[Debian-med-packaging] Bug#1027629: python-biopython: FTBFS: Test DSSP generation from MMCIF with non-standard residues.
Lucas Nussbaum
lucas at debian.org
Sun Jan 1 14:20:12 GMT 2023
Source: python-biopython
Version: 1.80+dfsg-4
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20230101 ftbfs-bookworm
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
> mv: cannot stat 'Tests/test_NACCESS_tool.py': No such file or directory
> # 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 "3.11 3.10" --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:240: set -e; \
> mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/home; \
> mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples; \
> cp -a Doc/Tutorial.tex /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
> cp -a Doc/Tutorial /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
> cp -a Doc/examples /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
> cp -a Tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; \
> cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests; \
> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/home python3.11 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_Align_Alignment ... ok
> test_Align_a2m ... ok
> test_Align_bed ... ok
> test_Align_bigbed ... ok
> test_Align_bigmaf ... ok
> test_Align_bigpsl ... ok
> test_Align_clustal ... ok
> test_Align_emboss ... ok
> test_Align_exonerate ... ok
> test_Align_fasta ... ok
> test_Align_hhr ... ok
> test_Align_maf ... ok
> test_Align_mauve ... ok
> test_Align_msf ... ok
> test_Align_nexus ... ok
> test_Align_phylip ... ok
> test_Align_psl ... ok
> test_Align_sam ... ok
> test_Align_stockholm ... ok
> test_Align_tabular ... 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_Dialign_tool ... ok
> test_EMBL_unittest ... ok
> test_Emboss ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> ok
> test_EmbossPrimer ... ok
> test_Entrez ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Entrez/__init__.py:686: UserWarning:
> Email address is not specified.
>
> To make use of NCBI's E-utilities, NCBI requires you to specify your
> email address with each request. As an example, if your email address
> is A.N.Other at example.com, you can specify it as follows:
> from Bio import Entrez
> Entrez.email = 'A.N.Other at example.com'
> In case of excessive usage of the E-utilities, NCBI will attempt to contact
> a user at the email address provided before blocking access to the
> E-utilities.
> warnings.warn(
> ok
> test_Entrez_online ... skipping. internet not available
> test_Entrez_parser ... ok
> test_Enzyme ... ok
> test_ExPASy ... skipping. internet not available
> test_Fasttree_tool ... ok
> test_File ... ok
> test_GenBank ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> 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
> Error in setFont('Times-Roman',10) 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 ... ok
> test_Medline ... ok
> test_Muscle_tool ... ok
> test_NCBITextParser ... ok
> test_NCBIXML ... ok
> test_NCBI_BLAST_tools ... 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_PDBList ... skipping. internet not available
> test_PDB_CEAligner ... ok
> test_PDB_DSSP ... FAIL
> test_PDB_Dice ... ok
> test_PDB_Disordered ... ok
> test_PDB_Exposure ... ok
> test_PDB_FragmentMapper ... ok
> test_PDB_KDTree ... ok
> test_PDB_MMCIF2Dict ... ok
> test_PDB_MMCIFIO ... ok
> test_PDB_MMCIFParser ... ok
> test_PDB_NACCESS ... ok
> test_PDB_PDBIO ... ok
> test_PDB_PDBParser ... ok
> test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path
> test_PDB_Polypeptide ... ok
> test_PDB_QCSuperimposer ... ok
> test_PDB_SASA ... ok
> test_PDB_SMCRA ... ok
> test_PDB_Selection ... ok
> test_PDB_StructureAlignment ... ok
> test_PDB_Superimposer ... ok
> test_PDB_internal_coords ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/Polypeptide.py:161: BiopythonDeprecationWarning: 'one_to_three' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_1to3'.
