[Debian-med-packaging] Bug#1022307: python-biopython: FTBFS: mv: cannot stat 'Tests/test_NACCESS_tool.py': No such file or directory
Lucas Nussbaum
lucas at debian.org
Sun Oct 23 13:50:27 BST 2022
Source: python-biopython
Version: 1.79+dfsg-3
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20221023 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 3.10 --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_3.10/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
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests/run_tests.py:33: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
> import distutils.util
> /usr/lib/python3/dist-packages/_distutils_hack/__init__.py:18: UserWarning: Distutils was imported before Setuptools, but importing Setuptools also replaces the `distutils` module in `sys.modules`. This may lead to undesirable behaviors or errors. To avoid these issues, avoid using distutils directly, ensure that setuptools is installed in the traditional way (e.g. not an editable install), and/or make sure that setuptools is always imported before distutils.
> warnings.warn(
> /usr/lib/python3/dist-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils.
> warnings.warn("Setuptools is replacing distutils.")
> 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_Dialign_tool ... ok
> test_EMBL_unittest ... ok
> test_Emboss ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: mRNA
> warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
> 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_Fasttree_tool ... ok
> test_File ... ok
> test_GenBank ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: genomic DNA
> warnings.warn("Non-standard molecule type: %s" % 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 ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
> 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_DSSP ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:252: UserWarning: Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match
>
> warnings.warn(err)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:252: UserWarning: Unknown or untrusted program in REMARK 3, trying all parsers to see if there is a match
>
> warnings.warn(err)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:252: UserWarning: Invalid mmCIF file use --verbose option to see errors
>
> warnings.warn(err)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:252: UserWarning: Invalid mmCIF file use --verbose option to see errors
>
> warnings.warn(err)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:252: UserWarning: Invalid mmCIF file use --verbose option to see errors
>
> warnings.warn(err)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/PDB/DSSP.py:252: UserWarning: Invalid mmCIF file use --verbose option to see errors
>
> warnings.warn(err)
> ok
> 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_Polypeptide ... ok
> test_PDB_SASA ... ok
> test_PDB_SMCRA ... ok
> test_PDB_StructureAlignment ... 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_3.10/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:1256: BiopythonWarning: Non-standard molecule type: mRNA
> warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: unassigned DNA
> warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: genomic DNA
> warnings.warn("Non-standard molecule type: %s" % 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:1256: BiopythonWarning: Non-standard molecule type: unassigned DNA
> warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: genomic DNA
> warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: mRNA
> warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning)
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SeqIO/InsdcIO.py:548: 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_SubsMat ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/SubsMat/__init__.py:126: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.
> warnings.warn(
> ok
> test_SwissProt ... ok
> test_TCoffee_tool ... FAIL
> test_TogoWS ... skipping. internet not available
> test_TreeConstruction ... ok
> test_Tutorial ... /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/Seq.py:2008: BiopythonDeprecationWarning: UnknownSeq(length) is deprecated; please use Seq(None, length) instead.
> 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:2954: 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_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.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.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.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.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.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.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_TCoffee_clustalw (test_TCoffee_tool.TCoffeeApplication)
> Round-trip through app and read clustalw alignment from file.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests/test_TCoffee_tool.py", line 109, in test_TCoffee_clustalw
> stdout, stderr = cmdline()
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/Application/__init__.py", line 574, in __call__
> raise ApplicationError(return_code, str(self), stdout_str, stderr_str)
> Bio.Application.ApplicationError: Non-zero return code 11 from 't_coffee -output clustalw_aln -infile Fasta/fa01 -outfile Fasta/tc_out.aln -type protein -outorder input -gapopen -2 -gapext -5', message 'PROGRAM: T-COFFEE Version_13.45.0.4846264 (2020-09-21 17:25:40 - Revision 0818d8a - Build 619)'
>
> ======================================================================
> ERROR: test_TCoffee_fasta (test_TCoffee_tool.TCoffeeApplication)
> Round-trip through app and read clustal alignment from file.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests/test_TCoffee_tool.py", line 60, in test_TCoffee_fasta
> stdout, stderr = cmdline()
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/Application/__init__.py", line 574, in __call__
> raise ApplicationError(return_code, str(self), stdout_str, stderr_str)
> Bio.Application.ApplicationError: Non-zero return code 11 from 't_coffee -infile Fasta/fa01', message 'PROGRAM: T-COFFEE Version_13.45.0.4846264 (2020-09-21 17:25:40 - Revision 0818d8a - Build 619)'
>
> ======================================================================
> ERROR: test_TCoffee_msf (test_TCoffee_tool.TCoffeeApplication)
> Round-trip through app and read GCG MSF alignment from file.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests/test_TCoffee_tool.py", line 161, in test_TCoffee_msf
> stdout, stderr = cmdline()
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/Application/__init__.py", line 574, in __call__
> raise ApplicationError(return_code, str(self), stdout_str, stderr_str)
> Bio.Application.ApplicationError: Non-zero return code 11 from 't_coffee -output msf_aln -infile Fasta/fa01 -outfile Fasta/tc_out.msf -quiet', message '*************************************************************************************************'
>
> ======================================================================
> ERROR: test_TCoffee_phylip (test_TCoffee_tool.TCoffeeApplication)
> Round-trip through app and read PHYLIP alignment from file.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests/test_TCoffee_tool.py", line 134, in test_TCoffee_phylip
> stdout, stderr = cmdline()
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/Application/__init__.py", line 574, in __call__
> raise ApplicationError(return_code, str(self), stdout_str, stderr_str)
> Bio.Application.ApplicationError: Non-zero return code 11 from 't_coffee -output phylip_aln -infile Fasta/fa01 -outfile Fasta/tc_out.phy -quiet', message '*************************************************************************************************'
>
> ======================================================================
> ERROR: test_TCoffee_pir (test_TCoffee_tool.TCoffeeApplication)
> Round-trip through app and read pir alignment from file.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests/test_TCoffee_tool.py", line 82, in test_TCoffee_pir
> stdout, stderr = cmdline()
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Bio/Application/__init__.py", line 574, in __call__
> raise ApplicationError(return_code, str(self), stdout_str, stderr_str)
> Bio.Application.ApplicationError: Non-zero return code 11 from 't_coffee -output pir_aln -infile Fasta/fa01 -outfile Fasta/tc_out.pir -quiet', message '*************************************************************************************************'
>
> ----------------------------------------------------------------------
> Ran 513 tests in 322.404 seconds
>
> FAILED (failures = 1)
> Skipping any tests requiring internet access
> Python version: 3.10.7 (main, Oct 1 2022, 04:31:04) [GCC 12.2.0]
> Operating system: posix linux
> E: pybuild pybuild:379: 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-pKtyzKJo
> dh_auto_test: error: pybuild --test -i python{version} -p 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/2022/10/23/python-biopython_1.79+dfsg-3_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20221023;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221023&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 marking 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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