Mock Version: 1.4.14
Mock Version: 1.4.14
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/f31-build-110588-34027/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x15580c1cf8>timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1565913600
Wrote: /builddir/build/SRPMS/python-biopython-1.74-1.fc31.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/f31-build-110588-34027/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x15580c1cf8>timeout=432000uid=986gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1565913600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.tYvAir
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf python-biopython-1.74
+ /usr/bin/mkdir -p python-biopython-1.74
+ cd python-biopython-1.74
+ /usr/bin/tar -xof -
+ /usr/bin/gzip -dc /builddir/build/SOURCES/biopython-1.74.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ pushd biopython-1.74
~/build/BUILD/python-biopython-1.74/biopython-1.74 ~/build/BUILD/python-biopython-1.74
+ find Scripts -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec sed -i 's/\r//' '{}' ';'
+ find Bio -type f -exec chmod -x '{}' ';'
+ find Bio -type f -name '*.py' -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' '{}' ';'
+ popd
~/build/BUILD/python-biopython-1.74
+ cp -a biopython-1.74 python3
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.KeCmzq
+ umask 022
~/build/BUILD/python-biopython-1.74/python3 ~/build/BUILD/python-biopython-1.74
+ cd /builddir/build/BUILD
+ cd python-biopython-1.74
+ pushd python3
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -s'
running build
running build_py
creating build
creating build/lib.linux-riscv64-3.7
creating build/lib.linux-riscv64-3.7/Bio
copying Bio/bgzf.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/LogisticRegression.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/File.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/Index.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/pairwise2.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/MaxEntropy.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/__init__.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/SeqRecord.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/Seq.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/kNN.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/MarkovModel.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/SeqFeature.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/_utils.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/triefind.py -> build/lib.linux-riscv64-3.7/Bio
copying Bio/NaiveBayes.py -> build/lib.linux-riscv64-3.7/Bio
creating build/lib.linux-riscv64-3.7/Bio/Align
copying Bio/Align/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Align
copying Bio/Align/AlignInfo.py -> build/lib.linux-riscv64-3.7/Bio/Align
creating build/lib.linux-riscv64-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-riscv64-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-riscv64-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-riscv64-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> build/lib.linux-riscv64-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-riscv64-3.7/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-riscv64-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-riscv64-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-riscv64-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-riscv64-3.7/Bio/Align/Applications
creating build/lib.linux-riscv64-3.7/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-riscv64-3.7/Bio/AlignIO
copying Bio/AlignIO/MafIO.py -> build/lib.linux-riscv64-3.7/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-riscv64-3.7/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> build/lib.linux-riscv64-3.7/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> build/lib.linux-riscv64-3.7/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-riscv64-3.7/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-riscv64-3.7/Bio/AlignIO
copying Bio/AlignIO/MauveIO.py -> build/lib.linux-riscv64-3.7/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> build/lib.linux-riscv64-3.7/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> build/lib.linux-riscv64-3.7/Bio/AlignIO
creating build/lib.linux-riscv64-3.7/Bio/Alphabet
copying Bio/Alphabet/Reduced.py -> build/lib.linux-riscv64-3.7/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Alphabet
copying Bio/Alphabet/IUPAC.py -> build/lib.linux-riscv64-3.7/Bio/Alphabet
creating build/lib.linux-riscv64-3.7/Bio/Application
copying Bio/Application/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Application
creating build/lib.linux-riscv64-3.7/Bio/Blast
copying Bio/Blast/Record.py -> build/lib.linux-riscv64-3.7/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> build/lib.linux-riscv64-3.7/Bio/Blast
copying Bio/Blast/Applications.py -> build/lib.linux-riscv64-3.7/Bio/Blast
copying Bio/Blast/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Blast
copying Bio/Blast/NCBIXML.py -> build/lib.linux-riscv64-3.7/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-riscv64-3.7/Bio/Blast
creating build/lib.linux-riscv64-3.7/Bio/CAPS
copying Bio/CAPS/__init__.py -> build/lib.linux-riscv64-3.7/Bio/CAPS
creating build/lib.linux-riscv64-3.7/Bio/codonalign
copying Bio/codonalign/codonseq.py -> build/lib.linux-riscv64-3.7/Bio/codonalign
copying Bio/codonalign/__init__.py -> build/lib.linux-riscv64-3.7/Bio/codonalign
copying Bio/codonalign/codonalphabet.py -> build/lib.linux-riscv64-3.7/Bio/codonalign
copying Bio/codonalign/chisq.py -> build/lib.linux-riscv64-3.7/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> build/lib.linux-riscv64-3.7/Bio/codonalign
creating build/lib.linux-riscv64-3.7/Bio/Compass
copying Bio/Compass/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Compass
creating build/lib.linux-riscv64-3.7/Bio/Crystal
copying Bio/Crystal/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Crystal
creating build/lib.linux-riscv64-3.7/Bio/Data
copying Bio/Data/CodonTable.py -> build/lib.linux-riscv64-3.7/Bio/Data
copying Bio/Data/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Data
copying Bio/Data/IUPACData.py -> build/lib.linux-riscv64-3.7/Bio/Data
copying Bio/Data/SCOPData.py -> build/lib.linux-riscv64-3.7/Bio/Data
creating build/lib.linux-riscv64-3.7/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-riscv64-3.7/Bio/Emboss
copying Bio/Emboss/Primer3.py -> build/lib.linux-riscv64-3.7/Bio/Emboss
copying Bio/Emboss/Applications.py -> build/lib.linux-riscv64-3.7/Bio/Emboss
copying Bio/Emboss/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Emboss
creating build/lib.linux-riscv64-3.7/Bio/Entrez
copying Bio/Entrez/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Entrez
copying Bio/Entrez/Parser.py -> build/lib.linux-riscv64-3.7/Bio/Entrez
creating build/lib.linux-riscv64-3.7/Bio/ExPASy
copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-riscv64-3.7/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-riscv64-3.7/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> build/lib.linux-riscv64-3.7/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> build/lib.linux-riscv64-3.7/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> build/lib.linux-riscv64-3.7/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> build/lib.linux-riscv64-3.7/Bio/ExPASy
creating build/lib.linux-riscv64-3.7/Bio/FSSP
copying Bio/FSSP/__init__.py -> build/lib.linux-riscv64-3.7/Bio/FSSP
copying Bio/FSSP/FSSPTools.py -> build/lib.linux-riscv64-3.7/Bio/FSSP
copying Bio/FSSP/fssp_rec.py -> build/lib.linux-riscv64-3.7/Bio/FSSP
creating build/lib.linux-riscv64-3.7/Bio/GenBank
copying Bio/GenBank/Record.py -> build/lib.linux-riscv64-3.7/Bio/GenBank
copying Bio/GenBank/Scanner.py -> build/lib.linux-riscv64-3.7/Bio/GenBank
copying Bio/GenBank/__init__.py -> build/lib.linux-riscv64-3.7/Bio/GenBank
copying Bio/GenBank/utils.py -> build/lib.linux-riscv64-3.7/Bio/GenBank
creating build/lib.linux-riscv64-3.7/Bio/Geo
copying Bio/Geo/Record.py -> build/lib.linux-riscv64-3.7/Bio/Geo
copying Bio/Geo/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Geo
creating build/lib.linux-riscv64-3.7/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-riscv64-3.7/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> build/lib.linux-riscv64-3.7/Bio/Graphics
copying Bio/Graphics/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-riscv64-3.7/Bio/Graphics
copying Bio/Graphics/Comparative.py -> build/lib.linux-riscv64-3.7/Bio/Graphics
copying Bio/Graphics/Distribution.py -> build/lib.linux-riscv64-3.7/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-riscv64-3.7/Bio/Graphics
creating build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram
creating build/lib.linux-riscv64-3.7/Bio/HMM
copying Bio/HMM/Utilities.py -> build/lib.linux-riscv64-3.7/Bio/HMM
copying Bio/HMM/__init__.py -> build/lib.linux-riscv64-3.7/Bio/HMM
copying Bio/HMM/MarkovModel.py -> build/lib.linux-riscv64-3.7/Bio/HMM
copying Bio/HMM/Trainer.py -> build/lib.linux-riscv64-3.7/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-riscv64-3.7/Bio/HMM
creating build/lib.linux-riscv64-3.7/Bio/KEGG
copying Bio/KEGG/__init__.py -> build/lib.linux-riscv64-3.7/Bio/KEGG
copying Bio/KEGG/REST.py -> build/lib.linux-riscv64-3.7/Bio/KEGG
creating build/lib.linux-riscv64-3.7/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-riscv64-3.7/Bio/KEGG/Compound
creating build/lib.linux-riscv64-3.7/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-riscv64-3.7/Bio/KEGG/Enzyme
creating build/lib.linux-riscv64-3.7/Bio/KEGG/Gene
copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-riscv64-3.7/Bio/KEGG/Gene
creating build/lib.linux-riscv64-3.7/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> build/lib.linux-riscv64-3.7/Bio/KEGG/Map
creating build/lib.linux-riscv64-3.7/Bio/PDB
creating build/lib.linux-riscv64-3.7/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-riscv64-3.7/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-riscv64-3.7/Bio/PDB/mmtf
creating build/lib.linux-riscv64-3.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-riscv64-3.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-riscv64-3.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-riscv64-3.7/Bio/KEGG/KGML
creating build/lib.linux-riscv64-3.7/Bio/Medline
copying Bio/Medline/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Medline
creating build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/mast.py -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/xms.py -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/minimal.py -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/thresholds.py -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/__init__.py -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/clusterbuster.py -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/alignace.py -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/matrix.py -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/pfm.py -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/meme.py -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/motifs/transfac.py -> build/lib.linux-riscv64-3.7/Bio/motifs
creating build/lib.linux-riscv64-3.7/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> build/lib.linux-riscv64-3.7/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-riscv64-3.7/Bio/motifs/applications
creating build/lib.linux-riscv64-3.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> build/lib.linux-riscv64-3.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-riscv64-3.7/Bio/motifs/jaspar
creating build/lib.linux-riscv64-3.7/Bio/Nexus
copying Bio/Nexus/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Nexus
copying Bio/Nexus/Nexus.py -> build/lib.linux-riscv64-3.7/Bio/Nexus
copying Bio/Nexus/Trees.py -> build/lib.linux-riscv64-3.7/Bio/Nexus
copying Bio/Nexus/StandardData.py -> build/lib.linux-riscv64-3.7/Bio/Nexus
copying Bio/Nexus/Nodes.py -> build/lib.linux-riscv64-3.7/Bio/Nexus
creating build/lib.linux-riscv64-3.7/Bio/NMR
copying Bio/NMR/__init__.py -> build/lib.linux-riscv64-3.7/Bio/NMR
copying Bio/NMR/NOEtools.py -> build/lib.linux-riscv64-3.7/Bio/NMR
copying Bio/NMR/xpktools.py -> build/lib.linux-riscv64-3.7/Bio/NMR
creating build/lib.linux-riscv64-3.7/Bio/Pathway
copying Bio/Pathway/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Pathway
creating build/lib.linux-riscv64-3.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-riscv64-3.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-riscv64-3.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Pathway/Rep
copying Bio/PDB/Chain.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/NACCESS.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/Entity.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/Atom.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/HSExposure.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/__init__.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/Structure.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/Residue.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/Superimposer.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/vectors.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/PDBList.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/Dice.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/PSEA.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/DSSP.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/PDBIO.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/Polypeptide.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/mmcifio.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/Model.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/Selection.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/PDBParser.py -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-riscv64-3.7/Bio/PDB
creating build/lib.linux-riscv64-3.7/Bio/PopGen
copying Bio/PopGen/__init__.py -> build/lib.linux-riscv64-3.7/Bio/PopGen
creating build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Utils.py -> build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop
creating build/lib.linux-riscv64-3.7/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> build/lib.linux-riscv64-3.7/Bio/Restriction
copying Bio/Restriction/Restriction.py -> build/lib.linux-riscv64-3.7/Bio/Restriction
copying Bio/Restriction/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-riscv64-3.7/Bio/Restriction
creating build/lib.linux-riscv64-3.7/Bio/SCOP
copying Bio/SCOP/Residues.py -> build/lib.linux-riscv64-3.7/Bio/SCOP
copying Bio/SCOP/Dom.py -> build/lib.linux-riscv64-3.7/Bio/SCOP
copying Bio/SCOP/Raf.py -> build/lib.linux-riscv64-3.7/Bio/SCOP
copying Bio/SCOP/Hie.py -> build/lib.linux-riscv64-3.7/Bio/SCOP
copying Bio/SCOP/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SCOP
copying Bio/SCOP/Cla.py -> build/lib.linux-riscv64-3.7/Bio/SCOP
copying Bio/SCOP/Des.py -> build/lib.linux-riscv64-3.7/Bio/SCOP
creating build/lib.linux-riscv64-3.7/Bio/SearchIO
copying Bio/SearchIO/_index.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO
copying Bio/SearchIO/BlatIO.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO
copying Bio/SearchIO/FastaIO.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO
creating build/lib.linux-riscv64-3.7/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/NCBIStandalone.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/ParserSupport.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/_legacy
creating build/lib.linux-riscv64-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/_base.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/_model
creating build/lib.linux-riscv64-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/BlastIO
creating build/lib.linux-riscv64-3.7/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/HHsuiteIO
creating build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO
creating build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO
creating build/lib.linux-riscv64-3.7/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SearchIO/InterproscanIO
creating build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/NibIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/_index.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/AceIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/_convert.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-riscv64-3.7/Bio/SeqIO
creating build/lib.linux-riscv64-3.7/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-riscv64-3.7/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-riscv64-3.7/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-riscv64-3.7/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-riscv64-3.7/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-riscv64-3.7/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-riscv64-3.7/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-riscv64-3.7/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> build/lib.linux-riscv64-3.7/Bio/SeqUtils
creating build/lib.linux-riscv64-3.7/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> build/lib.linux-riscv64-3.7/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> build/lib.linux-riscv64-3.7/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Sequencing
creating build/lib.linux-riscv64-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-riscv64-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-riscv64-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-riscv64-3.7/Bio/Sequencing/Applications
creating build/lib.linux-riscv64-3.7/Bio/Statistics
copying Bio/Statistics/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Statistics
copying Bio/Statistics/lowess.py -> build/lib.linux-riscv64-3.7/Bio/Statistics
creating build/lib.linux-riscv64-3.7/Bio/SubsMat
copying Bio/SubsMat/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SubsMat
copying Bio/SubsMat/FreqTable.py -> build/lib.linux-riscv64-3.7/Bio/SubsMat
copying Bio/SubsMat/MatrixInfo.py -> build/lib.linux-riscv64-3.7/Bio/SubsMat
creating build/lib.linux-riscv64-3.7/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SVDSuperimposer
creating build/lib.linux-riscv64-3.7/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.linux-riscv64-3.7/Bio/PDB/QCPSuperimposer
creating build/lib.linux-riscv64-3.7/Bio/SwissProt
copying Bio/SwissProt/KeyWList.py -> build/lib.linux-riscv64-3.7/Bio/SwissProt
copying Bio/SwissProt/__init__.py -> build/lib.linux-riscv64-3.7/Bio/SwissProt
creating build/lib.linux-riscv64-3.7/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> build/lib.linux-riscv64-3.7/Bio/TogoWS
creating build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/Newick.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/BaseTree.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/NeXML.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/Consensus.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/_io.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/_utils.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
copying Bio/Phylo/CDAO.py -> build/lib.linux-riscv64-3.7/Bio/Phylo
creating build/lib.linux-riscv64-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/Applications
creating build/lib.linux-riscv64-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-riscv64-3.7/Bio/Phylo/PAML
creating build/lib.linux-riscv64-3.7/Bio/UniGene
copying Bio/UniGene/__init__.py -> build/lib.linux-riscv64-3.7/Bio/UniGene
creating build/lib.linux-riscv64-3.7/Bio/UniProt
copying Bio/UniProt/GOA.py -> build/lib.linux-riscv64-3.7/Bio/UniProt
copying Bio/UniProt/__init__.py -> build/lib.linux-riscv64-3.7/Bio/UniProt
creating build/lib.linux-riscv64-3.7/Bio/Wise
copying Bio/Wise/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Wise
copying Bio/Wise/dnal.py -> build/lib.linux-riscv64-3.7/Bio/Wise
copying Bio/Wise/psw.py -> build/lib.linux-riscv64-3.7/Bio/Wise
creating build/lib.linux-riscv64-3.7/Bio/_py3k
copying Bio/_py3k/__init__.py -> build/lib.linux-riscv64-3.7/Bio/_py3k
creating build/lib.linux-riscv64-3.7/BioSQL
copying BioSQL/Loader.py -> build/lib.linux-riscv64-3.7/BioSQL
copying BioSQL/DBUtils.py -> build/lib.linux-riscv64-3.7/BioSQL
copying BioSQL/__init__.py -> build/lib.linux-riscv64-3.7/BioSQL
copying BioSQL/BioSeq.py -> build/lib.linux-riscv64-3.7/BioSQL
copying BioSQL/BioSeqDatabase.py -> build/lib.linux-riscv64-3.7/BioSQL
creating build/lib.linux-riscv64-3.7/Bio/Affy
copying Bio/Affy/CelFile.py -> build/lib.linux-riscv64-3.7/Bio/Affy
copying Bio/Affy/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Affy
creating build/lib.linux-riscv64-3.7/Bio/Cluster
copying Bio/Cluster/__init__.py -> build/lib.linux-riscv64-3.7/Bio/Cluster
creating build/lib.linux-riscv64-3.7/Bio/KDTree
copying Bio/KDTree/KDTree.py -> build/lib.linux-riscv64-3.7/Bio/KDTree
copying Bio/KDTree/__init__.py -> build/lib.linux-riscv64-3.7/Bio/KDTree
creating build/lib.linux-riscv64-3.7/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> build/lib.linux-riscv64-3.7/Bio/phenotype
copying Bio/phenotype/phen_micro.py -> build/lib.linux-riscv64-3.7/Bio/phenotype
copying Bio/phenotype/__init__.py -> build/lib.linux-riscv64-3.7/Bio/phenotype
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
BUILDSTDERR: warning: no previously-included files matching '*.pyc' found anywhere in distribution
BUILDSTDERR: warning: no previously-included files matching '*.pyo' found anywhere in distribution
BUILDSTDERR: warning: no previously-included files matching '*.py{}' found anywhere in distribution
BUILDSTDERR: warning: no previously-included files matching '*.py-e' found anywhere in distribution
writing manifest file 'biopython.egg-info/SOURCES.txt'
copying Bio/cpairwise2module.c -> build/lib.linux-riscv64-3.7/Bio
copying Bio/trie.c -> build/lib.linux-riscv64-3.7/Bio
copying Bio/trie.h -> build/lib.linux-riscv64-3.7/Bio
copying Bio/triemodule.c -> build/lib.linux-riscv64-3.7/Bio
copying Bio/Align/_aligners.c -> build/lib.linux-riscv64-3.7/Bio/Align
creating build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs
creating build/lib.linux-riscv64-3.7/Bio/Entrez/XSDs
copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-riscv64-3.7/Bio/Entrez/XSDs
copying Bio/motifs/_pwm.c -> build/lib.linux-riscv64-3.7/Bio/motifs
copying Bio/Nexus/cnexus.c -> build/lib.linux-riscv64-3.7/Bio/Nexus
copying Bio/PDB/kdtrees.c -> build/lib.linux-riscv64-3.7/Bio/PDB
copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> build/lib.linux-riscv64-3.7/Bio/PDB/QCPSuperimposer
copying Bio/Cluster/cluster.c -> build/lib.linux-riscv64-3.7/Bio/Cluster
copying Bio/Cluster/cluster.h -> build/lib.linux-riscv64-3.7/Bio/Cluster
copying Bio/Cluster/clustermodule.c -> build/lib.linux-riscv64-3.7/Bio/Cluster
copying Bio/KDTree/KDTree.c -> build/lib.linux-riscv64-3.7/Bio/KDTree
copying Bio/KDTree/KDTree.h -> build/lib.linux-riscv64-3.7/Bio/KDTree
copying Bio/KDTree/KDTreemodule.c -> build/lib.linux-riscv64-3.7/Bio/KDTree
copying Bio/KDTree/Neighbor.h -> build/lib.linux-riscv64-3.7/Bio/KDTree
running build_ext
building 'Bio.Align._aligners' extension
creating build/temp.linux-riscv64-3.7
creating build/temp.linux-riscv64-3.7/Bio
creating build/temp.linux-riscv64-3.7/Bio/Align
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.7m -c Bio/Align/_aligners.c -o build/temp.linux-riscv64-3.7/Bio/Align/_aligners.o
BUILDSTDERR: Bio/Align/_aligners.c: In function ‘PathGenerator_length’:
BUILDSTDERR: Bio/Align/_aligners.c:700:22: warning: ‘count’ may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   700 |         self->length = length;
BUILDSTDERR:       |         ~~~~~~~~~~~~~^~~~~~~~
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-riscv64-3.7/Bio/Align/_aligners.o -L/usr/lib64 -lpython3.7m -o build/lib.linux-riscv64-3.7/Bio/Align/_aligners.cpython-37m-riscv64-linux-gnu.so
building 'Bio.cpairwise2' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.7m -c Bio/cpairwise2module.c -o build/temp.linux-riscv64-3.7/Bio/cpairwise2module.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-riscv64-3.7/Bio/cpairwise2module.o -L/usr/lib64 -lpython3.7m -o build/lib.linux-riscv64-3.7/Bio/cpairwise2.cpython-37m-riscv64-linux-gnu.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-riscv64-3.7/Bio/Nexus
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.7m -c Bio/Nexus/cnexus.c -o build/temp.linux-riscv64-3.7/Bio/Nexus/cnexus.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-riscv64-3.7/Bio/Nexus/cnexus.o -L/usr/lib64 -lpython3.7m -o build/lib.linux-riscv64-3.7/Bio/Nexus/cnexus.cpython-37m-riscv64-linux-gnu.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-riscv64-3.7/Bio/PDB
creating build/temp.linux-riscv64-3.7/Bio/PDB/QCPSuperimposer
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.7m -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-riscv64-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-riscv64-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib64 -lpython3.7m -o build/lib.linux-riscv64-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-riscv64-linux-gnu.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-riscv64-3.7/Bio/motifs
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.7m -c Bio/motifs/_pwm.c -o build/temp.linux-riscv64-3.7/Bio/motifs/_pwm.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-riscv64-3.7/Bio/motifs/_pwm.o -L/usr/lib64 -lpython3.7m -o build/lib.linux-riscv64-3.7/Bio/motifs/_pwm.cpython-37m-riscv64-linux-gnu.so
building 'Bio.Cluster._cluster' extension
creating build/temp.linux-riscv64-3.7/Bio/Cluster
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.7m -c Bio/Cluster/cluster.c -o build/temp.linux-riscv64-3.7/Bio/Cluster/cluster.o
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.7m -c Bio/Cluster/clustermodule.c -o build/temp.linux-riscv64-3.7/Bio/Cluster/clustermodule.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-riscv64-3.7/Bio/Cluster/cluster.o build/temp.linux-riscv64-3.7/Bio/Cluster/clustermodule.o -L/usr/lib64 -lpython3.7m -o build/lib.linux-riscv64-3.7/Bio/Cluster/_cluster.cpython-37m-riscv64-linux-gnu.so
building 'Bio.PDB.kdtrees' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.7m -c Bio/PDB/kdtrees.c -o build/temp.linux-riscv64-3.7/Bio/PDB/kdtrees.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-riscv64-3.7/Bio/PDB/kdtrees.o -L/usr/lib64 -lpython3.7m -o build/lib.linux-riscv64-3.7/Bio/PDB/kdtrees.cpython-37m-riscv64-linux-gnu.so
building 'Bio.KDTree._CKDTree' extension
creating build/temp.linux-riscv64-3.7/Bio/KDTree
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.7m -c Bio/KDTree/KDTree.c -o build/temp.linux-riscv64-3.7/Bio/KDTree/KDTree.o
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.7m -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-riscv64-3.7/Bio/KDTree/KDTreemodule.o