> warnings.warn(
> 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_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_3.11/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> ok
> test_SeqIO_NibIO ... ok
> test_SeqIO_PdbIO ... ok
> test_SeqIO_QualityIO ... ok
> test_SeqIO_SeqXML ... ok
> test_SeqIO_SnapGene ... ok
> test_SeqIO_TwoBitIO ... ok
> test_SeqIO_Xdna ... ok
> test_SeqIO_features ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/SeqIO/InsdcIO.py:550: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line
> warnings.warn(
> 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_SwissProt ... ok
> test_TCoffee_tool ... ok
> test_TogoWS ... skipping. internet not available
> test_TreeConstruction ... ok
> test_Tutorial ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
> warnings.warn(
> 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_3.11/build/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython.
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/Seq.py:3457: 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(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA)
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA)
> warnings.warn(
> ok
> test_geo ... ok
> test_kNN ... ok
> test_motifs ... ok
> test_motifs_online ... skipping. internet not available
> test_pairwise2 ... ok
> test_pairwise2_no_C ... ok
> test_pairwise_aligner ... ok
> test_pairwise_alignment_map ... ok
> test_phenotype ... ok
> test_phenotype_fit ... ok
> test_phyml_tool ... ok
> test_prodoc ... ok
> test_prosite ... 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.a2m docstring test ... ok
> Bio.Align.bed docstring test ... ok
> Bio.Align.bigbed docstring test ... ok
> Bio.Align.bigmaf docstring test ... ok
> Bio.Align.bigpsl docstring test ... ok
> Bio.Align.clustal docstring test ... ok
> Bio.Align.emboss docstring test ... ok
> Bio.Align.exonerate docstring test ... ok
> Bio.Align.fasta docstring test ... ok
> Bio.Align.hhr docstring test ... ok
> Bio.Align.interfaces docstring test ... ok
> Bio.Align.maf docstring test ... ok
> Bio.Align.mauve docstring test ... ok
> Bio.Align.msf docstring test ... ok
> Bio.Align.nexus docstring test ... ok
> Bio.Align.phylip docstring test ... ok
> Bio.Align.psl docstring test ... ok
> Bio.Align.sam docstring test ... ok
> Bio.Align.stockholm docstring test ... ok
> Bio.Align.substitution_matrices docstring test ... ok
> Bio.Align.tabular 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.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.Data docstring test ... ok
> Bio.Data.CodonTable docstring test ... ok
> Bio.Data.IUPACData docstring test ... ok
> Bio.Data.PDBData 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.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.SASA 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.ccealign docstring test ... ok
> Bio.PDB.cealign 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.qcprot 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.TwoBitIO docstring test ... ok
> Bio.SeqIO.UniprotIO docstring test ... ok
> Bio.SeqIO.XdnaIO docstring test ... ok
> Bio.SeqIO._index docstring test ... ok
> Bio.SeqIO._twoBitIO 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.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.codonalignment 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
> ======================================================================
> ERROR: test_dssp_with_mmcif_file_and_nonstandard_residues (test_PDB_DSSP.DSSP_tool_test.test_dssp_with_mmcif_file_and_nonstandard_residues)
> Test DSSP generation from MMCIF with non-standard residues.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests/test_PDB_DSSP.py", line 130, in test_dssp_with_mmcif_file_and_nonstandard_residues
> dssp = DSSP(model, pdbfile)
> ^^^^^^^^^^^^^^^^^^^^
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/DSSP.py", line 389, in __init__
> dssp_dict, dssp_keys = dssp_dict_from_pdb_file(
> ^^^^^^^^^^^^^^^^^^^^^^^^
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Bio/PDB/DSSP.py", line 201, in dssp_dict_from_pdb_file
> raise Exception("DSSP failed to produce an output")
> Exception: DSSP failed to produce an output
>
> ----------------------------------------------------------------------
> Ran 554 tests in 412.516 seconds
>
> FAILED (failures = 1)
> Skipping any tests requiring internet access
> Python version: 3.11.1 (main, Dec 31 2022, 10:23:59) [GCC 12.2.0]
> Operating system: posix linux
> E: pybuild pybuild:388: test: plugin custom failed with: exit code=1: set -e; \
> mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/home; \
> mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc/examples; \
> cp -a Doc/Tutorial.tex /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
> cp -a Doc/Tutorial /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
> cp -a Doc/examples /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Doc; \
