fix implemented by zruan:

	https://github.com/biopython/biopython/issues/2993
	https://github.com/biopython/biopython/pull/2998

This test failure will thus most likely be solved with the next
upstream version of biopython.

Thanks for having caught that issue.
Kind Regards,
-- 
Étienne Mollier <etienne.mollier@mailoo.org>
Old rsa/3072: 5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
New rsa/4096: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/12, please excuse my verbosity.

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#1020629

On Mon, Aug 03, 2020 at 11:15:02PM +0200, Étienne Mollier wrote:
> Control: tags -1 fixed-upstream

Thanks for your research - I just uploaded with the pull request
connected patches to get rid of the nasty RC bug as soon as possible.

Kind regards

       Andreas.

-- 
http://fam-tille.de

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