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-riscv64-3.7/Bio/KDTree/KDTree.o build/temp.linux-riscv64-3.7/Bio/KDTree/KDTreemodule.o -L/usr/lib64 -lpython3.7m -o build/lib.linux-riscv64-3.7/Bio/KDTree/_CKDTree.cpython-37m-riscv64-linux-gnu.so
building 'Bio.trie' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -IBio -I/usr/include/python3.7m -c Bio/triemodule.c -o build/temp.linux-riscv64-3.7/Bio/triemodule.o
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -IBio -I/usr/include/python3.7m -c Bio/trie.c -o build/temp.linux-riscv64-3.7/Bio/trie.o
BUILDSTDERR: In file included from /usr/include/string.h:494,
BUILDSTDERR:                  from Bio/trie.c:17:
BUILDSTDERR: In function ‘strncat’,
BUILDSTDERR:     inlined from ‘_with_prefix_helper.constprop’ at Bio/trie.c:595:6:
BUILDSTDERR: /usr/include/bits/string_fortified.h:136:10: warning: ‘__builtin___strncat_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
BUILDSTDERR:   136 |   return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
BUILDSTDERR:       |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: Bio/trie.c: In function ‘_with_prefix_helper.constprop’:
BUILDSTDERR: Bio/trie.c:561:14: note: length computed here
BUILDSTDERR:   561 |  suffixlen = strlen(suffix);
BUILDSTDERR:       |              ^~~~~~~~~~~~~~
gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-riscv64-3.7/Bio/triemodule.o build/temp.linux-riscv64-3.7/Bio/trie.o -L/usr/lib64 -lpython3.7m -o build/lib.linux-riscv64-3.7/Bio/trie.cpython-37m-riscv64-linux-gnu.so
+ popd
~/build/BUILD/python-biopython-1.74
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.J3ORgq
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64
BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64
+ cd python-biopython-1.74
~/build/BUILD/python-biopython-1.74/python3 ~/build/BUILD/python-biopython-1.74
+ pushd python3
+ /usr/bin/python3 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64 --install-data=/usr/share/python-biopython
running install
running install_lib
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/NibIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/_convert.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-riscv64-3.7/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Alphabet
copying build/lib.linux-riscv64-3.7/Bio/Alphabet/Reduced.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Alphabet
copying build/lib.linux-riscv64-3.7/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Alphabet
copying build/lib.linux-riscv64-3.7/Bio/Alphabet/IUPAC.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Alphabet
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-riscv64-3.7/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
copying build/lib.linux-riscv64-3.7/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-riscv64-3.7/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-riscv64-3.7/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-riscv64-3.7/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-riscv64-3.7/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-riscv64-3.7/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-riscv64-3.7/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-riscv64-3.7/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-riscv64-3.7/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-riscv64-3.7/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-riscv64-3.7/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Compass
copying build/lib.linux-riscv64-3.7/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Compass
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-riscv64-3.7/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-riscv64-3.7/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-riscv64-3.7/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-riscv64-3.7/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Emboss
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SubsMat
copying build/lib.linux-riscv64-3.7/Bio/SubsMat/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SubsMat
copying build/lib.linux-riscv64-3.7/Bio/SubsMat/FreqTable.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SubsMat
copying build/lib.linux-riscv64-3.7/Bio/SubsMat/MatrixInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SubsMat
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-riscv64-3.7/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-riscv64-3.7/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-riscv64-3.7/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-riscv64-3.7/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-riscv64-3.7/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-riscv64-3.7/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-riscv64-3.7/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/TogoWS
copying build/lib.linux-riscv64-3.7/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/TogoWS
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Application
copying build/lib.linux-riscv64-3.7/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Application
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/NMR
copying build/lib.linux-riscv64-3.7/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/NMR
copying build/lib.linux-riscv64-3.7/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/NMR
copying build/lib.linux-riscv64-3.7/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/NMR
copying build/lib.linux-riscv64-3.7/Bio/trie.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-riscv64-3.7/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-riscv64-3.7/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-riscv64-3.7/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-riscv64-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-riscv64-3.7/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-riscv64-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-riscv64-3.7/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/kdtrees.cpython-37m-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PDB
copying build/lib.linux-riscv64-3.7/Bio/cpairwise2.cpython-37m-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-riscv64-3.7/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-riscv64-3.7/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-riscv64-3.7/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-riscv64-3.7/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/GenBank
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Geo
copying build/lib.linux-riscv64-3.7/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Geo
copying build/lib.linux-riscv64-3.7/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Geo
copying build/lib.linux-riscv64-3.7/Bio/Index.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SVDSuperimposer
copying build/lib.linux-riscv64-3.7/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SVDSuperimposer
copying build/lib.linux-riscv64-3.7/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
copying build/lib.linux-riscv64-3.7/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/HHsuiteIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/InterproscanIO
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/ExonerateIO
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/_legacy/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/_legacy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-riscv64-3.7/Bio/SearchIO/_legacy/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SearchIO/_legacy
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/FSSP
copying build/lib.linux-riscv64-3.7/Bio/FSSP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/FSSP
copying build/lib.linux-riscv64-3.7/Bio/FSSP/FSSPTools.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/FSSP
copying build/lib.linux-riscv64-3.7/Bio/FSSP/fssp_rec.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/FSSP
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-riscv64-3.7/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-riscv64-3.7/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-riscv64-3.7/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/xms.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/clusterbuster.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs/applications
copying build/lib.linux-riscv64-3.7/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs/applications
copying build/lib.linux-riscv64-3.7/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs/applications
copying build/lib.linux-riscv64-3.7/Bio/motifs/_pwm.cpython-37m-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/pfm.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs
copying build/lib.linux-riscv64-3.7/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PopGen
copying build/lib.linux-riscv64-3.7/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop/Utils.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-riscv64-3.7/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/PopGen/GenePop
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Sequencing
copying build/lib.linux-riscv64-3.7/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Sequencing
copying build/lib.linux-riscv64-3.7/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Sequencing
copying build/lib.linux-riscv64-3.7/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-riscv64-3.7/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-riscv64-3.7/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-riscv64-3.7/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-riscv64-3.7/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Sequencing/Applications
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/Enzyme
copying build/lib.linux-riscv64-3.7/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/Enzyme
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/Gene
copying build/lib.linux-riscv64-3.7/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/Gene
copying build/lib.linux-riscv64-3.7/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-riscv64-3.7/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-riscv64-3.7/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-riscv64-3.7/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/KGML
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/Map
copying build/lib.linux-riscv64-3.7/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/Map
copying build/lib.linux-riscv64-3.7/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/Compound
copying build/lib.linux-riscv64-3.7/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KEGG/Compound
copying build/lib.linux-riscv64-3.7/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
copying build/lib.linux-riscv64-3.7/Bio/triemodule.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/HMM
copying build/lib.linux-riscv64-3.7/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/HMM
copying build/lib.linux-riscv64-3.7/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/HMM
copying build/lib.linux-riscv64-3.7/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/HMM
copying build/lib.linux-riscv64-3.7/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/HMM
copying build/lib.linux-riscv64-3.7/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/HMM
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-riscv64-3.7/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-riscv64-3.7/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-riscv64-3.7/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-riscv64-3.7/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-riscv64-3.7/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-riscv64-3.7/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-riscv64-3.7/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SCOP
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Statistics
copying build/lib.linux-riscv64-3.7/Bio/Statistics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Statistics
copying build/lib.linux-riscv64-3.7/Bio/Statistics/lowess.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Statistics
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-riscv64-3.7/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-riscv64-3.7/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-riscv64-3.7/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-riscv64-3.7/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-riscv64-3.7/Bio/Cluster/_cluster.cpython-37m-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Cluster
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SwissProt
copying build/lib.linux-riscv64-3.7/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SwissProt
copying build/lib.linux-riscv64-3.7/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SwissProt
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Medline
copying build/lib.linux-riscv64-3.7/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Medline
copying build/lib.linux-riscv64-3.7/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
copying build/lib.linux-riscv64-3.7/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-riscv64-3.7/Bio/Nexus/cnexus.cpython-37m-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-riscv64-3.7/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-riscv64-3.7/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-riscv64-3.7/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-riscv64-3.7/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-riscv64-3.7/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-riscv64-3.7/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-riscv64-3.7/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/UniGene
copying build/lib.linux-riscv64-3.7/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/UniGene
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-riscv64-3.7/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-riscv64-3.7/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-riscv64-3.7/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-riscv64-3.7/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-riscv64-3.7/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-riscv64-3.7/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-riscv64-3.7/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Blast
copying build/lib.linux-riscv64-3.7/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Blast
copying build/lib.linux-riscv64-3.7/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Blast
copying build/lib.linux-riscv64-3.7/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Blast
copying build/lib.linux-riscv64-3.7/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Blast
copying build/lib.linux-riscv64-3.7/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Blast
copying build/lib.linux-riscv64-3.7/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Blast
copying build/lib.linux-riscv64-3.7/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Wise
copying build/lib.linux-riscv64-3.7/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Wise
copying build/lib.linux-riscv64-3.7/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Wise
copying build/lib.linux-riscv64-3.7/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Wise
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Data
copying build/lib.linux-riscv64-3.7/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Data
copying build/lib.linux-riscv64-3.7/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Data
copying build/lib.linux-riscv64-3.7/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Data
copying build/lib.linux-riscv64-3.7/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Data
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Crystal
copying build/lib.linux-riscv64-3.7/Bio/Crystal/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Crystal
copying build/lib.linux-riscv64-3.7/Bio/trie.h -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
copying build/lib.linux-riscv64-3.7/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
copying build/lib.linux-riscv64-3.7/Bio/triefind.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/_py3k
copying build/lib.linux-riscv64-3.7/Bio/_py3k/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/_py3k
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-riscv64-3.7/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-riscv64-3.7/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-riscv64-3.7/Bio/codonalign/codonalphabet.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-riscv64-3.7/Bio/codonalign/chisq.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-riscv64-3.7/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/codonalign
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-riscv64-3.7/Bio/KDTree/KDTree.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-riscv64-3.7/Bio/KDTree/KDTreemodule.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-riscv64-3.7/Bio/KDTree/_CKDTree.cpython-37m-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-riscv64-3.7/Bio/KDTree/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-riscv64-3.7/Bio/KDTree/Neighbor.h -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-riscv64-3.7/Bio/KDTree/KDTree.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-riscv64-3.7/Bio/KDTree/KDTree.h -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-riscv64-3.7/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/PAML
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-riscv64-3.7/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-riscv64-3.7/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-riscv64-3.7/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-riscv64-3.7/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-riscv64-3.7/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-riscv64-3.7/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/XSDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/XSDs
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-riscv64-3.7/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez
copying build/lib.linux-riscv64-3.7/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/phenotype
copying build/lib.linux-riscv64-3.7/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/phenotype
copying build/lib.linux-riscv64-3.7/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/phenotype
copying build/lib.linux-riscv64-3.7/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/phenotype
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/CAPS
copying build/lib.linux-riscv64-3.7/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/CAPS
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-riscv64-3.7/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-riscv64-3.7/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-riscv64-3.7/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-riscv64-3.7/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Restriction
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align
copying build/lib.linux-riscv64-3.7/Bio/Align/_aligners.c -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align
copying build/lib.linux-riscv64-3.7/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-riscv64-3.7/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align
copying build/lib.linux-riscv64-3.7/Bio/Align/_aligners.cpython-37m-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Affy
copying build/lib.linux-riscv64-3.7/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Affy
copying build/lib.linux-riscv64-3.7/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Affy
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/UniProt
copying build/lib.linux-riscv64-3.7/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/UniProt
copying build/lib.linux-riscv64-3.7/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/UniProt
copying build/lib.linux-riscv64-3.7/Bio/trie.cpython-37m-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Pathway
copying build/lib.linux-riscv64-3.7/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-riscv64-3.7/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-riscv64-3.7/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-riscv64-3.7/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/Pathway/Rep
creating /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/BioSQL
copying build/lib.linux-riscv64-3.7/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/BioSQL
copying build/lib.linux-riscv64-3.7/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/BioSQL
copying build/lib.linux-riscv64-3.7/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/BioSQL
copying build/lib.linux-riscv64-3.7/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/BioSQL
copying build/lib.linux-riscv64-3.7/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/BioSQL
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/_index.py to _index.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/_convert.py to _convert.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-37.pyc
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explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs/_pwm.cpython-37m-riscv64-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/motifs/_pwm.cpython-37m-riscv64-linux-gnu.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/trie.cpython-37m-riscv64-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages/Bio/trie.cpython-37m-riscv64-linux-gnu.so
original debug info size: 1332kB, size after compression: 1256kB
/usr/lib/rpm/sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match.
BUILDSTDERR: 1193 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/redhat/brp-python-bytecompile /usr/bin/python 1 0
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib/debug/usr/lib64/python3.7 using /usr/bin/python3.7
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7 using /usr/bin/python3.7
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.xZc79s
+ umask 022
~/build/BUILD/python-biopython-1.74/python3/Tests ~/build/BUILD/python-biopython-1.74
+ cd /builddir/build/BUILD
+ cd python-biopython-1.74
+ pushd python3/Tests
+ find . -name run_tests.py
+ xargs sed -i '1s|^#!/usr/bin/env python|#!/usr/bin/python3|'
BUILDSTDERR: ++ grep -v Tutorial
BUILDSTDERR: ++ grep -v Phylo
BUILDSTDERR: ++ grep -v Nexus
BUILDSTDERR: ++ ls test_Ace.py test_Affy.py test_AlignIO.py test_AlignIO_ClustalIO.py test_AlignIO_EmbossIO.py test_AlignIO_FastaIO.py test_AlignIO_MauveIO.py test_AlignIO_PhylipIO.py test_AlignIO_convert.py test_AlignInfo.py test_Application.py test_BWA_tool.py test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb_online.py test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector_online.py test_BioSQL_psycopg2.py test_BioSQL_psycopg2_online.py test_BioSQL_sqlite3.py test_BioSQL_sqlite3_online.py test_CAPS.py test_CelFile.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_ColorSpiral.py test_Compass.py test_Consensus.py test_Crystal.py test_DSSP_tool.py test_Dialign_tool.py test_EMBL_unittest.py test_Emboss.py test_EmbossPhylipNew.py test_EmbossPrimer.py test_Entrez.py test_Entrez_online.py test_Entrez_parser.py test_Enzyme.py test_ExPASy.py test_FSSP.py test_Fasttree_tool.py test_File.py test_GenBank.py test_GenomeDiagram.py test_GraphicsBitmaps.py test_GraphicsChromosome.py test_GraphicsDistribution.py test_GraphicsGeneral.py test_HMMCasino.py test_HMMGeneral.py test_KDTree.py test_KEGG.py test_KEGG_online.py test_KGML_graphics.py test_KGML_graphics_online.py test_KGML_nographics.py test_KeyWList.py test_LogisticRegression.py test_MSAProbs_tool.py test_MafIO_index.py test_Mafft_tool.py test_MarkovModel.py test_Medline.py test_Muscle_tool.py test_NACCESS_tool.py test_NCBITextParser.py test_NCBIXML.py test_NCBI_BLAST_tools.py test_NCBI_qblast.py test_NMR.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDB.py test_PDBList.py test_PDB_Dice.py test_PDB_FragmentMapper.py test_PDB_KDTree.py test_PDB_MMCIF2Dict.py test_PDB_MMCIFParser.py test_PDB_Polypetide.py test_PDB_ResidueDepth.py test_PDB_StructureAlignment.py test_PDB_Superimposer.py test_PDB_parse_pdb_header.py test_PDB_vectors.py test_Pathway.py test_Phd.py test_Phylo.py test_PhyloXML.py test_Phylo_CDAO.py test_Phylo_NeXML.py test_Phylo_matplotlib.py test_Phylo_networkx.py test_PopGen_GenePop.py test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_nodepend.py test_Prank_tool.py test_Probcons_tool.py test_ProtParam.py test_QCPSuperimposer.py test_RCSBFormats.py test_Restriction.py test_SCOP_Astral.py test_SCOP_Cla.py test_SCOP_Des.py test_SCOP_Dom.py test_SCOP_Hie.py test_SCOP_Raf.py test_SCOP_Residues.py test_SCOP_Scop.py test_SCOP_online.py test_SVDSuperimposer.py test_SearchIO_blast_tab.py test_SearchIO_blast_tab_index.py test_SearchIO_blast_text.py test_SearchIO_blast_xml.py test_SearchIO_blast_xml_index.py test_SearchIO_blat_psl.py test_SearchIO_blat_psl_index.py test_SearchIO_exonerate.py test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_vulgar_index.py test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10_index.py test_SearchIO_hhsuite2_text.py test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text_index.py test_SearchIO_interproscan_xml.py test_SearchIO_legacy.py test_SearchIO_model.py test_SearchIO_write.py test_SeqFeature.py test_SeqIO.py test_SeqIO_AbiIO.py test_SeqIO_FastaIO.py test_SeqIO_Insdc.py test_SeqIO_NibIO.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_convert.py test_SeqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SubsMat.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_Uniprot.py test_Wise.py test_XXmotif_tool.py test_align.py test_bgzf.py test_cellosaurus.py test_codonalign.py test_geo.py test_kNN.py test_lowess.py test_mmtf.py test_mmtf_online.py test_motifs.py test_motifs_online.py test_pairwise2.py test_pairwise2_no_C.py test_pairwise_aligner.py test_phenotype.py test_phenotype_fit.py test_phyml_tool.py test_prodoc.py test_prosite1.py test_prosite2.py test_psw.py test_raxml_tool.py test_samtools_tool.py test_seq.py test_translate.py test_trie.py
BUILDSTDERR: ++ grep -v bgzf
BUILDSTDERR: ++ grep -v SearchIO_blast
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Ace.py
BUILDSTDERR: test_Ace ... ok
BUILDSTDERR: test_check_ACEParser (test_Ace.AceTestOne)
BUILDSTDERR: Test to check that ACEParser can parse the whole file into one record. ... ok
BUILDSTDERR: test_check_record_parser (test_Ace.AceTestOne)
BUILDSTDERR: Test to check that contig parser parses each contig into a contig. ... ok
BUILDSTDERR: test_check_ACEParser (test_Ace.AceTestThree)
BUILDSTDERR: Test to check that ACEParser can parse the whole file into one record. ... ok
BUILDSTDERR: test_check_record_parser (test_Ace.AceTestThree)