> cp -a Tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; \
> cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/Tests; \
> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/home python3.11 run_tests.py --offline
> I: pybuild base:240: set -e; \
> mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/home; \
> mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc/examples; \
> cp -a Doc/Tutorial.tex /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc; \
> cp -a Doc/Tutorial /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc; \
> cp -a Doc/examples /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc; \
> cp -a Tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build; \
> cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests; \
> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/home python3.10 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_Align_Alignment ... ok
> test_Align_a2m ... ok
> test_Align_bed ... ok
> test_Align_bigbed ... ok
> test_Align_bigmaf ... ok
> test_Align_bigpsl ... ok
> test_Align_clustal ... ok
> test_Align_emboss ... ok
> test_Align_exonerate ... ok
> test_Align_fasta ... ok
> test_Align_hhr ... ok
> test_Align_maf ... ok
> test_Align_mauve ... ok
> test_Align_msf ... ok
> test_Align_nexus ... ok
> test_Align_phylip ... ok
> test_Align_psl ... ok
> test_Align_sam ... ok
> test_Align_stockholm ... ok
> test_Align_tabular ... 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_Dialign_tool ... ok
> test_EMBL_unittest ... ok
> test_Emboss ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> ok
> test_EmbossPrimer ... ok
> test_Entrez ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/Entrez/__init__.py:686: UserWarning:
> Email address is not specified.
>
> To make use of NCBI's E-utilities, NCBI requires you to specify your
> email address with each request. As an example, if your email address
> is A.N.Other at example.com, you can specify it as follows:
> from Bio import Entrez
> Entrez.email = 'A.N.Other at example.com'
> In case of excessive usage of the E-utilities, NCBI will attempt to contact
> a user at the email address provided before blocking access to the
> E-utilities.
> warnings.warn(
> ok
> test_Entrez_online ... skipping. internet not available
> test_Entrez_parser ... ok
> test_Enzyme ... ok
> test_ExPASy ... skipping. internet not available
> test_Fasttree_tool ... ok
> test_File ... ok
> test_GenBank ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> 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
> Error in setFont('Times-Roman',10) 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 ... ok
> test_Medline ... ok
> test_Muscle_tool ... ok
> test_NCBITextParser ... ok
> test_NCBIXML ... ok
> test_NCBI_BLAST_tools ... 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_PDBList ... skipping. internet not available
> test_PDB_CEAligner ... ok
> test_PDB_DSSP ... FAIL
> test_PDB_Dice ... ok
> test_PDB_Disordered ... ok
> test_PDB_Exposure ... ok
> test_PDB_FragmentMapper ... ok
> test_PDB_KDTree ... ok
> test_PDB_MMCIF2Dict ... ok
> test_PDB_MMCIFIO ... ok
> test_PDB_MMCIFParser ... ok
> test_PDB_NACCESS ... ok
> test_PDB_PDBIO ... ok
> test_PDB_PDBParser ... ok
> test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path
> test_PDB_Polypeptide ... ok
> test_PDB_QCSuperimposer ... ok
> test_PDB_SASA ... ok
> test_PDB_SMCRA ... ok
> test_PDB_Selection ... ok
> test_PDB_StructureAlignment ... ok
> test_PDB_Superimposer ... ok
> test_PDB_internal_coords ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/Polypeptide.py:144: BiopythonDeprecationWarning: 'three_to_one' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_3to1'.
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/Polypeptide.py:161: BiopythonDeprecationWarning: 'one_to_three' will be deprecated in a future release of Biopython in favor of 'Bio.PDB.Polypeptide.protein_letters_1to3'.
> warnings.warn(
> 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_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_3.10/build/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> ok
> test_SeqIO_NibIO ... ok
> test_SeqIO_PdbIO ... ok
> test_SeqIO_QualityIO ... ok
> test_SeqIO_SeqXML ... ok
> test_SeqIO_SnapGene ... ok
> test_SeqIO_TwoBitIO ... ok
> test_SeqIO_Xdna ... ok
> test_SeqIO_features ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA
> warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:550: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line
> warnings.warn(
> 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_SwissProt ... ok
> test_TCoffee_tool ... ok
> test_TogoWS ... skipping. internet not available
> test_TreeConstruction ... ok
> test_Tutorial ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
> warnings.warn(
> 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_3.10/build/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython.