BUILDSTDERR: Test to check that record parser parses each contig into a record. ... ok
BUILDSTDERR: test_check_ACEParser (test_Ace.AceTestTwo)
BUILDSTDERR: Test to check that ACEParser can parse the whole file into one record. ... ok
BUILDSTDERR: test_check_record_parser (test_Ace.AceTestTwo)
BUILDSTDERR: Test to check that record parser parses each contig into a record. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 4.662 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Affy.py
BUILDSTDERR: test_Affy ... ok
BUILDSTDERR: testAffy3 (test_Affy.AffyTest) ... ok
BUILDSTDERR: testAffy3Backwards (test_Affy.AffyTest) ... ok
BUILDSTDERR: testAffy4 (test_Affy.AffyTest) ... ok
BUILDSTDERR: testAffyBadHeader (test_Affy.AffyTest) ... ok
BUILDSTDERR: testAffyStrict (test_Affy.AffyTest) ... ok
BUILDSTDERR: testAffyWrongModeRead (test_Affy.AffyTest) ... ok
BUILDSTDERR: testAffyWrongModeReadV4 (test_Affy.AffyTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1.019 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO.py
BUILDSTDERR: test_AlignIO ... ok
BUILDSTDERR: test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions)
BUILDSTDERR: Check that parsing an empty file returns an empty list. ... ok
BUILDSTDERR: test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions)
BUILDSTDERR: Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok
BUILDSTDERR: test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions)
BUILDSTDERR: Check that writers can cope with no alignments. ... ok
BUILDSTDERR: test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions)
BUILDSTDERR: Check that writers reject records that are not alignments. ... ok
BUILDSTDERR: test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 252.119 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_ClustalIO.py
BUILDSTDERR: test_AlignIO_ClustalIO ... ok
BUILDSTDERR: test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO) ... ok
BUILDSTDERR: test_empy (test_AlignIO_ClustalIO.TestClustalIO)
BUILDSTDERR: Checking empty file. ... ok
BUILDSTDERR: test_kalign_header (test_AlignIO_ClustalIO.TestClustalIO)
BUILDSTDERR: Make sure we can parse the Kalign header. ... ok
BUILDSTDERR: test_one (test_AlignIO_ClustalIO.TestClustalIO) ... ok
BUILDSTDERR: test_three (test_AlignIO_ClustalIO.TestClustalIO) ... ok
BUILDSTDERR: test_two (test_AlignIO_ClustalIO.TestClustalIO) ... ok
BUILDSTDERR: test_write_read (test_AlignIO_ClustalIO.TestClustalIO)
BUILDSTDERR: Checking write/read. ... ok
BUILDSTDERR: test_write_read_single (test_AlignIO_ClustalIO.TestClustalIO)
BUILDSTDERR: Testing write/read when there is only one sequence. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 5.512 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_EmbossIO.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_AlignIO_EmbossIO ... ok
BUILDSTDERR: test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
BUILDSTDERR: test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
BUILDSTDERR: test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
BUILDSTDERR: test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
BUILDSTDERR: test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.089 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_FastaIO.py
BUILDSTDERR: test_AlignIO_FastaIO ... ok
BUILDSTDERR: test_output001 (test_AlignIO_FastaIO.FastaIOTests)
BUILDSTDERR: Check output001.m10 file. ... ok
BUILDSTDERR: test_output002 (test_AlignIO_FastaIO.FastaIOTests)
BUILDSTDERR: Check output002.m10 file. ... ok
BUILDSTDERR: test_output003 (test_AlignIO_FastaIO.FastaIOTests)
BUILDSTDERR: Check output003.m10 file. ... ok
BUILDSTDERR: test_output004 (test_AlignIO_FastaIO.FastaIOTests)
BUILDSTDERR: Check output004.m10 file. ... ok
BUILDSTDERR: test_output005 (test_AlignIO_FastaIO.FastaIOTests)
BUILDSTDERR: Check output005.m10 file. ... ok
BUILDSTDERR: test_output006 (test_AlignIO_FastaIO.FastaIOTests)
BUILDSTDERR: Check output006.m10 file. ... ok
BUILDSTDERR: test_output007 (test_AlignIO_FastaIO.FastaIOTests)
BUILDSTDERR: Check output007.m10 file. ... ok
BUILDSTDERR: test_output008 (test_AlignIO_FastaIO.FastaIOTests)
BUILDSTDERR: Check output008.m10 file. ... ok
BUILDSTDERR: test_output009 (test_AlignIO_FastaIO.FastaIOTests)
BUILDSTDERR: Check output009.m10 file. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.099 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_MauveIO.py
BUILDSTDERR: test_AlignIO_MauveIO ... ok
BUILDSTDERR: test_one (test_AlignIO_MauveIO.TestMauveIO) ... ok
BUILDSTDERR: test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO) ... ok
BUILDSTDERR: test_write_read (test_AlignIO_MauveIO.TestMauveIO) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 9.512 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_PhylipIO.py
BUILDSTDERR: test_AlignIO_PhylipIO ... ok
BUILDSTDERR: test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
BUILDSTDERR: test_five (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
BUILDSTDERR: test_five_a (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
BUILDSTDERR: test_four (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
BUILDSTDERR: test_one (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
BUILDSTDERR: test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
BUILDSTDERR: test_write_read (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.423 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_convert.py
BUILDSTDERR: test_AlignIO_convert ... ok
BUILDSTDERR: test_Clustalw_hedgehog_aln_clustal_to_clustal (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Clustalw/hedgehog.aln from clustal to clustal ... ok
BUILDSTDERR: test_Clustalw_hedgehog_aln_clustal_to_fasta (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Clustalw/hedgehog.aln from clustal to fasta ... ok
BUILDSTDERR: test_Clustalw_hedgehog_aln_clustal_to_maf (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Clustalw/hedgehog.aln from clustal to maf ... ok
BUILDSTDERR: test_Clustalw_hedgehog_aln_clustal_to_mauve (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Clustalw/hedgehog.aln from clustal to mauve ... ok
BUILDSTDERR: test_Clustalw_hedgehog_aln_clustal_to_nexus (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Clustalw/hedgehog.aln from clustal to nexus ... ok
BUILDSTDERR: test_Clustalw_hedgehog_aln_clustal_to_phylip (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Clustalw/hedgehog.aln from clustal to phylip ... ok
BUILDSTDERR: test_Clustalw_hedgehog_aln_clustal_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Clustalw/hedgehog.aln from clustal to phylip-relaxed ... ok
BUILDSTDERR: test_Clustalw_hedgehog_aln_clustal_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Clustalw/hedgehog.aln from clustal to phylip-sequential ... ok
BUILDSTDERR: test_Clustalw_hedgehog_aln_clustal_to_stockholm (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Clustalw/hedgehog.aln from clustal to stockholm ... ok
BUILDSTDERR: test_Fasta_output001_m10_fasta-m10_to_clustal (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Fasta/output001.m10 from fasta-m10 to clustal ... ok
BUILDSTDERR: test_Fasta_output001_m10_fasta-m10_to_fasta (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Fasta/output001.m10 from fasta-m10 to fasta ... ok
BUILDSTDERR: test_Fasta_output001_m10_fasta-m10_to_maf (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Fasta/output001.m10 from fasta-m10 to maf ... ok
BUILDSTDERR: test_Fasta_output001_m10_fasta-m10_to_mauve (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Fasta/output001.m10 from fasta-m10 to mauve ... ok
BUILDSTDERR: test_Fasta_output001_m10_fasta-m10_to_nexus (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Fasta/output001.m10 from fasta-m10 to nexus ... ok
BUILDSTDERR: test_Fasta_output001_m10_fasta-m10_to_phylip (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Fasta/output001.m10 from fasta-m10 to phylip ... ok
BUILDSTDERR: test_Fasta_output001_m10_fasta-m10_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Fasta/output001.m10 from fasta-m10 to phylip-relaxed ... ok
BUILDSTDERR: test_Fasta_output001_m10_fasta-m10_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Fasta/output001.m10 from fasta-m10 to phylip-sequential ... ok
BUILDSTDERR: test_Fasta_output001_m10_fasta-m10_to_stockholm (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Fasta/output001.m10 from fasta-m10 to stockholm ... ok
BUILDSTDERR: test_GFF_multi_fna_fasta_to_clustal (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert GFF/multi.fna from fasta to clustal ... ok
BUILDSTDERR: test_GFF_multi_fna_fasta_to_fasta (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert GFF/multi.fna from fasta to fasta ... ok
BUILDSTDERR: test_GFF_multi_fna_fasta_to_maf (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert GFF/multi.fna from fasta to maf ... ok
BUILDSTDERR: test_GFF_multi_fna_fasta_to_mauve (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert GFF/multi.fna from fasta to mauve ... ok
BUILDSTDERR: test_GFF_multi_fna_fasta_to_nexus (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert GFF/multi.fna from fasta to nexus ... ok
BUILDSTDERR: test_GFF_multi_fna_fasta_to_phylip (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert GFF/multi.fna from fasta to phylip ... ok
BUILDSTDERR: test_GFF_multi_fna_fasta_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert GFF/multi.fna from fasta to phylip-relaxed ... ok
BUILDSTDERR: test_GFF_multi_fna_fasta_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert GFF/multi.fna from fasta to phylip-sequential ... ok
BUILDSTDERR: test_GFF_multi_fna_fasta_to_stockholm (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert GFF/multi.fna from fasta to stockholm ... ok
BUILDSTDERR: test_IntelliGenetics_VIF_mase-pro_txt_ig_to_clustal (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert IntelliGenetics/VIF_mase-pro.txt from ig to clustal ... ok
BUILDSTDERR: test_IntelliGenetics_VIF_mase-pro_txt_ig_to_fasta (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert IntelliGenetics/VIF_mase-pro.txt from ig to fasta ... ok
BUILDSTDERR: test_IntelliGenetics_VIF_mase-pro_txt_ig_to_maf (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert IntelliGenetics/VIF_mase-pro.txt from ig to maf ... ok
BUILDSTDERR: test_IntelliGenetics_VIF_mase-pro_txt_ig_to_mauve (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert IntelliGenetics/VIF_mase-pro.txt from ig to mauve ... ok
BUILDSTDERR: test_IntelliGenetics_VIF_mase-pro_txt_ig_to_nexus (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert IntelliGenetics/VIF_mase-pro.txt from ig to nexus ... ok
BUILDSTDERR: test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip ... ok
BUILDSTDERR: test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip-relaxed ... ok
BUILDSTDERR: test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip-sequential ... ok
BUILDSTDERR: test_IntelliGenetics_VIF_mase-pro_txt_ig_to_stockholm (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert IntelliGenetics/VIF_mase-pro.txt from ig to stockholm ... ok
BUILDSTDERR: test_NBRF_clustalw_pir_pir_to_clustal (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert NBRF/clustalw.pir from pir to clustal ... ok
BUILDSTDERR: test_NBRF_clustalw_pir_pir_to_fasta (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert NBRF/clustalw.pir from pir to fasta ... ok
BUILDSTDERR: test_NBRF_clustalw_pir_pir_to_maf (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert NBRF/clustalw.pir from pir to maf ... ok
BUILDSTDERR: test_NBRF_clustalw_pir_pir_to_mauve (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert NBRF/clustalw.pir from pir to mauve ... ok
BUILDSTDERR: test_NBRF_clustalw_pir_pir_to_nexus (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert NBRF/clustalw.pir from pir to nexus ... ok
BUILDSTDERR: test_NBRF_clustalw_pir_pir_to_phylip (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert NBRF/clustalw.pir from pir to phylip ... ok
BUILDSTDERR: test_NBRF_clustalw_pir_pir_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert NBRF/clustalw.pir from pir to phylip-relaxed ... ok
BUILDSTDERR: test_NBRF_clustalw_pir_pir_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert NBRF/clustalw.pir from pir to phylip-sequential ... ok
BUILDSTDERR: test_NBRF_clustalw_pir_pir_to_stockholm (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert NBRF/clustalw.pir from pir to stockholm ... ok
BUILDSTDERR: test_Nexus_test_Nexus_input_nex_nexus_to_clustal (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Nexus/test_Nexus_input.nex from nexus to clustal ... ok
BUILDSTDERR: test_Nexus_test_Nexus_input_nex_nexus_to_fasta (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Nexus/test_Nexus_input.nex from nexus to fasta ... ok
BUILDSTDERR: test_Nexus_test_Nexus_input_nex_nexus_to_maf (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Nexus/test_Nexus_input.nex from nexus to maf ... ok
BUILDSTDERR: test_Nexus_test_Nexus_input_nex_nexus_to_mauve (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Nexus/test_Nexus_input.nex from nexus to mauve ... ok
BUILDSTDERR: test_Nexus_test_Nexus_input_nex_nexus_to_nexus (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Nexus/test_Nexus_input.nex from nexus to nexus ... ok
BUILDSTDERR: test_Nexus_test_Nexus_input_nex_nexus_to_phylip (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Nexus/test_Nexus_input.nex from nexus to phylip ... ok
BUILDSTDERR: test_Nexus_test_Nexus_input_nex_nexus_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Nexus/test_Nexus_input.nex from nexus to phylip-relaxed ... ok
BUILDSTDERR: test_Nexus_test_Nexus_input_nex_nexus_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Nexus/test_Nexus_input.nex from nexus to phylip-sequential ... ok
BUILDSTDERR: test_Nexus_test_Nexus_input_nex_nexus_to_stockholm (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Nexus/test_Nexus_input.nex from nexus to stockholm ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_clustal (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to clustal ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_fasta (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to fasta ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_maf (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to maf ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_mauve (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to mauve ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_nexus (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to nexus ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_phylip (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to phylip ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to phylip-relaxed ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to phylip-sequential ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_stockholm (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to stockholm ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_clustal (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to clustal ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_fasta (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_maf (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to maf ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_mauve (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to mauve ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_nexus (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to nexus ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_phylip (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to phylip ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to phylip-relaxed ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to phylip-sequential ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_stockholm (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to stockholm ... ok
BUILDSTDERR: test_Stockholm_simple_sth_stockholm_to_clustal (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Stockholm/simple.sth from stockholm to clustal ... ok
BUILDSTDERR: test_Stockholm_simple_sth_stockholm_to_fasta (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Stockholm/simple.sth from stockholm to fasta ... ok
BUILDSTDERR: test_Stockholm_simple_sth_stockholm_to_maf (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Stockholm/simple.sth from stockholm to maf ... ok
BUILDSTDERR: test_Stockholm_simple_sth_stockholm_to_mauve (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Stockholm/simple.sth from stockholm to mauve ... ok
BUILDSTDERR: test_Stockholm_simple_sth_stockholm_to_nexus (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Stockholm/simple.sth from stockholm to nexus ... ok
BUILDSTDERR: test_Stockholm_simple_sth_stockholm_to_phylip (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Stockholm/simple.sth from stockholm to phylip ... ok
BUILDSTDERR: test_Stockholm_simple_sth_stockholm_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Stockholm/simple.sth from stockholm to phylip-relaxed ... ok
BUILDSTDERR: test_Stockholm_simple_sth_stockholm_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Stockholm/simple.sth from stockholm to phylip-sequential ... ok
BUILDSTDERR: test_Stockholm_simple_sth_stockholm_to_stockholm (test_AlignIO_convert.ConvertTests)
BUILDSTDERR: Convert Stockholm/simple.sth from stockholm to stockholm ... ok
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 39.097 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignInfo.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_AlignInfo ... ok
BUILDSTDERR: test_nucleotides (test_AlignInfo.AlignInfoTests) ... ok
BUILDSTDERR: test_proteins (test_AlignInfo.AlignInfoTests) ... ok
BUILDSTDERR: test_pseudo_count (test_AlignInfo.AlignInfoTests) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.984 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Application.py
BUILDSTDERR: test_Application ... ok
BUILDSTDERR: test_echo (test_Application.TestApp) ... ok
BUILDSTDERR: test_echo_capture_both (test_Application.TestApp) ... ok
BUILDSTDERR: test_echo_capture_neither (test_Application.TestApp) ... ok
BUILDSTDERR: test_echo_capture_stderr (test_Application.TestApp) ... ok
BUILDSTDERR: test_echo_capture_stdout (test_Application.TestApp) ... ok
BUILDSTDERR: test_echo_file_both (test_Application.TestApp) ... ok
BUILDSTDERR: test_echo_file_same (test_Application.TestApp) ... ok
BUILDSTDERR: test_echo_file_stderr (test_Application.TestApp) ... ok
BUILDSTDERR: test_echo_file_stdout (test_Application.TestApp) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 3.213 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BWA_tool.py
BUILDSTDERR: test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1.965 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb.py
BUILDSTDERR: test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 11.280 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb_online.py
BUILDSTDERR: test_BioSQL_MySQLdb_online ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.852 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector.py
BUILDSTDERR: test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.306 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector_online.py
BUILDSTDERR: test_BioSQL_mysql_connector_online ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.326 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.847 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2_online.py
BUILDSTDERR: test_BioSQL_psycopg2_online ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.715 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3.py
BUILDSTDERR: test_BioSQL_sqlite3 ... ok
BUILDSTDERR: test_SeqIO_loading (common_BioSQL.AutoSeqIOTests) ... ok
BUILDSTDERR: test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest)
BUILDSTDERR: Check can re-use an old BioSQL SQLite3 database. ... ok
BUILDSTDERR: test_NC_000932 (common_BioSQL.ClosedLoopTest)
BUILDSTDERR: From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok
BUILDSTDERR: test_NC_005816 (common_BioSQL.ClosedLoopTest)
BUILDSTDERR: From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok
BUILDSTDERR: test_NT_019265 (common_BioSQL.ClosedLoopTest)
BUILDSTDERR: From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok
BUILDSTDERR: test_arab1 (common_BioSQL.ClosedLoopTest)
BUILDSTDERR: From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok
BUILDSTDERR: test_cor6_6 (common_BioSQL.ClosedLoopTest)
BUILDSTDERR: From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok
BUILDSTDERR: test_no_ref (common_BioSQL.ClosedLoopTest)
BUILDSTDERR: From GenBank file to BioSQL and back to a GenBank file, noref. ... ok
BUILDSTDERR: test_one_of (common_BioSQL.ClosedLoopTest)
BUILDSTDERR: From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok
BUILDSTDERR: test_protein_refseq2 (common_BioSQL.ClosedLoopTest)
BUILDSTDERR: From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok
BUILDSTDERR: test_del_db_items (common_BioSQL.DeleteTest)
BUILDSTDERR: Check all associated data is deleted from an item. ... ok
BUILDSTDERR: test_server (common_BioSQL.DeleteTest)
BUILDSTDERR: Check BioSeqDatabase methods. ... ok
BUILDSTDERR: test_duplicate_id_load (common_BioSQL.DupLoadTest)
BUILDSTDERR: Make sure can't import records with same ID (in one go). ... ok
BUILDSTDERR: test_duplicate_load (common_BioSQL.DupLoadTest)
BUILDSTDERR: Make sure can't import a single record twice (in one go). ... ok
BUILDSTDERR: test_duplicate_load2 (common_BioSQL.DupLoadTest)
BUILDSTDERR: Make sure can't import a single record twice (in steps). ... ok
BUILDSTDERR: test_record_loading (common_BioSQL.InDepthLoadTest)
BUILDSTDERR: Make sure all records are correctly loaded. ... ok
BUILDSTDERR: test_reload (common_BioSQL.InDepthLoadTest)
BUILDSTDERR: Make sure can't reimport existing records. ... ok
BUILDSTDERR: test_seq_feature (common_BioSQL.InDepthLoadTest)
BUILDSTDERR: In depth check that SeqFeatures are transmitted through the db. ... ok
BUILDSTDERR: test_transfer (common_BioSQL.InDepthLoadTest)
BUILDSTDERR: Make sure can load record into another namespace. ... ok
BUILDSTDERR: test_load_database (common_BioSQL.LoaderTest)
BUILDSTDERR: Load SeqRecord objects into a BioSQL database. ... ok
BUILDSTDERR: test_cross_retrieval_of_items (common_BioSQL.MultiReadTest)
BUILDSTDERR: Test that valid ids can't be retrieved between namespaces. ... ok
BUILDSTDERR: test_get_db_items (common_BioSQL.MultiReadTest)
BUILDSTDERR: Check list, keys, length etc. ... ok
BUILDSTDERR: test_server (common_BioSQL.MultiReadTest)
BUILDSTDERR: Check BioSeqDatabase methods. ... ok
BUILDSTDERR: test_get_db_items (common_BioSQL.ReadTest)
BUILDSTDERR: Check list, keys, length etc. ... ok
BUILDSTDERR: test_lookup_items (common_BioSQL.ReadTest)
BUILDSTDERR: Test retrieval of items using various ids. ... ok
BUILDSTDERR: test_server (common_BioSQL.ReadTest)
BUILDSTDERR: Check BioSeqDatabase methods. ... ok
BUILDSTDERR: test_addition (common_BioSQL.SeqInterfaceTest)
BUILDSTDERR: Check can add DBSeq objects together. ... ok
BUILDSTDERR: test_convert (common_BioSQL.SeqInterfaceTest)
BUILDSTDERR: Check can turn a DBSeq object into a Seq or MutableSeq. ... ok
BUILDSTDERR: test_multiplication (common_BioSQL.SeqInterfaceTest)
BUILDSTDERR: Check can multiply DBSeq objects by integers. ... ok
BUILDSTDERR: test_record_slicing (common_BioSQL.SeqInterfaceTest)
BUILDSTDERR: Check that slices of DBSeqRecord are retrieved properly. ... ok
BUILDSTDERR: test_seq (common_BioSQL.SeqInterfaceTest)
BUILDSTDERR: Make sure Seqs from BioSQL implement the right interface. ... ok
BUILDSTDERR: test_seq_features (common_BioSQL.SeqInterfaceTest)
BUILDSTDERR: Check SeqFeatures of a sequence. ... ok
BUILDSTDERR: test_seq_record (common_BioSQL.SeqInterfaceTest)
BUILDSTDERR: Make sure SeqRecords from BioSQL implement the right interface. ... ok
BUILDSTDERR: test_seq_slicing (common_BioSQL.SeqInterfaceTest)
BUILDSTDERR: Check that slices of sequences are retrieved properly. ... ok
BUILDSTDERR: test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest)
BUILDSTDERR: Loaded uniprot-xml with ambiguous location in BioSQL. ... ok
BUILDSTDERR: test_NC_000932 (common_BioSQL.TransferTest)
BUILDSTDERR: From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok
BUILDSTDERR: test_NC_005816 (common_BioSQL.TransferTest)
BUILDSTDERR: From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok
BUILDSTDERR: test_NT_019265 (common_BioSQL.TransferTest)
BUILDSTDERR: From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok
BUILDSTDERR: test_arab1 (common_BioSQL.TransferTest)
BUILDSTDERR: From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok
BUILDSTDERR: test_cor6_6 (common_BioSQL.TransferTest)
BUILDSTDERR: From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok
BUILDSTDERR: test_no_ref (common_BioSQL.TransferTest)
BUILDSTDERR: From GenBank file to BioSQL, then again to a new namespace, noref. ... ok
BUILDSTDERR: test_one_of (common_BioSQL.TransferTest)
BUILDSTDERR: From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok
BUILDSTDERR: test_protein_refseq2 (common_BioSQL.TransferTest)
BUILDSTDERR: From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 862.836 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3_online.py
BUILDSTDERR: test_BioSQL_sqlite3_online ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 9.254 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CAPS.py
BUILDSTDERR: test_CAPS ... ok
BUILDSTDERR: test (test_CAPS.TestCAPS) ... ok
BUILDSTDERR: testNoCAPS (test_CAPS.TestCAPS) ... ok
BUILDSTDERR: test_trivial (test_CAPS.TestCAPS) ... ok
BUILDSTDERR: test_uneven (test_CAPS.TestCAPS) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 39.082 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CelFile.py
BUILDSTDERR: test_CelFile ... ok
BUILDSTDERR: test_read (test_CelFile.testCelFile) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.561 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Chi2.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_Chi2 ... ok
BUILDSTDERR: test_cdf_chi2 (test_Chi2.ModTest) ... ok
BUILDSTDERR: test_incomplete_gamma (test_Chi2.ModTest) ... ok
BUILDSTDERR: test_ln_gamma (test_Chi2.ModTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 12.534 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ClustalOmega_tool.py
BUILDSTDERR: test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 11.046 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Clustalw_tool.py
BUILDSTDERR: test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 10.632 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Cluster.py
BUILDSTDERR: test_Cluster ... ok
BUILDSTDERR: test_clusterdistance (test_Cluster.TestCluster) ... ok
BUILDSTDERR: test_distancematrix_kmedoids (test_Cluster.TestCluster) ... ok
BUILDSTDERR: test_kcluster (test_Cluster.TestCluster) ... ok
BUILDSTDERR: test_mask_parse (test_Cluster.TestCluster) ... ok
BUILDSTDERR: test_matrix_parse (test_Cluster.TestCluster) ... ok
BUILDSTDERR: test_pca (test_Cluster.TestCluster) ... ok
BUILDSTDERR: test_somcluster (test_Cluster.TestCluster) ... ok
BUILDSTDERR: test_tree (test_Cluster.TestCluster) ... ok
BUILDSTDERR: test_treecluster (test_Cluster.TestCluster) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 3.379 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CodonTable.py
BUILDSTDERR: test_CodonTable ... ok
BUILDSTDERR: test_coding (test_CodonTable.AmbiguousCodonsTests)
BUILDSTDERR: Check a few ambiguous codons for correct coding. ... ok
BUILDSTDERR: test_list_ambiguous_codons (test_CodonTable.AmbiguousCodonsTests)
BUILDSTDERR: Check if stop codons are properly extended. ... ok
BUILDSTDERR: test_start_codons (test_CodonTable.AmbiguousCodonsTests)
BUILDSTDERR: Test various ambiguous codons as start codon. ... ok
BUILDSTDERR: test_stop_codons (test_CodonTable.AmbiguousCodonsTests)
BUILDSTDERR: Test various ambiguous codons as stop codon. ... ok
BUILDSTDERR: test_ambiguous_tables (test_CodonTable.BasicSanityTests)
BUILDSTDERR: Check if all IDs and all names are present in ambiguous tables. ... ok
BUILDSTDERR: test_complete_tables (test_CodonTable.BasicSanityTests)
BUILDSTDERR: Check if all unambiguous codon tables have all entries. ... ok
BUILDSTDERR: test_number_of_tables (test_CodonTable.BasicSanityTests)
BUILDSTDERR: Check if we have the same number of tables for each type. ... ok
BUILDSTDERR: test_ambiguous_forward_table (test_CodonTable.ErrorConditions)
BUILDSTDERR: Raise errors in AmbiguousForwardTable. ... ok
BUILDSTDERR: test_list_possible_proteins (test_CodonTable.ErrorConditions)
BUILDSTDERR: Raise errors in list_possible proteins. ... ok
BUILDSTDERR: test_print_table (test_CodonTable.PrintTable)
BUILDSTDERR: Test output of __str__ function. ... ok
BUILDSTDERR: test_table01 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 1: Standard. ... ok
BUILDSTDERR: test_table02 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 2: Vertebrate Mitochondrial. ... ok
BUILDSTDERR: test_table03 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 3: Yeast Mitochondrial. ... ok
BUILDSTDERR: test_table04 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 4: Mold Mitochondrial and others. ... ok
BUILDSTDERR: test_table05 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 5: Invertebrate Mitochondrial. ... ok
BUILDSTDERR: test_table06 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 6: Ciliate and Other Nuclear. ... ok
BUILDSTDERR: test_table09 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 9: Echinoderm and Flatworm Mitochondrial. ... ok
BUILDSTDERR: test_table10 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 10: Euplotid Nuclear. ... ok
BUILDSTDERR: test_table11 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 11: Bacterial, Archaeal and Plant Plastid. ... ok
BUILDSTDERR: test_table12 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 12: Alternative Yeast Nuclear. ... ok
BUILDSTDERR: test_table13 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 13: Ascidian Mitochondrial. ... ok
BUILDSTDERR: test_table14 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 14: Alternative Flatworm Mitochondrial. ... ok
BUILDSTDERR: test_table16 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 16: Chlorophycean Mitochondrial. ... ok
BUILDSTDERR: test_table21 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 21: Trematode Mitochondrial. ... ok
BUILDSTDERR: test_table22 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 22: Scenedesmus obliquus Mitochondrial. ... ok
BUILDSTDERR: test_table23 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 9: Thraustochytrium Mitochondrial. ... ok
BUILDSTDERR: test_table24 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 24: Pterobranchia Mitochondrial. ... ok
BUILDSTDERR: test_table25 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 25: Candidate Division SR1 and Gracilibacteria. ... ok
BUILDSTDERR: test_table26 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 26: Pachysolen tannophilus Nuclear. ... ok
BUILDSTDERR: test_table27 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 27: Karyorelict Nuclear. ... ok
BUILDSTDERR: test_table28 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 28: Condylostoma Nuclear. ... ok
BUILDSTDERR: test_table29 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 29: Mesodinium Nuclear. ... ok
BUILDSTDERR: test_table30 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 30: Peritrich Nuclear. ... ok
BUILDSTDERR: test_table31 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 31: Blastocrithidia Nuclear. ... ok
BUILDSTDERR: test_table32 (test_CodonTable.SingleTableTests)
BUILDSTDERR: Check table 32: Balanophoraceae Plastid. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.606 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ColorSpiral.py
BUILDSTDERR: test_ColorSpiral ... ok
BUILDSTDERR: test_dict (test_ColorSpiral.DictTest)
BUILDSTDERR: get_color_dict() for classes A-D, no jitter. ... ok
BUILDSTDERR: test_colorlist (test_ColorSpiral.SpiralTest)
BUILDSTDERR: Get set of eight colours, no jitter, using ColorSpiral. ... ok
BUILDSTDERR: test_colorspiral (test_ColorSpiral.SpiralTest)
BUILDSTDERR: Get set of 16 colours, no jitter, using ColorSpiral. ... ok
BUILDSTDERR: test_colorspiral (test_ColorSpiral.SquareTest)
BUILDSTDERR: Set of 625 colours, with jitter, using get_colors(). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 5.634 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Compass.py
BUILDSTDERR: test_Compass ... ok
BUILDSTDERR: testAlignmentParsingOne (test_Compass.CompassTest) ... ok
BUILDSTDERR: testAlignmentParsingTwo (test_Compass.CompassTest) ... ok
BUILDSTDERR: testCompassIteratorEasy (test_Compass.CompassTest) ... ok
BUILDSTDERR: testCompassIteratorHard (test_Compass.CompassTest) ... ok
BUILDSTDERR: testCompassParser (test_Compass.CompassTest) ... ok
BUILDSTDERR: testCompassScanAndConsume (test_Compass.CompassTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.965 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Consensus.py
BUILDSTDERR: test_Consensus ... ok
BUILDSTDERR: test_bitstring (test_Consensus.BitStringTest) ... ok
BUILDSTDERR: test_bootstrap (test_Consensus.BootstrapTest) ... ok
BUILDSTDERR: test_bootstrap_consensus (test_Consensus.BootstrapTest) ... ok
BUILDSTDERR: test_bootstrap_trees (test_Consensus.BootstrapTest) ... ok
BUILDSTDERR: test_adam_consensus (test_Consensus.ConsensusTest) ... ok
BUILDSTDERR: test_count_clades (test_Consensus.ConsensusTest) ... ok
BUILDSTDERR: test_get_support (test_Consensus.ConsensusTest) ... ok
BUILDSTDERR: test_majority_consensus (test_Consensus.ConsensusTest) ... ok
BUILDSTDERR: test_strict_consensus (test_Consensus.ConsensusTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 226.891 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Crystal.py
BUILDSTDERR: test_Crystal ... ok
BUILDSTDERR: testAdd (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testAppend (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testContains (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testCount (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testDelItem (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testDelSlice (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testEquals (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testGetItem (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testGetSlice (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testIndex (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testInsert (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testLen (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testRemove (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testSetItem (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testSetSlice (test_Crystal.ChainTestCase) ... ok
BUILDSTDERR: testClear (test_Crystal.CrystalTestCase) ... ok
BUILDSTDERR: testDelItem (test_Crystal.CrystalTestCase) ... ok
BUILDSTDERR: testGetItem (test_Crystal.CrystalTestCase) ... ok
BUILDSTDERR: testHasKey (test_Crystal.CrystalTestCase) ... ok
BUILDSTDERR: testItems (test_Crystal.CrystalTestCase) ... ok
BUILDSTDERR: testKeys (test_Crystal.CrystalTestCase) ... ok
BUILDSTDERR: testLen (test_Crystal.CrystalTestCase) ... ok
BUILDSTDERR: testSetItem (test_Crystal.CrystalTestCase) ... ok
BUILDSTDERR: testValues (test_Crystal.CrystalTestCase) ... ok
BUILDSTDERR: testEquals (test_Crystal.HeteroTestCase) ... ok
BUILDSTDERR: testInit (test_Crystal.HeteroTestCase) ... ok
BUILDSTDERR: testLen (test_Crystal.HeteroTestCase) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1.552 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_DSSP_tool.py
BUILDSTDERR: test_DSSP_tool ... skipping. Install dssp if you want to use it from Biopython.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 9.800 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Dialign_tool.py
BUILDSTDERR: test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 5.017 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EMBL_unittest.py
BUILDSTDERR: test_EMBL_unittest ... ok
BUILDSTDERR: test_embl_0_line (test_EMBL_unittest.EMBLTests)
BUILDSTDERR: Test SQ line with 0 length sequence. ... ok
BUILDSTDERR: test_embl_content_after_co (test_EMBL_unittest.EMBLTests)
BUILDSTDERR: Test a ValueError is thrown by content after a CO line. ... ok
BUILDSTDERR: test_embl_no_coords (test_EMBL_unittest.EMBLTests)
BUILDSTDERR: Test sequence lines without coordinates. ... ok
BUILDSTDERR: test_embl_wrong_dr_line (test_EMBL_unittest.EMBLTests)
BUILDSTDERR: Test files with wrong DR lines. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 9.729 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Emboss.py
BUILDSTDERR: test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 10.807 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPhylipNew.py
BUILDSTDERR: test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7.797 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPrimer.py
BUILDSTDERR: test_EmbossPrimer ... ok
BUILDSTDERR: test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest)
BUILDSTDERR: Make sure we get info right from a single primer find. ... ok
BUILDSTDERR: test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest)
BUILDSTDERR: Make sure we get the data from normal primer3 files okay. ... ok
BUILDSTDERR: test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest)
BUILDSTDERR: Make sure we can parse an internal oligo file correctly. ... ok
BUILDSTDERR: test_mutli_record_full (test_EmbossPrimer.Primer3ParseTest)
BUILDSTDERR: Test parsing multiple primer sets (NirK full). ... ok
BUILDSTDERR: test_mutli_record_fwd (test_EmbossPrimer.Primer3ParseTest)
BUILDSTDERR: Test parsing multiple primer sets (NirK forward). ... ok
BUILDSTDERR: test_simple_parse (test_EmbossPrimer.Primer3ParseTest)
BUILDSTDERR: Make sure that we can use all single target primer3 files. ... ok
BUILDSTDERR: test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest)
BUILDSTDERR: Make sure we can output primer information correctly. ... ok
BUILDSTDERR: test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest)
BUILDSTDERR: Make sure the output from a simple primersearch file is correct. ... ok
BUILDSTDERR: test_simple_parse (test_EmbossPrimer.PrimersearchParseTest)
BUILDSTDERR: Make sure that we can parse all primersearch files. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1.249 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_Entrez ... ok
BUILDSTDERR: test_custom_directory (test_Entrez.CustomDirectoryTest) ... ok
BUILDSTDERR: test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction) ... ok
BUILDSTDERR: test_construct_cgi_efetch (test_Entrez.TestURLConstruction) ... ok
BUILDSTDERR: test_construct_cgi_einfo (test_Entrez.TestURLConstruction)
BUILDSTDERR: Test constructed url for request to Entrez. ... ok
BUILDSTDERR: test_construct_cgi_elink1 (test_Entrez.TestURLConstruction) ... ok
BUILDSTDERR: test_construct_cgi_elink2 (test_Entrez.TestURLConstruction)
BUILDSTDERR: Commas: Link from protein to gene. ... ok
BUILDSTDERR: test_construct_cgi_elink3 (test_Entrez.TestURLConstruction)
BUILDSTDERR: Multiple ID entries: Find one-to-one links from protein to gene. ... ok
BUILDSTDERR: test_construct_cgi_epost1 (test_Entrez.TestURLConstruction) ... ok
BUILDSTDERR: test_construct_cgi_epost2 (test_Entrez.TestURLConstruction) ... ok
BUILDSTDERR: test_email_warning (test_Entrez.TestURLConstruction)
BUILDSTDERR: Test issuing warning when user does not specify email address. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1.499 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez_online.py
BUILDSTDERR: test_Entrez_online ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.869 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez_parser.py
BUILDSTDERR: test_Entrez_parser ... ok
BUILDSTDERR: test_efetch_schemas (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML using Schemas. ... ok
BUILDSTDERR: test_fasta (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test error handling when presented with Fasta non-XML data. ... ok
BUILDSTDERR: test_genbank (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test error handling when presented with GenBank non-XML data. ... ok
BUILDSTDERR: test_nucleotide1 (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok
BUILDSTDERR: test_nucleotide2 (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok
BUILDSTDERR: test_omim (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, OMIM database. ... ok
BUILDSTDERR: test_protein (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, Protein database. ... ok
BUILDSTDERR: test_pubmed1 (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, PubMed database (first test). ... ok
BUILDSTDERR: test_pubmed2 (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, PubMed database (second test). ... ok
BUILDSTDERR: test_pubmed_html (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test error handling when presented with HTML (so XML-like) data. ... ok
BUILDSTDERR: test_pubmed_html_escaping (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok
BUILDSTDERR: test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok
BUILDSTDERR: test_pubmed_html_tags (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok
BUILDSTDERR: test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok
BUILDSTDERR: test_taxonomy (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test parsing XML returned by EFetch, Taxonomy database. ... ok
BUILDSTDERR: test_truncated_xml (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test error handling for a truncated XML declaration. ... ok
BUILDSTDERR: test_xml_without_declaration (test_Entrez_parser.EFetchTest)
BUILDSTDERR: Test error handling for a missing XML declaration. ... ok
BUILDSTDERR: test_egquery1 (test_Entrez_parser.EGQueryTest)
BUILDSTDERR: Test parsing XML output returned by EGQuery (first test). ... ok
BUILDSTDERR: test_egquery2 (test_Entrez_parser.EGQueryTest)
BUILDSTDERR: Test parsing XML output returned by EGQuery (second test). ... ok
BUILDSTDERR: test_corrupted (test_Entrez_parser.EInfoTest)
BUILDSTDERR: Test if corrupted XML is handled correctly. ... ok
BUILDSTDERR: test_list (test_Entrez_parser.EInfoTest)
BUILDSTDERR: Test parsing database list returned by EInfo. ... ok
BUILDSTDERR: test_pubmed1 (test_Entrez_parser.EInfoTest)
BUILDSTDERR: Test parsing database info returned by EInfo. ... ok
BUILDSTDERR: test_pubmed2 (test_Entrez_parser.EInfoTest)
BUILDSTDERR: Test validating the XML against the DTD. ... ok
BUILDSTDERR: test_pubmed3 (test_Entrez_parser.EInfoTest)
BUILDSTDERR: Test non-validating parser on XML with an inconsistent DTD. ... ok
BUILDSTDERR: test_medline (test_Entrez_parser.ELinkTest)
BUILDSTDERR: Test parsing medline indexed articles returned by ELink. ... ok
BUILDSTDERR: test_nucleotide (test_Entrez_parser.ELinkTest)
BUILDSTDERR: Test parsing Nucleotide to Protein links returned by ELink. ... ok
BUILDSTDERR: test_pubmed1 (test_Entrez_parser.ELinkTest)
BUILDSTDERR: Test parsing pubmed links returned by ELink (first test). ... ok
BUILDSTDERR: test_pubmed2 (test_Entrez_parser.ELinkTest)
BUILDSTDERR: Test parsing pubmed links returned by ELink (second test). ... ok
BUILDSTDERR: test_pubmed3 (test_Entrez_parser.ELinkTest)
BUILDSTDERR: Test parsing pubmed link returned by ELink (third test). ... ok
BUILDSTDERR: test_pubmed4 (test_Entrez_parser.ELinkTest)
BUILDSTDERR: Test parsing pubmed links returned by ELink (fourth test). ... ok
BUILDSTDERR: test_pubmed5 (test_Entrez_parser.ELinkTest)
BUILDSTDERR: Test parsing pubmed links returned by ELink (fifth test). ... ok
BUILDSTDERR: test_pubmed6 (test_Entrez_parser.ELinkTest)
BUILDSTDERR: Test parsing pubmed links returned by ELink (sixth test). ... ok
BUILDSTDERR: test_epost (test_Entrez_parser.EPostTest)
BUILDSTDERR: Test parsing XML returned by EPost. ... ok
BUILDSTDERR: test_invalid (test_Entrez_parser.EPostTest)
BUILDSTDERR: Test parsing XML returned by EPost with invalid id (overflow tag). ... ok
BUILDSTDERR: test_wrong (test_Entrez_parser.EPostTest)
BUILDSTDERR: Test parsing XML returned by EPost with incorrect arguments. ... ok
BUILDSTDERR: test_journals (test_Entrez_parser.ESearchTest)
BUILDSTDERR: Test parsing XML returned by ESearch from the Journals database. ... ok
BUILDSTDERR: test_notfound (test_Entrez_parser.ESearchTest)
BUILDSTDERR: Test parsing XML returned by ESearch when no items were found. ... ok
BUILDSTDERR: test_nucleotide (test_Entrez_parser.ESearchTest)
BUILDSTDERR: Test parsing XML returned by ESearch from the Nucleotide database. ... ok
BUILDSTDERR: test_pmc (test_Entrez_parser.ESearchTest)
BUILDSTDERR: Test parsing XML returned by ESearch from PubMed Central. ... ok
BUILDSTDERR: test_protein (test_Entrez_parser.ESearchTest)
BUILDSTDERR: Test parsing XML returned by ESearch from the Protein database. ... ok
BUILDSTDERR: test_pubmed1 (test_Entrez_parser.ESearchTest)
BUILDSTDERR: Test parsing XML returned by ESearch from PubMed (first test). ... ok
BUILDSTDERR: test_pubmed2 (test_Entrez_parser.ESearchTest)
BUILDSTDERR: Test parsing XML returned by ESearch from PubMed (second test). ... ok
BUILDSTDERR: test_pubmed3 (test_Entrez_parser.ESearchTest)
BUILDSTDERR: Test parsing XML returned by ESearch from PubMed (third test). ... ok
BUILDSTDERR: test_espell (test_Entrez_parser.ESpellTest)
BUILDSTDERR: Test parsing XML output returned by ESpell. ... ok
BUILDSTDERR: test_integer_none (test_Entrez_parser.ESummaryTest)
BUILDSTDERR: Test parsing ESummary XML where an Integer is not defined. ... ok
BUILDSTDERR: test_journals (test_Entrez_parser.ESummaryTest)
BUILDSTDERR: Test parsing XML returned by ESummary from the Journals database. ... ok
BUILDSTDERR: test_nucleotide (test_Entrez_parser.ESummaryTest)
BUILDSTDERR: Test parsing XML returned by ESummary from the Nucleotide database. ... ok
BUILDSTDERR: test_protein (test_Entrez_parser.ESummaryTest)
BUILDSTDERR: Test parsing XML returned by ESummary from the Protein database. ... ok
BUILDSTDERR: test_pubmed (test_Entrez_parser.ESummaryTest)
BUILDSTDERR: Test parsing XML returned by ESummary from PubMed. ... ok
BUILDSTDERR: test_structure (test_Entrez_parser.ESummaryTest)
BUILDSTDERR: Test parsing XML returned by ESummary from the Structure database. ... ok
BUILDSTDERR: test_taxonomy (test_Entrez_parser.ESummaryTest)
BUILDSTDERR: Test parsing XML returned by ESummary from the Taxonomy database. ... ok
BUILDSTDERR: test_unists (test_Entrez_parser.ESummaryTest)
BUILDSTDERR: Test parsing XML returned by ESummary from the UniSTS database. ... ok
BUILDSTDERR: test_wrong (test_Entrez_parser.ESummaryTest)
BUILDSTDERR: Test parsing XML returned by ESummary with incorrect arguments. ... ok
BUILDSTDERR: test_BytesIO (test_Entrez_parser.GeneralTests)
BUILDSTDERR: Test parsing a BytesIO handle (bytes not unicode). ... ok
BUILDSTDERR: test_StringIO (test_Entrez_parser.GeneralTests)
BUILDSTDERR: Test parsing a StringIO handle (unicode not bytes). ... ok
BUILDSTDERR: test_bytes_handle (test_Entrez_parser.GeneralTests)
BUILDSTDERR: Test parsing a handle opened in binary mode. ... ok
BUILDSTDERR: test_closed_handle (test_Entrez_parser.GeneralTests)
BUILDSTDERR: Test parsing closed handle fails gracefully. ... ok
BUILDSTDERR: test_text_handle (test_Entrez_parser.GeneralTests)
BUILDSTDERR: Test parsing a handle opened in text mode. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 30.399 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Enzyme.py
BUILDSTDERR: test_Enzyme ... ok
BUILDSTDERR: test_lactate (test_Enzyme.TestEnzyme)
BUILDSTDERR: Parsing ENZYME record for lactate racemase (5.1.2.1). ... ok
BUILDSTDERR: test_lipoprotein (test_Enzyme.TestEnzyme)
BUILDSTDERR: Parsing ENZYME record for lipoprotein lipase (3.1.1.34). ... ok
BUILDSTDERR: test_parse_many (test_Enzyme.TestEnzyme)
BUILDSTDERR: Check parse function with multiple records. ... ok
BUILDSTDERR: test_parse_one (test_Enzyme.TestEnzyme)
BUILDSTDERR: Check parse function with one record. ... ok
BUILDSTDERR: test_parse_zero (test_Enzyme.TestEnzyme) ... ok
BUILDSTDERR: test_proline (test_Enzyme.TestEnzyme)
BUILDSTDERR: Parsing ENZYME record for proline racemase (5.1.1.4). ... ok
BUILDSTDERR: test_valine (test_Enzyme.TestEnzyme)
BUILDSTDERR: Parsing ENZYME record for valine decarboxylase (4.1.1.14). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.689 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ExPASy.py
BUILDSTDERR: test_ExPASy ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.640 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_FSSP.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_FSSP ... ok
BUILDSTDERR: test_alignment (test_FSSP.TestGeo) ... ok
BUILDSTDERR: test_attributes (test_FSSP.TestGeo) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 159.445 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Fasttree_tool.py
BUILDSTDERR: test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 12.764 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_File.py
BUILDSTDERR: test_File ... ok
BUILDSTDERR: test_custom_path_like_object (test_File.AsHandleTestCase)
BUILDSTDERR: Test as_handle with a custom path-like object. ... ok
BUILDSTDERR: test_handle (test_File.AsHandleTestCase)
BUILDSTDERR: Test as_handle with a file-like object argument. ... ok
BUILDSTDERR: test_path_object (test_File.AsHandleTestCase)
BUILDSTDERR: Test as_handle with a pathlib.Path object. ... ok
BUILDSTDERR: test_string_path (test_File.AsHandleTestCase)
BUILDSTDERR: Test as_handle with a string path argument. ... ok
BUILDSTDERR: test_stringio (test_File.AsHandleTestCase)
BUILDSTDERR: Testing passing StringIO handles. ... ok
BUILDSTDERR: test_bgzf (test_File.RandomAccess)
BUILDSTDERR: Test BGZF compressed file. ... ok
BUILDSTDERR: test_gzip (test_File.RandomAccess)
BUILDSTDERR: Test gzip compressed file. ... ok
BUILDSTDERR: test_plain (test_File.RandomAccess)
BUILDSTDERR: Test plain text file. ... ok
BUILDSTDERR: test_one (test_File.UndoHandleTests)
BUILDSTDERR: First test. ... ok
BUILDSTDERR: test_read (test_File.UndoHandleTests)
BUILDSTDERR: Test read method. ... ok
BUILDSTDERR: test_undohandle_read_block (test_File.UndoHandleTests)
BUILDSTDERR: Test reading in blocks. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.999 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenBank.py
BUILDSTDERR: test_GenBank ... ok
BUILDSTDERR: test_embl_cds_interaction (test_GenBank.GenBankScannerTests)
BUILDSTDERR: Test EMBL CDS interaction, parse CDS features on embl files. ... ok
BUILDSTDERR: test_embl_record_interaction (test_GenBank.GenBankScannerTests)
BUILDSTDERR: Test EMBL Record interaction on embl files. ... ok
BUILDSTDERR: test_genbank_cds_interaction (test_GenBank.GenBankScannerTests)
BUILDSTDERR: Test CDS interaction, parse CDS features on gb(k) files. ... ok
BUILDSTDERR: test_genbank_interaction (test_GenBank.GenBankScannerTests)
BUILDSTDERR: Test GenBank records interaction on gbk files. ... ok
BUILDSTDERR: test_000_genbank_bad_loc_wrap_warning (test_GenBank.GenBankTests)
BUILDSTDERR: Feature line wrapping warning. ... ok
BUILDSTDERR: test_001_genbank_bad_origin_wrapping_location (test_GenBank.GenBankTests)
BUILDSTDERR: Bad origin wrapping. ... ok
BUILDSTDERR: test_001_negative_location_warning (test_GenBank.GenBankTests)
BUILDSTDERR: Un-parsable feature location warning. ... ok
BUILDSTDERR: test_dbline_embl_gb (test_GenBank.GenBankTests)
BUILDSTDERR: Parse GenBank/EMBL paired records with PR project entry: EMBL. ... ok
BUILDSTDERR: test_dbline_gb_embl (test_GenBank.GenBankTests)
BUILDSTDERR: Parse GenBank/EMBL paired records with PR project entry: GenBank. ... ok
BUILDSTDERR: test_dblink (test_GenBank.GenBankTests)
BUILDSTDERR: Parse GenBank record with old DBLINK project entry. ... ok
BUILDSTDERR: test_dblink_two (test_GenBank.GenBankTests)
BUILDSTDERR: Parse GenBank record with old and new DBLINK project entries. ... ok
BUILDSTDERR: test_dot_lineage (test_GenBank.GenBankTests)
BUILDSTDERR: Missing taxonomy lineage. ... ok
BUILDSTDERR: test_extremely_long_sequence (test_GenBank.GenBankTests)
BUILDSTDERR: Tests if extremely long sequences can be read. ... ok
BUILDSTDERR: test_fuzzy_origin_wrap (test_GenBank.GenBankTests)
BUILDSTDERR: Test features that wrap an origin, and have fuzzy location. ... ok
BUILDSTDERR: test_genbank_bad_loc_wrap_parsing (test_GenBank.GenBankTests)
BUILDSTDERR: Bad location wrapping. ... ok
BUILDSTDERR: test_genbank_date_correct (test_GenBank.GenBankTests)
BUILDSTDERR: Check if user provided date is inserted correctly. ... ok
BUILDSTDERR: test_genbank_date_datetime (test_GenBank.GenBankTests)
BUILDSTDERR: Check if datetime objects are handled correctly. ... ok
BUILDSTDERR: test_genbank_date_default (test_GenBank.GenBankTests)
BUILDSTDERR: Check if default date is handled correctly. ... ok
BUILDSTDERR: test_genbank_date_invalid (test_GenBank.GenBankTests)
BUILDSTDERR: Check if invalid dates are treated as default. ... ok
BUILDSTDERR: test_genbank_date_list (test_GenBank.GenBankTests)
BUILDSTDERR: Check if date lists are handled correctly. ... ok
BUILDSTDERR: test_genbank_read (test_GenBank.GenBankTests)
BUILDSTDERR: GenBank.read(...) simple test. ... ok
BUILDSTDERR: test_genbank_read_invalid (test_GenBank.GenBankTests)
BUILDSTDERR: GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok
BUILDSTDERR: test_genbank_read_multirecord (test_GenBank.GenBankTests)
BUILDSTDERR: GenBank.read(...) error on multiple record input. ... ok