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/Seq.py:3457: 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(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA)
> warnings.warn(
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA)
> warnings.warn(
> ok
> test_geo ... ok
> test_kNN ... ok
> test_motifs ... ok
> test_motifs_online ... skipping. internet not available
> test_pairwise2 ... ok
> test_pairwise2_no_C ... ok
> test_pairwise_aligner ... ok
> test_pairwise_alignment_map ... ok
> test_phenotype ... ok
> test_phenotype_fit ... ok
> test_phyml_tool ... ok
> test_prodoc ... ok
> test_prosite ... 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.a2m docstring test ... ok
> Bio.Align.bed docstring test ... ok
> Bio.Align.bigbed docstring test ... ok
> Bio.Align.bigmaf docstring test ... ok
> Bio.Align.bigpsl docstring test ... ok
> Bio.Align.clustal docstring test ... ok
> Bio.Align.emboss docstring test ... ok
> Bio.Align.exonerate docstring test ... ok
> Bio.Align.fasta docstring test ... ok
> Bio.Align.hhr docstring test ... ok
> Bio.Align.interfaces docstring test ... ok
> Bio.Align.maf docstring test ... ok
> Bio.Align.mauve docstring test ... ok
> Bio.Align.msf docstring test ... ok
> Bio.Align.nexus docstring test ... ok
> Bio.Align.phylip docstring test ... ok
> Bio.Align.psl docstring test ... ok
> Bio.Align.sam docstring test ... ok
> Bio.Align.stockholm docstring test ... ok
> Bio.Align.substitution_matrices docstring test ... ok
> Bio.Align.tabular 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.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.Data docstring test ... ok
> Bio.Data.CodonTable docstring test ... ok
> Bio.Data.IUPACData docstring test ... ok
> Bio.Data.PDBData 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.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.SASA 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.ccealign docstring test ... ok
> Bio.PDB.cealign 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.qcprot 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.TwoBitIO docstring test ... ok
> Bio.SeqIO.UniprotIO docstring test ... ok
> Bio.SeqIO.XdnaIO docstring test ... ok
> Bio.SeqIO._index docstring test ... ok
> Bio.SeqIO._twoBitIO 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.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.codonalignment 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
> ======================================================================
> ERROR: test_dssp_with_mmcif_file_and_nonstandard_residues (test_PDB_DSSP.DSSP_tool_test)
> Test DSSP generation from MMCIF with non-standard residues.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests/test_PDB_DSSP.py", line 130, in test_dssp_with_mmcif_file_and_nonstandard_residues
> dssp = DSSP(model, pdbfile)
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py", line 389, in __init__
> dssp_dict, dssp_keys = dssp_dict_from_pdb_file(
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py", line 201, in dssp_dict_from_pdb_file
> raise Exception("DSSP failed to produce an output")
> Exception: DSSP failed to produce an output
>
> ----------------------------------------------------------------------
> Ran 554 tests in 427.062 seconds
>
> FAILED (failures = 1)
> Skipping any tests requiring internet access
> Python version: 3.10.9 (main, Dec 7 2022, 13:47:07) [GCC 12.2.0]
> Operating system: posix linux
> E: pybuild pybuild:388: test: plugin custom failed with: exit code=1: set -e; \
> mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/home; \
> mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc/examples; \
> cp -a Doc/Tutorial.tex /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc; \
> cp -a Doc/Tutorial /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc; \
> cp -a Doc/examples /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc; \
> cp -a Tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build; \
> cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests; \
> env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/home python3.10 run_tests.py --offline
> rm -fr -- /tmp/dh-xdg-rundir-SDL8yfPf
> dh_auto_test: error: pybuild --test -i python{version} -p "3.11 3.10" --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/2023/01/01/python-biopython_1.80+dfsg-4_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230101;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230101&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
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!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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