BUILDSTDERR: test_genbank_read_no_origin_no_end (test_GenBank.GenBankTests)
BUILDSTDERR: GenBank.read(...) error on malformed file. ... ok
BUILDSTDERR: test_implicit_orign_wrap_extract_and_translate (test_GenBank.GenBankTests)
BUILDSTDERR: Test that features wrapped around origin give expected data. ... ok
BUILDSTDERR: test_implicit_orign_wrap_fix (test_GenBank.GenBankTests)
BUILDSTDERR: Attempt to fix implied origin wrapping. ... ok
BUILDSTDERR: test_invalid_product_line_raises_value_error (test_GenBank.GenBankTests)
BUILDSTDERR: Parsing invalid product line. ... ok
BUILDSTDERR: test_locus_line_topogoly (test_GenBank.GenBankTests)
BUILDSTDERR: Test if chromosome topology is conserved. ... ok
BUILDSTDERR: test_long_names (test_GenBank.GenBankTests)
BUILDSTDERR: Various GenBank names which push the column based LOCUS line. ... ok
BUILDSTDERR: test_longer_locus_line (test_GenBank.GenBankTests)
BUILDSTDERR: Check that we can read and write files with longer locus lines. ... ok
BUILDSTDERR: test_negative_location (test_GenBank.GenBankTests)
BUILDSTDERR: Negative feature locations. ... ok
BUILDSTDERR: test_qualifier_escaping_read (test_GenBank.GenBankTests)
BUILDSTDERR: Check qualifier escaping is preserved when parsing. ... ok
BUILDSTDERR: test_qualifier_escaping_write (test_GenBank.GenBankTests)
BUILDSTDERR: Check qualifier escaping is preserved when writing. ... ok
BUILDSTDERR: test_qualifier_order (test_GenBank.GenBankTests)
BUILDSTDERR: Check the qualifier order is preserved. ... ok
BUILDSTDERR: test_structured_comment_parsing (test_GenBank.GenBankTests)
BUILDSTDERR: Structued comment parsing. ... ok
BUILDSTDERR: test_first_line_imgt (test_GenBank.LineOneTests)
BUILDSTDERR: Check IMGT ID line parsing. ... ok
BUILDSTDERR: test_topology_embl (test_GenBank.LineOneTests)
BUILDSTDERR: Check EMBL ID line parsing. ... ok
BUILDSTDERR: test_topology_genbank (test_GenBank.LineOneTests)
BUILDSTDERR: Check GenBank LOCUS line parsing. ... ok
BUILDSTDERR: test_000_write_invalid_but_parsed_locus_line (test_GenBank.OutputTests)
BUILDSTDERR: Make sure we survive writing slightly invalid LOCUS lines we could parse. ... ok
BUILDSTDERR: test_mad_dots (test_GenBank.OutputTests)
BUILDSTDERR: Writing and reading back accesssion.version variants. ... ok
BUILDSTDERR: test_seqrecord_default_description (test_GenBank.OutputTests)
BUILDSTDERR: Read in file using SeqRecord default description. ... ok
BUILDSTDERR: test_cleaning_features (test_GenBank.TestBasics)
BUILDSTDERR: Test the ability to clean up feature values. ... ok
BUILDSTDERR: test_ensembl_locus (test_GenBank.TestBasics)
BUILDSTDERR: Test the ENSEMBL locus line. ... ok
BUILDSTDERR: test_write_format (test_GenBank.TestBasics)
BUILDSTDERR: Test writing to the difference formats. ... ok
BUILDSTDERR: test_feature_parser_01 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_02 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_03 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_04 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_05 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_06 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_07 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_08 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_09 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_10 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_11 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_12 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_13 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_14 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_15 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_16 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_17 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_18 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_19 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_feature_parser_20 (test_GenBank.TestFeatureParser) ... ok
BUILDSTDERR: test_record_parser_01 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_02 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_03 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_04 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_05 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_06 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_07 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_08 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_09 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_10 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_11 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_12 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_13 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_14 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_15 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_16 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_17 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_18 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_19 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: test_record_parser_20 (test_GenBank.TestRecordParser) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 50.394 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenomeDiagram.py
BUILDSTDERR: x_order_2: colinear!
BUILDSTDERR: x_order_2: colinear!
BUILDSTDERR: x_order_2: colinear!
BUILDSTDERR: test_GenomeDiagram ... ok
BUILDSTDERR: test_color_conversions (test_GenomeDiagram.ColorsTest)
BUILDSTDERR: Test color translations. ... ok
BUILDSTDERR: test_add_track (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Add track. ... ok
BUILDSTDERR: test_add_track_error (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Test adding unspecified track. ... ok
BUILDSTDERR: test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Add track to occupied level. ... ok
BUILDSTDERR: test_del_tracks (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Delete track. ... ok
BUILDSTDERR: test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Construct and draw PDF using method approach. ... ok
BUILDSTDERR: test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Construct and draw PDF using object approach. ... ok
BUILDSTDERR: test_get_tracks (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Get track. ... ok
BUILDSTDERR: test_move_track (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Move a track. ... ok
BUILDSTDERR: test_partial_diagram (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Construct and draw SVG and PDF for just part of a SeqRecord. ... ok
BUILDSTDERR: test_renumber (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Test renumbering tracks. ... ok
BUILDSTDERR: test_str (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Test diagram's info as string. ... ok
BUILDSTDERR: test_write_arguments (test_GenomeDiagram.DiagramTest)
BUILDSTDERR: Check how the write methods respond to output format arguments. ... ok
BUILDSTDERR: test_limits (test_GenomeDiagram.GraphTest)
BUILDSTDERR: Check line graphs. ... ok
BUILDSTDERR: test_slicing (test_GenomeDiagram.GraphTest)
BUILDSTDERR: Check GraphData slicing. ... ok
BUILDSTDERR: test_label_default (test_GenomeDiagram.LabelTest)
BUILDSTDERR: Feature labels - default. ... ok
BUILDSTDERR: test_all_sigils (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: All sigils. ... ok
BUILDSTDERR: test_arrow_heads (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature arrow sigils, varying heads. ... ok
BUILDSTDERR: test_arrow_shafts (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature arrow sigils, varying shafts. ... ok
BUILDSTDERR: test_big_arrow_shafts (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature big-arrow sigils, varying shafts. ... ok
BUILDSTDERR: test_labels (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature labels. ... ok
BUILDSTDERR: test_long_arrow_heads (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature ARROW sigil heads within bounding box. ... ok
BUILDSTDERR: test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature BIGARROW sigil heads within bounding box. ... ok
BUILDSTDERR: test_long_jaggy (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature JAGGY sigil heads within bounding box. ... ok
BUILDSTDERR: test_long_octo_heads (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature OCTO sigil heads within bounding box. ... ok
BUILDSTDERR: test_short_arrow (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature arrow sigil heads within bounding box. ... ok
BUILDSTDERR: test_short_bigarrow (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature big-arrow sigil heads within bounding box. ... ok
BUILDSTDERR: test_short_jaggy (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature arrow sigil heads within bounding box. ... ok
BUILDSTDERR: test_short_octo (test_GenomeDiagram.SigilsTest)
BUILDSTDERR: Feature big-arrow sigil heads within bounding box. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 345.645 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsBitmaps.py
BUILDSTDERR: test_GraphicsBitmaps ... ok
BUILDSTDERR: test_simple_scatter_plot (test_GraphicsBitmaps.ComparativeTest)
BUILDSTDERR: Test creation of a simple PNG scatter plot. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 58.005 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsChromosome.py
BUILDSTDERR: test_GraphicsChromosome ... ok
BUILDSTDERR: test_add_count (test_GraphicsChromosome.ChromosomeCountTest)
BUILDSTDERR: Add counts to specific chromosome segments. ... ok
BUILDSTDERR: test_add_label (test_GraphicsChromosome.ChromosomeCountTest)
BUILDSTDERR: Add labels to chromosome segments. ... ok
BUILDSTDERR: test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest)
BUILDSTDERR: Retrieve a color from a count number with the default color scheme. ... ok
BUILDSTDERR: test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest)
BUILDSTDERR: Test filling out the information on a chromosome. ... ok
BUILDSTDERR: test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest)
BUILDSTDERR: Test retrieval of segment information. ... ok
BUILDSTDERR: test_set_scale (test_GraphicsChromosome.ChromosomeCountTest)
BUILDSTDERR: Set the scale for a chromosome segment. ... ok
BUILDSTDERR: test_random_organism (test_GraphicsChromosome.OrganismGraphicTest)
BUILDSTDERR: Generate an organism with random chromosome info. ... ok
BUILDSTDERR: test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest)
BUILDSTDERR: Test the basic functionality of drawing an organism. ... ok
BUILDSTDERR: test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest)
BUILDSTDERR: Output a simple organism to a PDF file. ... ok
BUILDSTDERR: test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest)
BUILDSTDERR: Output a simple organism to a postscript file. ... ok
BUILDSTDERR: test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest)
BUILDSTDERR: Output a simple organism to an SVG file. ... ok
BUILDSTDERR: test_widget (test_GraphicsChromosome.OrganismGraphicTest)
BUILDSTDERR: Try widget derived functionality. ... ok
BUILDSTDERR: test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest)
BUILDSTDERR: Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis. ... ok
BUILDSTDERR: test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest)
BUILDSTDERR: Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 113.306 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsDistribution.py
BUILDSTDERR: test_GraphicsDistribution ... ok
BUILDSTDERR: test_multi_page (test_GraphicsDistribution.BarChartTest)
BUILDSTDERR: Create a page with multiple distributions on it. ... ok
BUILDSTDERR: test_simple_page (test_GraphicsDistribution.BarChartTest)
BUILDSTDERR: Test displaying a page with single distribution. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 21.236 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsGeneral.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_GraphicsGeneral ... ok
BUILDSTDERR: test_simple_scatter_plot_1 (test_GraphicsGeneral.ComparativeTest)
BUILDSTDERR: Test creation of a simple ScatterPlot with one list. ... ok
BUILDSTDERR: test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest)
BUILDSTDERR: Test creation of a simple ScatterPlot with more lists. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 133.723 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMCasino.py
BUILDSTDERR: test_HMMCasino ... ok
BUILDSTDERR: test_baum_welch_training_standard (test_HMMCasino.TestHMMCasino)
BUILDSTDERR: Standard Training with known states. ... ok
BUILDSTDERR: test_baum_welch_training_without (test_HMMCasino.TestHMMCasino)
BUILDSTDERR: Baum-Welch training without known state sequences. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 34.332 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMGeneral.py
BUILDSTDERR: test_HMMGeneral ... ok
BUILDSTDERR: test_log_likelihood (test_HMMGeneral.AbstractTrainerTest)
BUILDSTDERR: Calculate log likelihood. ... ok
BUILDSTDERR: test_ml_estimator (test_HMMGeneral.AbstractTrainerTest)
BUILDSTDERR: Test the maximum likelihood estimator for simple cases. ... ok
BUILDSTDERR: test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest)
BUILDSTDERR: Testing allow_transition. ... ok
BUILDSTDERR: test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest)
BUILDSTDERR: Non-ergodic model (meaning that some transitions are not allowed). ... ok
BUILDSTDERR: test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest)
BUILDSTDERR: Test a simple model with 2 states and 2 symbols. ... ok
BUILDSTDERR: test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest)
BUILDSTDERR: Testing the calculation of transitions_from. ... ok
BUILDSTDERR: test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest)
BUILDSTDERR: Testing the calculation of transitions_to. ... ok
BUILDSTDERR: test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest)
BUILDSTDERR: Testing allow_all_transitions. ... ok
BUILDSTDERR: test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
BUILDSTDERR: test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
BUILDSTDERR: test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
BUILDSTDERR: test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest)
BUILDSTDERR: Making sure MarkovModelBuilder is initialized correctly. ... ok
BUILDSTDERR: test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest)
BUILDSTDERR: Testing the calculation of s values. ... ok
BUILDSTDERR: test_empty_state_training_sequence (test_HMMGeneral.TrainingSequenceTest) ... ok
BUILDSTDERR: test_invalid_training_sequence (test_HMMGeneral.TrainingSequenceTest) ... ok
BUILDSTDERR: test_valid_training_sequence (test_HMMGeneral.TrainingSequenceTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.533 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KDTree.py
BUILDSTDERR: test_KDTree ... ok
BUILDSTDERR: test_KDTree (test_KDTree.KDTreeTest) ... ok
BUILDSTDERR: test_KDTree_exceptions (test_KDTree.KDTreeTest) ... ok
BUILDSTDERR: test_KDTree_neighbour (test_KDTree.KDTreeTest) ... ok
BUILDSTDERR: test_all_search (test_KDTree.KDTreeTest) ... ok
BUILDSTDERR: test_search (test_KDTree.KDTreeTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 190.433 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG.py
BUILDSTDERR: test_KEGG ... ok
BUILDSTDERR: test_irregular (test_KEGG.CompoundTests) ... ok
BUILDSTDERR: test_sample (test_KEGG.CompoundTests) ... ok
BUILDSTDERR: test_4letter (test_KEGG.EnzymeTests) ... ok
BUILDSTDERR: test_exceptions (test_KEGG.EnzymeTests) ... ok
BUILDSTDERR: test_irregular (test_KEGG.EnzymeTests) ... ok
BUILDSTDERR: test_new (test_KEGG.EnzymeTests) ... ok
BUILDSTDERR: test_sample (test_KEGG.EnzymeTests) ... ok
BUILDSTDERR: test_map00950 (test_KEGG.MapTests) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 19.237 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG_online.py
BUILDSTDERR: test_KEGG_online ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 10.029 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics.py
BUILDSTDERR: test_KGML_graphics ... ok
BUILDSTDERR: test_render_KGML_basic (test_KGML_graphics.KGMLPathwayTest)
BUILDSTDERR: Basic rendering of KGML: write to PDF without modification. ... ok
BUILDSTDERR: test_render_KGML_modify (test_KGML_graphics.KGMLPathwayTest)
BUILDSTDERR: Rendering of KGML to PDF, with modification. ... ok
BUILDSTDERR: test_render_KGML_transparency (test_KGML_graphics.KGMLPathwayTest)
BUILDSTDERR: Rendering of KGML to PDF, with color alpha channel. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 974.977 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics_online.py
BUILDSTDERR: test_KGML_graphics_online ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 3.360 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_nographics.py
BUILDSTDERR: test_KGML_nographics ... ok
BUILDSTDERR: test_read_and_write_KGML_files (test_KGML_nographics.KGMLPathwayTest)
BUILDSTDERR: Read KGML from, and write KGML to, local files. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 171.937 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KeyWList.py
BUILDSTDERR: test_KeyWList ... ok
BUILDSTDERR: test_parse (test_KeyWList.KeyWListTest)
BUILDSTDERR: Test parsing keywlist.txt works. ... ok
BUILDSTDERR: test_parse2 (test_KeyWList.KeyWListTest)
BUILDSTDERR: Parsing keywlist2.txt (without header and footer). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.644 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_LogisticRegression.py
BUILDSTDERR: test_LogisticRegression ... ok
BUILDSTDERR: test_calculate_model (test_LogisticRegression.TestLogisticRegression) ... ok
BUILDSTDERR: test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression) ... ok
BUILDSTDERR: test_calculate_probability (test_LogisticRegression.TestLogisticRegression) ... ok
BUILDSTDERR: test_classify (test_LogisticRegression.TestLogisticRegression) ... ok
BUILDSTDERR: test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression) ... ok
BUILDSTDERR: test_leave_one_out (test_LogisticRegression.TestLogisticRegression) ... ok
BUILDSTDERR: test_model_accuracy (test_LogisticRegression.TestLogisticRegression) ... ok
BUILDSTDERR: test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression) ... ok
BUILDSTDERR: test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 9.583 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MSAProbs_tool.py
BUILDSTDERR: test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 10.173 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MafIO_index.py
BUILDSTDERR: test_MafIO_index ... ok
BUILDSTDERR: test_bundle_without_target (test_MafIO_index.NewIndexTest) ... ok
BUILDSTDERR: test_good_big (test_MafIO_index.NewIndexTest) ... ok
BUILDSTDERR: test_good_small (test_MafIO_index.NewIndexTest) ... ok
BUILDSTDERR: test_length_coords_mismatch (test_MafIO_index.NewIndexTest) ... ok
BUILDSTDERR: test_old (test_MafIO_index.PreBuiltIndexTest) ... ok
BUILDSTDERR: test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest) ... ok
BUILDSTDERR: test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest) ... ok
BUILDSTDERR: test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest) ... ok
BUILDSTDERR: test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest) ... ok
BUILDSTDERR: test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest) ... ok
BUILDSTDERR: test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest) ... ok
BUILDSTDERR: test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest) ... ok
BUILDSTDERR: test_region2bin (test_MafIO_index.StaticMethodTest) ... ok
BUILDSTDERR: test_ucscbin (test_MafIO_index.StaticMethodTest) ... ok
BUILDSTDERR: test_records_begin (test_MafIO_index.TestGetRecord) ... ok
BUILDSTDERR: test_records_end (test_MafIO_index.TestGetRecord) ... ok
BUILDSTDERR: test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF) ... ok
BUILDSTDERR: test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF)
BUILDSTDERR: Following issues 504 and 1086. ... ok
BUILDSTDERR: test_correct_block_length (test_MafIO_index.TestSearchGoodMAF)
BUILDSTDERR: Following issues 504 and 1086. ... ok
BUILDSTDERR: test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF)
BUILDSTDERR: Correct retrieval of Cnksr3 in mouse. ... ok
BUILDSTDERR: test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF) ... ok
BUILDSTDERR: test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF)
BUILDSTDERR: Following issue 1083. ... ok
BUILDSTDERR: test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF)
BUILDSTDERR: Checking that spliced sequences are correct. ... ok
BUILDSTDERR: test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF)
BUILDSTDERR: Checking that spliced sequences are correct. ... ok
BUILDSTDERR: test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF) ... ok
BUILDSTDERR: test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF) ... ok
BUILDSTDERR: test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF) ... ok
BUILDSTDERR: test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF) ... ok
BUILDSTDERR: test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF) ... ok
BUILDSTDERR: test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF) ... ok
BUILDSTDERR: test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF)
BUILDSTDERR: Correct retrieval of Cnksr3 in mouse. ... ok
BUILDSTDERR: test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF) ... ok
BUILDSTDERR: test_no_alignment (test_MafIO_index.TestSpliceGoodMAF) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 155.970 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Mafft_tool.py
BUILDSTDERR: test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.166 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MarkovModel.py
BUILDSTDERR: test_MarkovModel ... ok
BUILDSTDERR: test_argmaxes (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_backward (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_baum_welch (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_forward (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_logsum_and_exp_logsum (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_logvecadd (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_mle (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_normalize_and_copy_and_check (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_random_norm (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_readline_and_check_start (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_save_and_load (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_topcoder1 (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_topcoder2 (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_topcoder3 (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_topcoder4 (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_topcoder5 (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_train_bw (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_train_visible (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_uniform_norm (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: test_viterbi (test_MarkovModel.TestMarkovModel) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 45.835 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Medline.py
C
BUILDSTDERR: test_Medline ... ok
BUILDSTDERR: test_multiline_mesh (test_Medline.TestMedline) ... ok
BUILDSTDERR: test_parse (test_Medline.TestMedline) ... ok
BUILDSTDERR: test_read (test_Medline.TestMedline) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.728 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Muscle_tool.py
BUILDSTDERR: test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 9.293 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NACCESS_tool.py
BUILDSTDERR: test_NACCESS_tool ... skipping. Install naccess if you want to use it from Biopython.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.883 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBITextParser.py
BUILDSTDERR: test_NCBITextParser ... ok
BUILDSTDERR: test_conversion (test_NCBITextParser.TestBlastRecord)
BUILDSTDERR: Converting a Blast record multiple alignment. ... ok
BUILDSTDERR: test_text_2010L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.0.10 output (text_2010L_blastn_001). ... ok
BUILDSTDERR: test_text_2010L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.0.10 output without alignments (text_2010L_blastn_002). ... ok
BUILDSTDERR: test_text_2010L_blastn_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.0.10 output without descriptions (text_2010L_blastn_003). ... ok
BUILDSTDERR: test_text_2010L_blastn_004 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.0.10 output (text_2010L_blastn_004). ... ok
BUILDSTDERR: test_text_2010L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.10 output (text_2010L_blastp_001). ... ok
BUILDSTDERR: test_text_2010L_blastp_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.10 output without hits (text_2010L_blastp_002). ... ok
BUILDSTDERR: test_text_2010L_blastp_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.10 output (text_2010L_blastp_003). ... ok
BUILDSTDERR: test_text_2010L_blastp_004 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.10 output without descriptions (text_2010L_blastp_004). ... ok
BUILDSTDERR: test_text_2010L_blastp_005 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.10 output without alignments (text_2010L_blastp_005). ... ok
BUILDSTDERR: test_text_2010L_blastp_006 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.10 output (text_2010L_blastp_006). ... ok
BUILDSTDERR: test_text_2010L_blastp_007 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.10 output (text_2010L_blastp_007). ... ok
BUILDSTDERR: test_text_2010L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.0.10 output (text_2010L_blastx_001). ... ok
BUILDSTDERR: test_text_2010L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.0.10 output without hits (text_2010L_blastx_002). ... ok
BUILDSTDERR: test_text_2010L_phiblast_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing PHI-BLAST, BLASTP 2.0.10 output, one round (text_2010L_phiblast_001). ... ok
BUILDSTDERR: test_text_2010L_phiblast_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (text_2010L_phiblast_002). ... ok
BUILDSTDERR: test_text_2010L_phiblast_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (text_2010L_phiblast_003). ... ok
BUILDSTDERR: test_text_2010L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTN 2.0.10 output (text_2010L_tblastn_001). ... ok
BUILDSTDERR: test_text_2010L_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTN 2.0.10 output without hits (text_2010L_tblastn_002). ... ok
BUILDSTDERR: test_text_2010L_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTX 2.0.10 output (text_2010L_tblastx_001). ... ok
BUILDSTDERR: test_text_2011L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.0.11 output (text_2011L_blastn_001). ... ok
BUILDSTDERR: test_text_2011L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.0.11 output without alignments (text_2011L_blastn_002). ... ok
BUILDSTDERR: test_text_2011L_blastn_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.0.11 output without descriptions (text_2011L_blastn_003). ... ok
BUILDSTDERR: test_text_2011L_blastn_004 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.0.11 output (text_2011L_blastn_004). ... ok
BUILDSTDERR: test_text_2011L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.11 output (text_2011L_blastp_001). ... ok
BUILDSTDERR: test_text_2011L_blastp_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.11 output without hits (text_2011L_blastp_002). ... ok
BUILDSTDERR: test_text_2011L_blastp_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.11 output (text_2011L_blastp_003). ... ok
BUILDSTDERR: test_text_2011L_blastp_004 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.11 output without descriptions (text_2011L_blastp_004). ... ok
BUILDSTDERR: test_text_2011L_blastp_005 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.11 output without alignments (text_2011L_blastp_005). ... ok
BUILDSTDERR: test_text_2011L_blastp_006 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.11 output (text_2011L_blastp_006). ... ok
BUILDSTDERR: test_text_2011L_blastp_007 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.11 output (text_2011L_blastp_007). ... ok
BUILDSTDERR: test_text_2011L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.0.11 output (text_2011L_blastx_001). ... ok
BUILDSTDERR: test_text_2011L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.0.11 output without hits (text_2011L_blastx_002). ... ok
BUILDSTDERR: test_text_2011L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_001). ... ok
BUILDSTDERR: test_text_2011L_psiblast_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_002). ... ok
BUILDSTDERR: test_text_2011L_psiblast_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.11 output (text_2011L_psiblast_003). ... ok
BUILDSTDERR: test_text_2011L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTN 2.0.11 output (text_2011L_tblastn_001). ... ok
BUILDSTDERR: test_text_2011L_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTN 2.0.11 output without hits (text_2011L_tblastn_002). ... ok
BUILDSTDERR: test_text_2011L_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTX 2.0.11 output (text_2011L_tblastx_001). ... ok
BUILDSTDERR: test_text_2012L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.12 output (text_2012L_psiblast_001). ... ok
BUILDSTDERR: test_text_2014L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.0.14 output (text_2014L_blastn_001). ... ok
BUILDSTDERR: test_text_2014L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.0.14 output (text_2014L_psiblast_001). ... ok
BUILDSTDERR: test_text_2201L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.2.1 output (text_2201L_blastx_001). ... ok
BUILDSTDERR: test_text_2202L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.2.2 output with error messages (text_2202L_blastn_001). ... ok
BUILDSTDERR: test_text_2202L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.2.2 output with missing error messages (text_2202L_blastn_002). ... ok
BUILDSTDERR: test_text_2202L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.2.2 output with multiple records (text_2202L_blastp_001). ... ok
BUILDSTDERR: test_text_2208L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.2.8 output (text_2208L_psiblast_001). ... ok
BUILDSTDERR: test_text_2215L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.2.15 output with no hits (text_2215L_blastx_001). ... ok
BUILDSTDERR: test_text_2216L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTN 2.2.16 output (text_2216L_tblastn_001). ... ok
BUILDSTDERR: test_text_2220L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.2.20 output (text_2220L_blastx_001). ... ok
BUILDSTDERR: test_text_2220L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.2.20 output with multiple queries (text_2220L_blastx_002). ... ok
BUILDSTDERR: test_text_2221L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.2.21 output with multiple queries (text_2221L_blastp_001). ... ok
BUILDSTDERR: test_text_2222L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.2.22 output with multiple queries (text_2222L_blastx_001). ... ok
BUILDSTDERR: test_text_2222_blastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.2.22+ output with multiple queries (text_2222_blastx_001). ... ok
BUILDSTDERR: test_text_2226_blastn_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.2.26+ output with no results. ... ok
BUILDSTDERR: test_text_2226_blastn_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.2.26+ output with single hsp results. ... ok
BUILDSTDERR: test_text_2226_blastn_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTN 2.2.26+ output with multiple hsp results present. ... ok
BUILDSTDERR: test_text_2226_blastp_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.2.26+ with no results. ... ok
BUILDSTDERR: test_text_2226_blastp_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.2.26+ with single hsp results. ... ok
BUILDSTDERR: test_text_2226_blastp_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
BUILDSTDERR: test_text_2226_blastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.2.26+ with no results. ... ok
BUILDSTDERR: test_text_2226_blastx_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTX 2.2.26+ with single hsp results. ... ok
BUILDSTDERR: test_text_2226_blastx_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
BUILDSTDERR: test_text_2226_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTN 2.2.26+ output with no results. ... ok
BUILDSTDERR: test_text_2226_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTN 2.2.26+ output with single hsp results. ... ok
BUILDSTDERR: test_text_2226_tblastn_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTN 2.2.26+ output with multiple hsp results present. ... ok
BUILDSTDERR: test_text_2226_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTX 2.2.26+ output with no results. ... ok
BUILDSTDERR: test_text_2226_tblastx_002 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTX 2.2.26+ output with single hsp results. ... ok
BUILDSTDERR: test_text_2226_tblastx_003 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing TBLASTX 2.2.26+ output with multiple hsp results present. ... ok
BUILDSTDERR: test_text_2230_blastp_001 (test_NCBITextParser.TestNCBITextParser)
BUILDSTDERR: Parsing BLASTP 2.2.30+ output with line of dashes. ... ok
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 65.671 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBIXML.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_NCBIXML ... ok
BUILDSTDERR: test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001). ... ok
BUILDSTDERR: test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001). ... ok
BUILDSTDERR: test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001). ... ok
BUILDSTDERR: test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001). ... ok
BUILDSTDERR: test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001). ... ok
BUILDSTDERR: test_xml_2218L_blastp_001 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001). ... ok
BUILDSTDERR: test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001). ... ok
BUILDSTDERR: test_xml_2218_blastp_001 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001). ... ok
BUILDSTDERR: test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002). ... ok
BUILDSTDERR: test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001). ... ok
BUILDSTDERR: test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML)
BUILDSTDERR: Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001). ... ok
BUILDSTDERR: test_xml_2900_blastn_001_v1 (test_NCBIXML.TestNCBIXML) ... ok
BUILDSTDERR: test_xml_2900_blastn_001_v2 (test_NCBIXML.TestNCBIXML) ... ok
BUILDSTDERR: test_xml_2900_blastp_001_v1 (test_NCBIXML.TestNCBIXML) ... ok
BUILDSTDERR: test_xml_2900_blastp_001_v2 (test_NCBIXML.TestNCBIXML) ... ok
BUILDSTDERR: test_xml_2900_blastx_001_v1 (test_NCBIXML.TestNCBIXML) ... ok
BUILDSTDERR: test_xml_2900_blastx_001_v2 (test_NCBIXML.TestNCBIXML) ... ok
BUILDSTDERR: test_xml_2900_tblastn_001_v1 (test_NCBIXML.TestNCBIXML) ... ok
BUILDSTDERR: test_xml_2900_tblastn_001_v2 (test_NCBIXML.TestNCBIXML) ... ok
BUILDSTDERR: test_xml_2900_tblastx_001_v1 (test_NCBIXML.TestNCBIXML) ... ok
BUILDSTDERR: test_xml_2900_tblastx_001_v2 (test_NCBIXML.TestNCBIXML) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 273.613 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBI_BLAST_tools.py
BUILDSTDERR: test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1.257 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBI_qblast.py
BUILDSTDERR: test_NCBI_qblast ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 5.722 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NMR.py
BUILDSTDERR: test_NMR ... ok
BUILDSTDERR: test_noetools (test_NMR.NmrTests)
BUILDSTDERR: Self test for NMR.NOEtools. ... ok
BUILDSTDERR: test_xpktools (test_NMR.NmrTests)
BUILDSTDERR: Self test for NMR.xpktools. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1.891 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NaiveBayes.py
BUILDSTDERR: test_NaiveBayes ... ok
BUILDSTDERR: test_car_data (test_NaiveBayes.CarTest)
BUILDSTDERR: Simple example using car data. ... ok
BUILDSTDERR: test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest) ... ok
BUILDSTDERR: test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest) ... ok
BUILDSTDERR: test_classify_function (test_NaiveBayes.NaiveBayesTest) ... ok
BUILDSTDERR: test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest) ... ok
BUILDSTDERR: test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest) ... ok
BUILDSTDERR: test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest) ... ok
BUILDSTDERR: test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.747 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_baseml.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_PAML_baseml ... ok
BUILDSTDERR: testAlignmentExists (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testAlignmentFileIsValid (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testAlignmentSpecified (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testCtlFileExistsOnRead (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testCtlFileExistsOnRun (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testCtlFileValidOnRead (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testCtlFileValidOnRun (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testOptionExists (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testOutputFileSpecified (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testPamlErrorsCaught (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testParseAllVersions (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testParseAlpha1Rho1 (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testParseModel (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testParseNhomo (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testParseSEs (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testResultsExist (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testResultsParsable (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testResultsValid (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testTreeExists (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testTreeFileValid (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testTreeSpecified (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: testWorkingDirValid (test_PAML_baseml.ModTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 20.826 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_codeml.py
BUILDSTDERR: test_PAML_codeml ... ok
BUILDSTDERR: testAlignmentExists (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testAlignmentFileIsValid (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testAlignmentSpecified (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testCtlFileExistsOnRead (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testCtlFileExistsOnRun (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testCtlFileValidOnRead (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testCtlFileValidOnRun (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testOptionExists (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testOutputFileSpecified (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testPamlErrorsCaught (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseAA (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseAAPairwise (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseAllNSsites (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseBranchSiteA (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseCladeModelC (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseFreeRatio (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseM2arel (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseNSsite3 (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseNgene2Mgene02 (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseNgene2Mgene1 (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseNgene2Mgene34 (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParsePairwise (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseSEs (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testParseSitesParamsForPairwise (test_PAML_codeml.ModTest)
BUILDSTDERR: Verify that pairwise site estimates are indeed parsed. Fixes #483. ... ok
BUILDSTDERR: testResultsExist (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testResultsParsable (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testResultsValid (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testTreeExists (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testTreeFileValid (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testTreeParseVersatility (test_PAML_codeml.ModTest)
BUILDSTDERR: Test finding trees in the results. ... ok
BUILDSTDERR: testTreeSpecified (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: testWorkingDirValid (test_PAML_codeml.ModTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 97.936 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_tools.py
BUILDSTDERR: test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 10.525 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_yn00.py
BUILDSTDERR: test_PAML_yn00 ... ok
BUILDSTDERR: testAlignmentExists (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testAlignmentFileIsValid (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testAlignmentSpecified (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testCtlFileExistsOnRead (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testCtlFileExistsOnRun (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testCtlFileValidOnRead (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testCtlFileValidOnRun (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testOptionExists (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testOutputFileSpecified (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testParseAllVersions (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testParseDottedNames (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testParseDottedNumNames (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testParseLongNames (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testResultsExist (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testResultsParsable (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testResultsValid (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: testWorkingDirValid (test_PAML_yn00.ModTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 12.601 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB.py
BUILDSTDERR: test_PDB ... ok
BUILDSTDERR: test_1_warnings (test_PDB.A_ExceptionTest)
BUILDSTDERR: Check warnings: Parse a flawed PDB file in permissive mode. ... ok
BUILDSTDERR: test_2_strict (test_PDB.A_ExceptionTest)
BUILDSTDERR: Check error: Parse a flawed PDB file in strict mode. ... ok
BUILDSTDERR: test_3_bad_xyz (test_PDB.A_ExceptionTest)
BUILDSTDERR: Check error: Parse an entry with bad x,y,z value. ... ok
BUILDSTDERR: test_4_occupancy (test_PDB.A_ExceptionTest)
BUILDSTDERR: Parse file with missing occupancy. ... ok
BUILDSTDERR: test_AtomElement (test_PDB.Atom_Element)
BUILDSTDERR: Atom Element. ... ok
BUILDSTDERR: test_hydrogens (test_PDB.Atom_Element) ... ok
BUILDSTDERR: test_ions (test_PDB.Atom_Element)
BUILDSTDERR: Element for magnesium is assigned correctly. ... ok
BUILDSTDERR: test_change_chain_id (test_PDB.ChangingIdTests)
BUILDSTDERR: Change the id of a model. ... ok
BUILDSTDERR: test_change_id_to_self (test_PDB.ChangingIdTests)
BUILDSTDERR: Changing the id to itself does nothing (does not raise). ... ok
BUILDSTDERR: test_change_model_id (test_PDB.ChangingIdTests)
BUILDSTDERR: Change the id of a model. ... ok
BUILDSTDERR: test_change_model_id_raises (test_PDB.ChangingIdTests)
BUILDSTDERR: Cannot change id to a value already in use by another child. ... ok
BUILDSTDERR: test_change_residue_id (test_PDB.ChangingIdTests)
BUILDSTDERR: Change the id of a residue. ... ok
BUILDSTDERR: test_full_id_is_updated_chain (test_PDB.ChangingIdTests)
BUILDSTDERR: Invalidate cached full_ids if an id is changed. ... ok
BUILDSTDERR: test_full_id_is_updated_residue (test_PDB.ChangingIdTests)
BUILDSTDERR: Invalidate cached full_ids if an id is changed. ... ok
BUILDSTDERR: test_atom_copy (test_PDB.CopyTests) ... ok
BUILDSTDERR: test_entity_copy (test_PDB.CopyTests)
BUILDSTDERR: Make a copy of a residue. ... ok
BUILDSTDERR: test_DSSP_RSA (test_PDB.DsspTests)
BUILDSTDERR: Tests the usage of different ASA tables. ... ok
BUILDSTDERR: test_DSSP_file (test_PDB.DsspTests)
BUILDSTDERR: Test parsing of pregenerated DSSP. ... ok
BUILDSTDERR: test_DSSP_hbonds (test_PDB.DsspTests)
BUILDSTDERR: Test parsing of DSSP hydrogen bond information. ... ok
BUILDSTDERR: test_DSSP_in_model_obj (test_PDB.DsspTests)
BUILDSTDERR: All elements correctly added to xtra attribute of input model object. ... ok
BUILDSTDERR: test_DSSP_noheader_file (test_PDB.DsspTests)
BUILDSTDERR: Test parsing of pregenerated DSSP missing header information. ... ok
BUILDSTDERR: test_ExposureCN (test_PDB.Exposure)
BUILDSTDERR: HSExposureCN. ... ok
BUILDSTDERR: test_HSExposureCA (test_PDB.Exposure)
BUILDSTDERR: HSExposureCA. ... ok
BUILDSTDERR: test_HSExposureCB (test_PDB.Exposure)
BUILDSTDERR: HSExposureCB. ... ok
BUILDSTDERR: test_capsid (test_PDB.HeaderTests)
BUILDSTDERR: Parse the header of a known PDB file (1A8O). ... ok
BUILDSTDERR: test_fibril (test_PDB.HeaderTests)
BUILDSTDERR: Parse the header of another PDB file (2BEG). ... ok
BUILDSTDERR: test_get_atoms (test_PDB.IterationTests)
BUILDSTDERR: Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok
BUILDSTDERR: test_get_chains (test_PDB.IterationTests)
BUILDSTDERR: Yields chains from different models separately. ... ok
BUILDSTDERR: test_get_residues (test_PDB.IterationTests)
BUILDSTDERR: Yields all residues from all models. ... ok
BUILDSTDERR: test_NACCESS_asa_file (test_PDB.NACCESSTests)
BUILDSTDERR: Test parsing of pregenerated asa NACCESS file. ... ok
BUILDSTDERR: test_NACCESS_rsa_file (test_PDB.NACCESSTests)
BUILDSTDERR: Test parsing of pregenerated rsa NACCESS file. ... ok
BUILDSTDERR: test_PDBParser (test_PDB.PDBParserTests)
BUILDSTDERR: Walk down the structure hierarchy and test parser reliability. ... ok
BUILDSTDERR: test_c_n (test_PDB.ParseReal)
BUILDSTDERR: Extract polypeptides from 1A80. ... ok
BUILDSTDERR: test_empty (test_PDB.ParseReal)
BUILDSTDERR: Parse an empty file. ... ok
BUILDSTDERR: test_model_numbering (test_PDB.ParseReal)
BUILDSTDERR: Preserve model serial numbers during I/O. ... ok
BUILDSTDERR: test_residue_sort (test_PDB.ParseReal)
BUILDSTDERR: Sorting atoms in residues. ... ok
BUILDSTDERR: test_strict (test_PDB.ParseReal)
BUILDSTDERR: Parse 1A8O.pdb file in strict mode. ... ok
BUILDSTDERR: test_c_n (test_PDB.ParseTest)
BUILDSTDERR: Extract polypeptides using C-N. ... ok
BUILDSTDERR: test_ca_ca (test_PDB.ParseTest)
BUILDSTDERR: Extract polypeptides using CA-CA. ... ok
BUILDSTDERR: test_comparison_entities (test_PDB.ParseTest)
BUILDSTDERR: Test comparing and sorting the several SMCRA objects. ... ok
BUILDSTDERR: test_details (test_PDB.ParseTest)
BUILDSTDERR: Verify details of the parsed example PDB file. ... ok
BUILDSTDERR: test_pdbio_write_truncated (test_PDB.ParseTest)
BUILDSTDERR: Test parsing of truncated lines. ... ok
BUILDSTDERR: test_structure (test_PDB.ParseTest)
BUILDSTDERR: Verify the structure of the parsed example PDB file. ... ok
BUILDSTDERR: test_pdb_to_xyzr (test_PDB.ResidueDepthTests)
BUILDSTDERR: Test generation of xyzr (atomic radii) file. ... ok
BUILDSTDERR: test_transform (test_PDB.TransformTests)
BUILDSTDERR: Transform entities (rotation and translation). ... ok
BUILDSTDERR: test_mmcifio_multimodel (test_PDB.WriteTest)
BUILDSTDERR: Write a multi-model, multi-chain mmCIF file. ... ok
BUILDSTDERR: test_mmcifio_select (test_PDB.WriteTest)
BUILDSTDERR: Write a selection of the structure using a Select subclass. ... ok
BUILDSTDERR: test_mmcifio_write_dict (test_PDB.WriteTest)
BUILDSTDERR: Write an mmCIF dictionary out, read it in and compare them. ... ok
BUILDSTDERR: test_mmcifio_write_residue (test_PDB.WriteTest)
BUILDSTDERR: Write a single residue using MMCIFIO. ... ok
BUILDSTDERR: test_mmcifio_write_structure (test_PDB.WriteTest)
BUILDSTDERR: Write a full structure using MMCIFIO. ... ok
BUILDSTDERR: test_pdbio_missing_occupancy (test_PDB.WriteTest)
BUILDSTDERR: Write PDB file with missing occupancy. ... ok
BUILDSTDERR: test_pdbio_select (test_PDB.WriteTest)
BUILDSTDERR: Write a selection of the structure using a Select subclass. ... ok
BUILDSTDERR: test_pdbio_write_custom_residue (test_PDB.WriteTest)
BUILDSTDERR: Write a chainless residue using PDBIO. ... ok
BUILDSTDERR: test_pdbio_write_residue (test_PDB.WriteTest)
BUILDSTDERR: Write a single residue using PDBIO. ... ok
BUILDSTDERR: test_pdbio_write_structure (test_PDB.WriteTest)
BUILDSTDERR: Write a full structure using PDBIO. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 346.231 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDBList.py
BUILDSTDERR: test_PDBList ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 5.451 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Dice.py
BUILDSTDERR: test_PDB_Dice ... ok
BUILDSTDERR: test_dice (test_PDB_Dice.DiceTests)
BUILDSTDERR: Self test for PDB.Dice module. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 14.029 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_FragmentMapper.py
BUILDSTDERR: test_PDB_FragmentMapper ... ok
BUILDSTDERR: test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests)
BUILDSTDERR: Self test for FragmentMapper module. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 17.522 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_KDTree.py
C
BUILDSTDERR: test_PDB_KDTree ... ok
BUILDSTDERR: test_KDTree_exceptions (test_PDB_KDTree.KDTreeTest) ... ok
BUILDSTDERR: test_KDTree_neighbor_search_manual (test_PDB_KDTree.KDTreeTest)
BUILDSTDERR: Test all fixed radius neighbor search. ... ok
BUILDSTDERR: test_KDTree_neighbor_search_simple (test_PDB_KDTree.KDTreeTest)
BUILDSTDERR: Test all fixed radius neighbor search. ... ok
BUILDSTDERR: test_KDTree_point_search (test_PDB_KDTree.KDTreeTest)
BUILDSTDERR: Test searching all points within a certain radius of center. ... ok
BUILDSTDERR: test_neighbor_search (test_PDB_KDTree.NeighborTest)
BUILDSTDERR: NeighborSearch: Find nearby randomly generated coordinates. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 406.248 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIF2Dict.py
BUILDSTDERR: test_PDB_MMCIF2Dict ... ok
BUILDSTDERR: test_MMCIF2dict (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
BUILDSTDERR: test_inline_comments (test_PDB_MMCIF2Dict.MMCIF2dictTests)
BUILDSTDERR: Comments may begin outside of column 1 if preceded by whitespace. ... ok
BUILDSTDERR: test_loop_keyword_case_insensitive (test_PDB_MMCIF2Dict.MMCIF2dictTests)
BUILDSTDERR: Comments may begin outside of column 1. ... ok
BUILDSTDERR: test_quotefix (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
BUILDSTDERR: test_splitline (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
BUILDSTDERR: test_underscores (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
BUILDSTDERR: test_verbatim_block (test_PDB_MMCIF2Dict.MMCIF2dictTests)
BUILDSTDERR: Verbatim bocks parsed correctly. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 14.238 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFParser.py
BUILDSTDERR: test_PDB_MMCIFParser ... ok
BUILDSTDERR: test_conversion (test_PDB_MMCIFParser.CIFtoPDB)
BUILDSTDERR: Parse 1A8O.cif, write 1A8O.pdb, parse again and compare. ... ok
BUILDSTDERR: testModels (test_PDB_MMCIFParser.ParseReal)
BUILDSTDERR: Test file with multiple models. ... ok
BUILDSTDERR: test_filehandle (test_PDB_MMCIFParser.ParseReal)
BUILDSTDERR: Test if the parser can handle file handle as well as filename. ... ok
BUILDSTDERR: test_insertions (test_PDB_MMCIFParser.ParseReal)
BUILDSTDERR: Test file with residue insertion codes. ... ok
BUILDSTDERR: test_parsers (test_PDB_MMCIFParser.ParseReal)
BUILDSTDERR: Extract polypeptides from 1A80. ... ok
BUILDSTDERR: test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal)
BUILDSTDERR: Test if FastMMCIFParser can parse point mutations correctly. ... ok
BUILDSTDERR: test_point_mutations_main (test_PDB_MMCIFParser.ParseReal)
BUILDSTDERR: Test if MMCIFParser parse point mutations correctly. ... ok
BUILDSTDERR: test_with_anisotrop (test_PDB_MMCIFParser.ParseReal) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 267.871 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Polypetide.py
BUILDSTDERR: test_PDB_Polypetide ... ok
BUILDSTDERR: test_polypeptide (test_PDB_Polypetide.PolypeptideTests)
BUILDSTDERR: Tests on polypetide class and methods. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 15.159 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_ResidueDepth.py
BUILDSTDERR: test_PDB_ResidueDepth ... skipping. Install MSMS if you want to use it in Biopython.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.906 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_StructureAlignment.py
BUILDSTDERR: test_PDB_StructureAlignment ... /builddir/build/BUILD/python-biopython-1.74/python3/build/lib.linux-riscv64-3.7/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298.
BUILDSTDERR:   PDBConstructionWarning)
BUILDSTDERR: /builddir/build/BUILD/python-biopython-1.74/python3/build/lib.linux-riscv64-3.7/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344.
BUILDSTDERR:   PDBConstructionWarning)
BUILDSTDERR: ok
BUILDSTDERR: test_StructAlign (test_PDB_StructureAlignment.StructureAlignTests)
BUILDSTDERR: Tests on module to align two proteins according to a FASTA alignment file. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 53.017 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Superimposer.py
BUILDSTDERR: test_PDB_Superimposer ... ok
BUILDSTDERR: test_Superimposer (test_PDB_Superimposer.SuperimposerTests)
BUILDSTDERR: Test on module that superimpose two protein structures. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 13.220 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_parse_pdb_header.py
BUILDSTDERR: test_PDB_parse_pdb_header ... ok
BUILDSTDERR: test_parse_header_line (test_PDB_parse_pdb_header.ParseReal)
BUILDSTDERR: Unit test for parsing and converting fields in HEADER record. ... ok
BUILDSTDERR: test_parse_pdb_with_remark_465 (test_PDB_parse_pdb_header.ParseReal)
BUILDSTDERR: Tests that parse_pdb_header now can identify some REMARK 465 entries. ... ok
BUILDSTDERR: test_parse_remark_465 (test_PDB_parse_pdb_header.ParseReal)
BUILDSTDERR: A UNIT-test for the private function _parse_remark_465. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7.492 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_vectors.py
BUILDSTDERR: test_PDB_vectors ... ok
BUILDSTDERR: test_Vector (test_PDB_vectors.VectorTests)
BUILDSTDERR: Test Vector object. ... ok
BUILDSTDERR: test_Vector_angles (test_PDB_vectors.VectorTests)
BUILDSTDERR: Test Vector angles. ... ok
BUILDSTDERR: test_division (test_PDB_vectors.VectorTests)
BUILDSTDERR: Confirm division works. ... ok
BUILDSTDERR: test_m2rotaxis_0 (test_PDB_vectors.VectorTests)
BUILDSTDERR: Test 0 deg rotation. Axis must be [1, 0, 0] as per Vector documentation. ... ok
BUILDSTDERR: test_m2rotaxis_180 (test_PDB_vectors.VectorTests)
BUILDSTDERR: Test 180 deg rotation. ... ok
BUILDSTDERR: test_m2rotaxis_90 (test_PDB_vectors.VectorTests)
BUILDSTDERR: Test 90 deg rotation. ... ok
BUILDSTDERR: test_normalization (test_PDB_vectors.VectorTests)
BUILDSTDERR: Test Vector normalization. ... ok
BUILDSTDERR: test_refmat (test_PDB_vectors.VectorTests) ... ok
BUILDSTDERR: test_rotmat_0 (test_PDB_vectors.VectorTests)
BUILDSTDERR: Test rotmat when the rotation is 0 deg (singularity). ... ok
BUILDSTDERR: test_rotmat_180 (test_PDB_vectors.VectorTests)
BUILDSTDERR: Test rotmat when the rotation is 180 deg (singularity). ... ok
BUILDSTDERR: test_rotmat_90 (test_PDB_vectors.VectorTests)
BUILDSTDERR: Test regular 90 deg rotation. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.445 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Pathway.py
BUILDSTDERR: test_Pathway ... ok
BUILDSTDERR: testAdditionalFunctions (test_Pathway.GraphTestCase) ... ok
BUILDSTDERR: test_Edges (test_Pathway.GraphTestCase) ... ok
BUILDSTDERR: test_Equals (test_Pathway.GraphTestCase) ... ok
BUILDSTDERR: test_Nodes (test_Pathway.GraphTestCase) ... ok
BUILDSTDERR: test_RemoveNode (test_Pathway.GraphTestCase) ... ok
BUILDSTDERR: testAdditionalFunctions (test_Pathway.MultiGraphTestCase) ... ok
BUILDSTDERR: test_Edges (test_Pathway.MultiGraphTestCase) ... ok
BUILDSTDERR: test_Equals (test_Pathway.MultiGraphTestCase) ... ok
BUILDSTDERR: test_Nodes (test_Pathway.MultiGraphTestCase) ... ok
BUILDSTDERR: test_RemoveNode (test_Pathway.MultiGraphTestCase) ... ok
BUILDSTDERR: test_eq (test_Pathway.ReactionTestCase) ... ok
BUILDSTDERR: test_rev (test_Pathway.ReactionTestCase) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.800 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Phd.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_Phd ... ok
BUILDSTDERR: test_check_SeqIO (test_Phd.PhdTest454)
BUILDSTDERR: Test phd_454 using parser via SeqIO. ... ok
BUILDSTDERR: test_check_SeqIO (test_Phd.PhdTestOne)
BUILDSTDERR: Test phd1 using parser via SeqIO. ... ok
BUILDSTDERR: test_check_record_parser (test_Phd.PhdTestOne)
BUILDSTDERR: Test phd1 file in detail. ... ok
BUILDSTDERR: test_check_SeqIO (test_Phd.PhdTestSolexa)
BUILDSTDERR: Test phd2 using parser via SeqIO. ... ok
BUILDSTDERR: test_check_SeqIO (test_Phd.PhdTestTwo)
BUILDSTDERR: Test phd2 using parser via SeqIO. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 9.893 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop.py
BUILDSTDERR: test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1.774 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py
BUILDSTDERR: test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.816 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_nodepend.py
BUILDSTDERR: test_PopGen_GenePop_nodepend ... ok
BUILDSTDERR: test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest)
BUILDSTDERR: Basic operation of the File Record Parser. ... ok
BUILDSTDERR: test_remove_features (test_PopGen_GenePop_nodepend.FileParserTest)
BUILDSTDERR: Testing the ability to remove population/loci via class methods. ... ok
BUILDSTDERR: test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest)
BUILDSTDERR: Testing the ability to deal with wrongly formatted files. ... ok
BUILDSTDERR: test_record_parser (test_PopGen_GenePop_nodepend.ParserTest)
BUILDSTDERR: Basic operation of the Record Parser. ... ok
BUILDSTDERR: test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest)
BUILDSTDERR: Testing the ability to deal with wrongly formatted files. ... ok
BUILDSTDERR: test_record_basic (test_PopGen_GenePop_nodepend.RecordTest)
BUILDSTDERR: Basic test on Record. ... ok
BUILDSTDERR: test_utils (test_PopGen_GenePop_nodepend.UtilsTest)
BUILDSTDERR: Basic operation of GenePop Utils. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 2.653 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Prank_tool.py
BUILDSTDERR: test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.218 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Probcons_tool.py
BUILDSTDERR: test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 5.660 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ProtParam.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_ProtParam ... ok
BUILDSTDERR: test_aromaticity (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate protein aromaticity. ... ok
BUILDSTDERR: test_count_amino_acids (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate amino acid counts. ... ok
BUILDSTDERR: test_flexibility (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate protein flexibility. ... ok
BUILDSTDERR: test_get_amino_acids_percent (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate amino acid percentages. ... ok
BUILDSTDERR: test_get_molecular_weight (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate protein molecular weight. ... ok
BUILDSTDERR: test_get_molecular_weight_identical (test_ProtParam.ProtParamTest)
BUILDSTDERR: Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
BUILDSTDERR: test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate monoisotopic molecular weight. ... ok
BUILDSTDERR: test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest)
BUILDSTDERR: Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
BUILDSTDERR: test_gravy (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate gravy. ... ok
BUILDSTDERR: test_instability_index (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate protein instability index. ... ok
BUILDSTDERR: test_isoelectric_point (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate the isoelectric point. ... ok
BUILDSTDERR: test_molar_extinction_coefficient (test_ProtParam.ProtParamTest)
BUILDSTDERR: Molar extinction coefficient. ... ok
BUILDSTDERR: test_protein_scale (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate the Kite Doolittle scale. ... ok
BUILDSTDERR: test_secondary_structure_fraction (test_ProtParam.ProtParamTest)
BUILDSTDERR: Calculate secondary structure fractions. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 4.564 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_QCPSuperimposer.py
BUILDSTDERR: test_QCPSuperimposer ... ok
BUILDSTDERR: test_get_init_rms (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
BUILDSTDERR: test_get_rms (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
BUILDSTDERR: test_get_rotran (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
BUILDSTDERR: test_get_transformed (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
BUILDSTDERR: test_oldTest (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
BUILDSTDERR: test_run (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
BUILDSTDERR: test_set (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 3.645 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_RCSBFormats.py
BUILDSTDERR: test_RCSBFormats ... ok
BUILDSTDERR: test_compare_chains (test_RCSBFormats.CompareStructures)
BUILDSTDERR: Compare parsed chains. ... ok
BUILDSTDERR: test_compare_models (test_RCSBFormats.CompareStructures)
BUILDSTDERR: Compared parsed models. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 97.938 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Restriction.py
BUILDSTDERR: test_Restriction ... ok
BUILDSTDERR: test_basic_isochizomers (test_Restriction.EnzymeComparison)
BUILDSTDERR: Test to be sure isochizomer and neoschizomers are as expected. ... ok
BUILDSTDERR: test_comparisons (test_Restriction.EnzymeComparison)
BUILDSTDERR: Test comparison operators between different enzymes. ... ok
BUILDSTDERR: test_change (test_Restriction.RestrictionBatchPrintTest)
BUILDSTDERR: Test that change() changes something. ... ok
BUILDSTDERR: test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest)
BUILDSTDERR: Test that print_as('map'); print_that() correctly wraps round. ... ok
BUILDSTDERR: test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest)
BUILDSTDERR: Test that print_as('map'); print_that() correctly wraps round. ... ok
BUILDSTDERR: test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest)
BUILDSTDERR: Test that print_as('map'); print_that() correctly wraps round. ... ok
BUILDSTDERR: test_analysis_restrictions (test_Restriction.RestrictionBatches)
BUILDSTDERR: Test Fancier restriction analysis. ... ok
BUILDSTDERR: test_batch_analysis (test_Restriction.RestrictionBatches)
BUILDSTDERR: Sequence analysis with a restriction batch. ... ok
BUILDSTDERR: test_creating_batch (test_Restriction.RestrictionBatches)
BUILDSTDERR: Creating and modifying a restriction batch. ... ok
BUILDSTDERR: test_premade_batches (test_Restriction.RestrictionBatches)
BUILDSTDERR: Test content of premade batches CommOnly, NoComm, AllEnzymes. ... ok
BUILDSTDERR: test_search_premade_batches (test_Restriction.RestrictionBatches)
BUILDSTDERR: Test search with pre-made batches CommOnly, NoComm, AllEnzymes. ... ok
BUILDSTDERR: test_formatted_seq (test_Restriction.SequenceTesting)
BUILDSTDERR: Test several methods of FormattedSeq. ... ok
BUILDSTDERR: test_non_iupac_letters (test_Restriction.SequenceTesting)
BUILDSTDERR: Test if non-IUPAC letters raise a TypeError. ... ok
BUILDSTDERR: test_sequence_object (test_Restriction.SequenceTesting)
BUILDSTDERR: Test if sequence must be a Seq or MutableSeq object. ... ok
BUILDSTDERR: test_circular_sequences (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Deal with cutting circular sequences. ... ok
BUILDSTDERR: test_cutting_border_positions (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Check if cutting after first and penultimate position works. ... ok
BUILDSTDERR: test_ear_cutting (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Test basic cutting with EarI (ambiguous overhang). ... ok
BUILDSTDERR: test_eco_cutting (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Test basic cutting with EcoRI (5'overhang). ... ok
BUILDSTDERR: test_init (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Check for error during __init__. ... ok
BUILDSTDERR: test_kpn_cutting (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Test basic cutting with KpnI (3'overhang). ... ok
BUILDSTDERR: test_overlapping_cut_sites (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Check if overlapping recognition sites are properly handled. ... ok
BUILDSTDERR: test_recognition_site_on_both_strands (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Check if recognition sites on both strands are properly handled. ... ok
BUILDSTDERR: test_shortcuts (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Check if '/' and '//' work as '.search' and '.catalyse'. ... ok
BUILDSTDERR: test_sma_cutting (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Test basic cutting with SmaI (blunt cutter). ... ok
BUILDSTDERR: test_sna_cutting (test_Restriction.SimpleEnzyme)
BUILDSTDERR: Test basic cutting with SnaI (unknown). ... ok
BUILDSTDERR: test_print_that (test_Restriction.TestPrintOutputs)
BUILDSTDERR: Test print_that function. ... ok
BUILDSTDERR: test_str_method (test_Restriction.TestPrintOutputs)
BUILDSTDERR: Test __str__ and __repr__ outputs. ... ok
BUILDSTDERR: test_supplier (test_Restriction.TestPrintOutputs)
BUILDSTDERR: Test output of supplier list for different enzyme types. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 25.423 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Astral.py
BUILDSTDERR: test_SCOP_Astral ... ok
BUILDSTDERR: testConstructWithCustomFile (test_SCOP_Astral.AstralTests) ... ok
BUILDSTDERR: testGetDomainsClustered (test_SCOP_Astral.AstralTests) ... ok
BUILDSTDERR: testGetDomainsFromFile (test_SCOP_Astral.AstralTests) ... ok
BUILDSTDERR: testGetSeq (test_SCOP_Astral.AstralTests) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 9.136 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Cla.py
BUILDSTDERR: test_SCOP_Cla ... ok
BUILDSTDERR: testError (test_SCOP_Cla.ClaTests)
BUILDSTDERR: Test if a corrupt record raises the appropriate exception. ... ok
BUILDSTDERR: testIndex (test_SCOP_Cla.ClaTests)
BUILDSTDERR: Test CLA file indexing. ... ok
BUILDSTDERR: testParse (test_SCOP_Cla.ClaTests)
BUILDSTDERR: Test if all records in a CLA file are being read. ... ok
BUILDSTDERR: testRecord (test_SCOP_Cla.ClaTests)
BUILDSTDERR: Test one record in detail. ... ok
BUILDSTDERR: testStr (test_SCOP_Cla.ClaTests)
BUILDSTDERR: Test if we can convert each record to a string correctly. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7.035 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Des.py
BUILDSTDERR: test_SCOP_Des ... ok
BUILDSTDERR: testError (test_SCOP_Des.DesTests)
BUILDSTDERR: Test if a corrupt record raises the appropriate exception. ... ok
BUILDSTDERR: testParse (test_SCOP_Des.DesTests)
BUILDSTDERR: Test if all records in a DES file are being read. ... ok
BUILDSTDERR: testRecord (test_SCOP_Des.DesTests)
BUILDSTDERR: Test one record in detail. ... ok
BUILDSTDERR: testStr (test_SCOP_Des.DesTests)
BUILDSTDERR: Test if we can convert each record to a string correctly. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.036 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Dom.py
BUILDSTDERR: test_SCOP_Dom ... ok
BUILDSTDERR: testError (test_SCOP_Dom.DomTests)
BUILDSTDERR: Test if a corrupt record raises the appropriate exception. ... ok
BUILDSTDERR: testParse (test_SCOP_Dom.DomTests)
BUILDSTDERR: Test if all records in a DOM file are being read. ... ok
BUILDSTDERR: testRecord (test_SCOP_Dom.DomTests)
BUILDSTDERR: Test one record in detail. ... ok
BUILDSTDERR: testStr (test_SCOP_Dom.DomTests)
BUILDSTDERR: Test if we can convert each record to a string correctly. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7.364 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Hie.py
BUILDSTDERR: test_SCOP_Hie ... ok
BUILDSTDERR: testError (test_SCOP_Hie.HieTests)
BUILDSTDERR: Test if a corrupt record raises the appropriate exception. ... ok
BUILDSTDERR: testParse (test_SCOP_Hie.HieTests)
BUILDSTDERR: Test if all records in a HIE file are being read. ... ok
BUILDSTDERR: testStr (test_SCOP_Hie.HieTests)
BUILDSTDERR: Test if we can convert each record to a string correctly. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.577 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Raf.py
BUILDSTDERR: test_SCOP_Raf ... ok
BUILDSTDERR: testParse (test_SCOP_Raf.RafTests)
BUILDSTDERR: Parse a RAF record. ... ok
BUILDSTDERR: testSeqMapAdd (test_SCOP_Raf.RafTests) ... ok
BUILDSTDERR: testSeqMapIndex (test_SCOP_Raf.RafTests) ... ok
BUILDSTDERR: testSeqMapSlice (test_SCOP_Raf.RafTests) ... ok
BUILDSTDERR: test_SeqMap_getAtoms_err (test_SCOP_Raf.RafTests) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.948 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Residues.py
BUILDSTDERR: test_SCOP_Residues ... ok
BUILDSTDERR: testAstralParse (test_SCOP_Residues.ResiduesTests)
BUILDSTDERR: Test if we can parse residue subsets enclosed in brackets. ... ok
BUILDSTDERR: testJustPdbId (test_SCOP_Residues.ResiduesTests) ... ok
BUILDSTDERR: testParse (test_SCOP_Residues.ResiduesTests) ... ok
BUILDSTDERR: testParseError (test_SCOP_Residues.ResiduesTests) ... ok
BUILDSTDERR: testPdbId (test_SCOP_Residues.ResiduesTests) ... ok
BUILDSTDERR: testStr (test_SCOP_Residues.ResiduesTests) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7.656 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Scop.py
BUILDSTDERR: test_SCOP_Scop ... ok
BUILDSTDERR: testConstructFromDirectory (test_SCOP_Scop.ScopTests) ... ok
BUILDSTDERR: testGetAscendent (test_SCOP_Scop.ScopTests) ... ok
BUILDSTDERR: testParse (test_SCOP_Scop.ScopTests) ... ok
BUILDSTDERR: testParseDomain (test_SCOP_Scop.ScopTests) ... ok
BUILDSTDERR: testSccsOrder (test_SCOP_Scop.ScopTests) ... ok
BUILDSTDERR: test_get_descendents (test_SCOP_Scop.ScopTests)
BUILDSTDERR: Test getDescendents method. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.537 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_online.py
BUILDSTDERR: test_SCOP_online ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7.637 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SVDSuperimposer.py
BUILDSTDERR: test_SVDSuperimposer ... ok
BUILDSTDERR: test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest) ... ok
BUILDSTDERR: test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.526 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl.py
BUILDSTDERR: test_SearchIO_blat_psl ... ok
BUILDSTDERR: test_psl_34_001 (test_SearchIO_blat_psl.BlatPslCases)
BUILDSTDERR: Test parsing blat output (psl_34_001.psl). ... ok
BUILDSTDERR: test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases)
BUILDSTDERR: Test parsing blat output (psl_34_001.psl). ... ok
BUILDSTDERR: test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases)
BUILDSTDERR: Test parsing blat output (psl_34_003.psl). ... ok
BUILDSTDERR: test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases)
BUILDSTDERR: Test parsing blat output (psl_34_004.psl). ... ok
BUILDSTDERR: test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases)
BUILDSTDERR: Test parsing blat output (psl_34_005.psl). ... ok
BUILDSTDERR: test_psl_35_001 (test_SearchIO_blat_psl.BlatPslCases)
BUILDSTDERR: Test parsing blat output (psl_35_001.psl). ... ok
BUILDSTDERR: test_psl_35_002 (test_SearchIO_blat_psl.BlatPslCases)
BUILDSTDERR: Test parsing blat output (psl_35_002.psl). ... ok
BUILDSTDERR: test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (psl_34_001.psl). ... ok
BUILDSTDERR: test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (psl_34_001.psl). ... ok
BUILDSTDERR: test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (psl_34_003.psl). ... ok
BUILDSTDERR: test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (psl_34_004.psl). ... ok
BUILDSTDERR: test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (psl_34_005.psl). ... ok
BUILDSTDERR: test_psl_35_001 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (psl_35_001.psl). ... ok
BUILDSTDERR: test_psl_35_002 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (psl_35_002.psl). ... ok
BUILDSTDERR: test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (pslx_34_001.pslx). ... ok
BUILDSTDERR: test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (pslx_34_002.pslx). ... ok
BUILDSTDERR: test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (pslx_34_003.pslx). ... ok
BUILDSTDERR: test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (pslx_34_004.pslx). ... ok
BUILDSTDERR: test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (pslx_34_005.pslx). ... ok
BUILDSTDERR: test_pslx_35_002 (test_SearchIO_blat_psl.BlatPslxCases)
BUILDSTDERR: Test parsing blat output (pslx_35_002.pslx). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 12.843 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl_index.py
BUILDSTDERR: test_SearchIO_blat_psl_index ... ok
BUILDSTDERR: test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
BUILDSTDERR: Test blat-psl indexing, multiple queries. ... ok
BUILDSTDERR: test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
BUILDSTDERR: Test blat-psl indexing, single query, no hits. ... ok
BUILDSTDERR: test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
BUILDSTDERR: Test blat-psl indexing, single query, single hit. ... ok
BUILDSTDERR: test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
BUILDSTDERR: Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok
BUILDSTDERR: test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
BUILDSTDERR: Test blat-psl indexing, multiple queries, no header. ... ok
BUILDSTDERR: test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
BUILDSTDERR: Test blat-pslx indexing, multiple queries. ... ok
BUILDSTDERR: test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
BUILDSTDERR: Test blat-pslx indexing, single query, no hits. ... ok
BUILDSTDERR: test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
BUILDSTDERR: Test blat-pslx indexing, single query, single hit. ... ok
BUILDSTDERR: test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
BUILDSTDERR: Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok
BUILDSTDERR: test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
BUILDSTDERR: Test blat-pslx indexing, multiple queries, no header. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 17.185 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate.py
BUILDSTDERR: test_SearchIO_exonerate ... ok
BUILDSTDERR: test_exn_22_o_vulgar_cigar (test_SearchIO_exonerate.ExonerateCigarCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_o_vulgar_cigar.exn). ... ok
BUILDSTDERR: test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases)
BUILDSTDERR: Compares vulgar-text coordinate parsing for the coding2coding model. ... ok
BUILDSTDERR: test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases)
BUILDSTDERR: Compares vulgar-text coordinate parsing for the genome2genome model. ... ok
BUILDSTDERR: test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases)
BUILDSTDERR: Compares vulgar-text coordinate parsing for the protein2dna model. ... ok
BUILDSTDERR: test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_affine_local.exn). ... ok
BUILDSTDERR: test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_cdna2genome.exn). ... ok
BUILDSTDERR: test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_coding2coding.exn). ... ok
BUILDSTDERR: test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn). ... ok
BUILDSTDERR: test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_coding2genome.exn). ... ok
BUILDSTDERR: test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_dna2protein.exn). ... ok
BUILDSTDERR: test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_est2genome.exn). ... ok
BUILDSTDERR: test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_genome2genome.exn). ... ok
BUILDSTDERR: test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_ner.exn). ... ok
BUILDSTDERR: test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn). ... ok
BUILDSTDERR: test_exn_22_m_protein2genome (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_protein2genome.exn). ... ok
BUILDSTDERR: test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_ungapped.exn). ... ok
BUILDSTDERR: test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_m_ungapped_trans.exn). ... ok
BUILDSTDERR: test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_q_multiple.exn). ... ok
BUILDSTDERR: test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_q_none.exn). ... ok
BUILDSTDERR: test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_o_vulgar.exn). ... ok
BUILDSTDERR: test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases)
BUILDSTDERR: Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 17.760 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_text_index.py
BUILDSTDERR: test_SearchIO_exonerate_text_index ... ok
BUILDSTDERR: test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases)
BUILDSTDERR: Test exonerate-text indexing, single. ... ok
BUILDSTDERR: test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases)
BUILDSTDERR: Test exonerate-text indexing, single. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7.258 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_vulgar_index.py
BUILDSTDERR: test_SearchIO_exonerate_vulgar_index ... ok
BUILDSTDERR: test_exn_22_m_est2genome (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases)
BUILDSTDERR: Test exonerate-vulgar indexing, single. ... ok
BUILDSTDERR: test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases)
BUILDSTDERR: Test exonerate-vulgar indexing, single. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.048 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10.py
BUILDSTDERR: test_SearchIO_fasta_m10 ... ok
BUILDSTDERR: test_output002 (test_SearchIO_fasta_m10.Fasta34Cases)
BUILDSTDERR: Test parsing fasta34 output (output002.m10). ... ok
BUILDSTDERR: test_output003 (test_SearchIO_fasta_m10.Fasta34Cases)
BUILDSTDERR: Test parsing fasta34 output (output003.m10). ... ok
BUILDSTDERR: test_output001 (test_SearchIO_fasta_m10.Fasta35Cases)
BUILDSTDERR: Test parsing fasta35 output (output001.m10). ... ok
BUILDSTDERR: test_output004 (test_SearchIO_fasta_m10.Fasta35Cases)
BUILDSTDERR: Test parsing fasta35 output (output004.m10). ... ok
BUILDSTDERR: test_output005 (test_SearchIO_fasta_m10.Fasta35Cases)
BUILDSTDERR: Test parsing ssearch35 output (output005.m10). ... ok
BUILDSTDERR: test_output006 (test_SearchIO_fasta_m10.Fasta35Cases)
BUILDSTDERR: Test parsing fasta35 output (output006.m10). ... ok
BUILDSTDERR: test_output007 (test_SearchIO_fasta_m10.Fasta36Cases)
BUILDSTDERR: Test parsing fasta36 output (output007.m10). ... ok
BUILDSTDERR: test_output008 (test_SearchIO_fasta_m10.Fasta36Cases)
BUILDSTDERR: Test parsing tfastx36 output (output008.m10). ... ok
BUILDSTDERR: test_output009 (test_SearchIO_fasta_m10.Fasta36Cases)
BUILDSTDERR: Test parsing fasta36 output (output009.m10). ... ok
BUILDSTDERR: test_output010 (test_SearchIO_fasta_m10.Fasta36Cases)
BUILDSTDERR: Test parsing fasta36 output (output010.m10). ... ok
BUILDSTDERR: test_output011 (test_SearchIO_fasta_m10.Fasta36Cases)
BUILDSTDERR: Test parsing fasta36 output (output011.m10). ... ok
BUILDSTDERR: test_output012 (test_SearchIO_fasta_m10.Fasta36Cases)
BUILDSTDERR: Test parsing fasta36 output (output012.m10). ... ok
BUILDSTDERR: test_output013 (test_SearchIO_fasta_m10.Fasta36Cases)
BUILDSTDERR: Test parsing fasta36 output (output013.m10). ... ok
BUILDSTDERR: test_output014 (test_SearchIO_fasta_m10.Fasta36Cases)
BUILDSTDERR: Test parsing fasta36 output (output014.m10). ... ok
BUILDSTDERR: test_output015 (test_SearchIO_fasta_m10.Fasta36Cases)
BUILDSTDERR: Test parsing fasta36 output (output015.m10). ... ok
BUILDSTDERR: test_output016 (test_SearchIO_fasta_m10.Fasta36Cases)
BUILDSTDERR: Test parsing fasta36 output (output016.m10). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 13.690 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10_index.py
BUILDSTDERR: test_SearchIO_fasta_m10_index ... ok
BUILDSTDERR: test_output_001 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
BUILDSTDERR: Test fasta-m10 indexing, fasta35, multiple queries. ... ok
BUILDSTDERR: test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
BUILDSTDERR: Test fasta-m10 indexing, fasta34, multiple queries. ... ok
BUILDSTDERR: test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
BUILDSTDERR: Test fasta-m10 indexing, ssearch35, multiple queries. ... ok
BUILDSTDERR: test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
BUILDSTDERR: Test fasta-m10 indexing, tfastx36, multiple queries. ... ok
BUILDSTDERR: test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
BUILDSTDERR: Test fasta-m10 indexing, fasta36, multiple queries. ... ok
BUILDSTDERR: test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
BUILDSTDERR: Test fasta-m10 indexing, fasta36, single query, no hits. ... ok
BUILDSTDERR: test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
BUILDSTDERR: Test fasta-m10 indexing, fasta36, single query, hits with single hsp. ... ok
BUILDSTDERR: test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
BUILDSTDERR: Test fasta-m10 indexing, fasta36, single query with multiple hsps. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 21.068 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hhsuite2_text.py
BUILDSTDERR: test_SearchIO_hhsuite2_text ... ok
BUILDSTDERR: test_2uvo (test_SearchIO_hhsuite2_text.HhsuiteCases)
BUILDSTDERR: Parsing 2uvo. ... ok
BUILDSTDERR: test_2uvo_emptytable (test_SearchIO_hhsuite2_text.HhsuiteCases)
BUILDSTDERR: Parsing 4uvo with empty results table. ... ok
BUILDSTDERR: test_2uvo_onlyheader (test_SearchIO_hhsuite2_text.HhsuiteCases)
BUILDSTDERR: Parsing 4uvo with only header present. ... ok
BUILDSTDERR: test_4p79 (test_SearchIO_hhsuite2_text.HhsuiteCases)
BUILDSTDERR: Parsing 4p79_hhsearch_server_NOssm.hhr file. ... ok
BUILDSTDERR: test_4y9h_nossm (test_SearchIO_hhsuite2_text.HhsuiteCases)
BUILDSTDERR: Parsing 4y9h_hhsearch_server_NOssm.hhr file. ... ok
BUILDSTDERR: test_9590198 (test_SearchIO_hhsuite2_text.HhsuiteCases)
BUILDSTDERR: Parsing hhpred_9590198.hhr file. ... ok
BUILDSTDERR: test_allx (test_SearchIO_hhsuite2_text.HhsuiteCases)
BUILDSTDERR: Parsing allx.hhr file. ... ok
BUILDSTDERR: test_q9bsu1 (test_SearchIO_hhsuite2_text.HhsuiteCases)
BUILDSTDERR: Parsing hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr file. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 22.715 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text.py
BUILDSTDERR: test_SearchIO_hmmer2_text ... ok
BUILDSTDERR: test_hmmpfam_21 (test_SearchIO_hmmer2_text.HmmpfamTests)
BUILDSTDERR: Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out). ... ok
BUILDSTDERR: test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests)
BUILDSTDERR: Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out). ... ok
BUILDSTDERR: test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests)
BUILDSTDERR: Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out). ... ok
BUILDSTDERR: test_hmmpfam_23_break_in_end_of_seq (test_SearchIO_hmmer2_text.HmmpfamTests)
BUILDSTDERR: Test parsing hmmpfam 2.3 file with a line break in the end of seq marker. ... ok
BUILDSTDERR: test_hmmpfam_23_missing_consensus (test_SearchIO_hmmer2_text.HmmpfamTests)
BUILDSTDERR: Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out). ... ok
BUILDSTDERR: test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests)
BUILDSTDERR: Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out). ... ok
BUILDSTDERR: test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests)
BUILDSTDERR: Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out). ... ok
BUILDSTDERR: test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests)
BUILDSTDERR: Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out). ... ok
BUILDSTDERR: test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests)
BUILDSTDERR: Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 26.965 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text_index.py
BUILDSTDERR: test_SearchIO_hmmer2_text_index ... ok
BUILDSTDERR: test_hmmertext_text_21_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
BUILDSTDERR: Test hmmer2-text indexing, HMMER 2.1. ... ok
BUILDSTDERR: test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
BUILDSTDERR: Test hmmer2-text indexing, HMMER 2.2. ... ok
BUILDSTDERR: test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
BUILDSTDERR: Test hmmer2-text indexing, HMMER 2.2. ... ok
BUILDSTDERR: test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
BUILDSTDERR: Test hmmer2-text indexing, HMMER 2.3. ... ok
BUILDSTDERR: test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
BUILDSTDERR: Test hmmer2-text indexing, HMMER 2.4. ... ok
BUILDSTDERR: test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
BUILDSTDERR: Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
BUILDSTDERR: test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
BUILDSTDERR: Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
BUILDSTDERR: test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
BUILDSTDERR: Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
BUILDSTDERR: test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
BUILDSTDERR: Test hmmer2-text raw string retrieval, single query, hmmpfam. ... ok
BUILDSTDERR: test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
BUILDSTDERR: Test hmmer2-text raw string retrieval, single query, hmmsearch. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 16.716 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab.py
BUILDSTDERR: test_SearchIO_hmmer3_domtab ... ok
BUILDSTDERR: test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases)
BUILDSTDERR: Parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001). ... ok
BUILDSTDERR: test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases)
BUILDSTDERR: Parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001). ... ok
BUILDSTDERR: test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases)
BUILDSTDERR: Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001). ... ok
BUILDSTDERR: test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases)
BUILDSTDERR: Parsing hmmscan-domtab, hmmscan 3.0, single query, no hits (domtab_30_hmmscan_002). ... ok
BUILDSTDERR: test_domtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab.HmmscanCases)
BUILDSTDERR: Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003). ... ok
BUILDSTDERR: test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases)
BUILDSTDERR: Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004). ... ok
BUILDSTDERR: test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases)
BUILDSTDERR: Parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7.917 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab_index.py
BUILDSTDERR: test_SearchIO_hmmer3_domtab_index ... ok
BUILDSTDERR: test_hmmerdomtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
BUILDSTDERR: Test hmmscan-domtab indexing, HMMER 3.0, multiple queries. ... ok
BUILDSTDERR: test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
BUILDSTDERR: Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits. ... ok
BUILDSTDERR: test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
BUILDSTDERR: Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits. ... ok
BUILDSTDERR: test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
BUILDSTDERR: Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments. ... ok
BUILDSTDERR: test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
BUILDSTDERR: Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments. ... ok
BUILDSTDERR: test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
BUILDSTDERR: Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, first (domtab_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_hmmerdomtab_30_multiple_last (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
BUILDSTDERR: Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, last (domtab_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_hmmerdomtab_30_multiple_middle (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
BUILDSTDERR: Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, middle (domtab_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_hmmerdomtab_30_single (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
BUILDSTDERR: Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 10.622 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab.py
BUILDSTDERR: test_SearchIO_hmmer3_tab ... ok
BUILDSTDERR: test_30_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases)
BUILDSTDERR: Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001). ... ok
BUILDSTDERR: test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases)
BUILDSTDERR: Test parsing hmmer3-tab, hmmscan 3.0, single query, no hits (tab_30_hmmscan_002). ... ok
BUILDSTDERR: test_30_hmmscan_003 (test_SearchIO_hmmer3_tab.HmmscanCases)
BUILDSTDERR: Test parsing hmmer3-tab, hmmscan 3.0, single query, single hit, single hsp (tab_30_hmmscan_003). ... ok
BUILDSTDERR: test_30_hmmscan_004 (test_SearchIO_hmmer3_tab.HmmscanCases)
BUILDSTDERR: Test parsing hmmer3-tab, hmmscan 3.0, single query, multiple hits (tab_30_hmmscan_004). ... ok
BUILDSTDERR: test_31b1_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases)
BUILDSTDERR: Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
BUILDSTDERR: test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases)
BUILDSTDERR: Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.776 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab_index.py
BUILDSTDERR: test_SearchIO_hmmer3_tab_index ... ok
BUILDSTDERR: test_hmmer3tab_30_hmmscan_001 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
BUILDSTDERR: Test hmmer3-tab indexing, HMMER 3.0, multiple queries. ... ok
BUILDSTDERR: test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
BUILDSTDERR: Test hmmer3-tab indexing, HMMER 3.0, single query, no hits. ... ok
BUILDSTDERR: test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
BUILDSTDERR: Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits. ... ok
BUILDSTDERR: test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
BUILDSTDERR: Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments. ... ok
BUILDSTDERR: test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
BUILDSTDERR: Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, first (tab_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_hmmer3tab_30_multiple_last (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
BUILDSTDERR: Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, last (tab_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_hmmer3tab_30_multiple_middle (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
BUILDSTDERR: Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, middle (tab_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_hmmer3tab_30_single (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
BUILDSTDERR: Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.488 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text.py
BUILDSTDERR: test_SearchIO_hmmer3_text ... ok
BUILDSTDERR: test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
BUILDSTDERR: Parsing hmmersearch 3.0 (text_30_hmmsearch_001). ... ok
BUILDSTDERR: test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases)
BUILDSTDERR: Parsing hmmersearch 3.0 (text_30_hmmsearch_002). ... ok
BUILDSTDERR: test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases)
BUILDSTDERR: Parsing hmmersearch 3.0 (text_30_hmmsearch_003). ... ok
BUILDSTDERR: test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases)
BUILDSTDERR: Parsing hmmersearch 3.0 (text_30_hmmsearch_004). ... ok
BUILDSTDERR: test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases)
BUILDSTDERR: Parsing hmmersearch 3.0 (text_30_hmmsearch_005). ... ok
BUILDSTDERR: test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
BUILDSTDERR: Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001). ... ok
BUILDSTDERR: test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
BUILDSTDERR: Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001). ... ok
BUILDSTDERR: test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
BUILDSTDERR: Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001). ... ok
BUILDSTDERR: test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases)
BUILDSTDERR: Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002). ... ok
BUILDSTDERR: test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.0 (text_30_hmmscan_001). ... ok
BUILDSTDERR: test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.0 (text_30_hmmscan_002). ... ok
BUILDSTDERR: test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.0 (text_30_hmmscan_003). ... ok
BUILDSTDERR: test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.0 (text_30_hmmscan_004). ... ok
BUILDSTDERR: test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.0 (text_30_hmmscan_005). ... ok
BUILDSTDERR: test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.0 (text_30_hmmscan_006). ... ok
BUILDSTDERR: test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.0 (text_30_hmmscan_007). ... ok
BUILDSTDERR: test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.0 (text_30_hmmscan_008). ... ok
BUILDSTDERR: test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.0 (text_30_hmmscan_009). ... ok
BUILDSTDERR: test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.0 (text_30_hmmscan_010). ... ok
BUILDSTDERR: test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases)
BUILDSTDERR: Parsing hmmscan 3.1b1 (text_31b1_hmmscan_001). ... ok
BUILDSTDERR: test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases)
BUILDSTDERR: Parsing phmmer 3.1b2 (text_31b2_phmmer_001). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 26.639 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text_index.py
BUILDSTDERR: test_SearchIO_hmmer3_text_index ... ok
BUILDSTDERR: test_hmmertext_text_30_hmmscan_001 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
BUILDSTDERR: Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok
BUILDSTDERR: test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
BUILDSTDERR: Test hmmer3-text indexing, HMMER 3.0, single query, no hits. ... ok
BUILDSTDERR: test_hmmertext_text_30_hmmscan_006 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
BUILDSTDERR: Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits. ... ok
BUILDSTDERR: test_hmmertext_text_30_hmmscan_007 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
BUILDSTDERR: Test hmmer3-text indexing, HMMER 3.0, single query, no alignments. ... ok
BUILDSTDERR: test_hmmertext_text_30_hmmscan_008 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
BUILDSTDERR: Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width. ... ok
BUILDSTDERR: test_hmmertext_text_30_hmmsearch_005 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
BUILDSTDERR: Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok
BUILDSTDERR: test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
BUILDSTDERR: Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_hmmer3text_30_multiple_last (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
BUILDSTDERR: Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_hmmer3text_30_multiple_middle (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
BUILDSTDERR: Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_hmmer3text_30_single (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
BUILDSTDERR: Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 14.501 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_interproscan_xml.py
BUILDSTDERR: test_SearchIO_interproscan_xml ... ok
BUILDSTDERR: test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.424 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_legacy.py
BUILDSTDERR: test_SearchIO_legacy ... ok
BUILDSTDERR: test_TaggingConsumer (test_SearchIO_legacy.TestParserSupport) ... ok
BUILDSTDERR: test_attempt_read_and_call (test_SearchIO_legacy.TestParserSupport) ... ok
BUILDSTDERR: test_is_blank_line (test_SearchIO_legacy.TestParserSupport) ... ok
BUILDSTDERR: test_read_and_call (test_SearchIO_legacy.TestParserSupport) ... ok
BUILDSTDERR: test_safe_peekline (test_SearchIO_legacy.TestParserSupport) ... ok
BUILDSTDERR: test_safe_readline (test_SearchIO_legacy.TestParserSupport) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.144 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_model.py
BUILDSTDERR: test_SearchIO_model ... ok
BUILDSTDERR: test_alphabet_no_seq (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment alphabet property, query and hit sequences not present. ... ok
BUILDSTDERR: test_alphabet_with_seq (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment alphabet property, query or hit sequences present. ... ok
BUILDSTDERR: test_coords_setters_getters (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment query and hit coordinate-related setters and getters. ... ok
BUILDSTDERR: test_coords_setters_readonly (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment query and hit coordinate-related read-only getters. ... ok
BUILDSTDERR: test_default_attrs (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment attributes' default values. ... ok
BUILDSTDERR: test_frame_set_error (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment query and hit frame setters, invalid values. ... ok
BUILDSTDERR: test_frame_set_ok (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment query and hit frame setters. ... ok
BUILDSTDERR: test_getitem (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment.__getitem__. ... ok
BUILDSTDERR: test_getitem_alignment_annot (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment.__getitem__, with alignment annotation. ... ok
BUILDSTDERR: test_getitem_attrs (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment.__getitem__, with attributes. ... ok
BUILDSTDERR: test_id_desc_set (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment query and hit id and description setters. ... ok
BUILDSTDERR: test_init_with_seqrecord (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment.__init__, with SeqRecord. ... ok
BUILDSTDERR: test_init_wrong_seqtypes (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment.__init__, wrong sequence argument types. ... ok
BUILDSTDERR: test_len (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment.__len__. ... ok
BUILDSTDERR: test_pickle (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test pickling and unpickling of HSPFragment. ... ok
BUILDSTDERR: test_repr (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment.__repr__. ... ok
BUILDSTDERR: test_seq_unequal_hit_query_len (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment sequence setter with unequal hit and query lengths. ... ok
BUILDSTDERR: test_seqmodel (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment sequence attribute types and default values. ... ok
BUILDSTDERR: test_strand_set_error (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment query and hit strand setters, invalid values. ... ok
BUILDSTDERR: test_strand_set_from_minus_frame (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment query and hit strand getters, from minus frame. ... ok
BUILDSTDERR: test_strand_set_from_plus_frame (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment query and hit strand getters, from plus frame. ... ok
BUILDSTDERR: test_strand_set_from_zero_frame (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment query and hit strand getters, from zero frame. ... ok
BUILDSTDERR: test_strand_set_ok (test_SearchIO_model.HSPFragmentCases)
BUILDSTDERR: Test HSPFragment query and hit strand setters. ... ok
BUILDSTDERR: test_getitem (test_SearchIO_model.HSPFragmentWithoutSeqCases)
BUILDSTDERR: Test HSPFragment.__getitem__, no alignments. ... ok
BUILDSTDERR: test_getitem_only_hit (test_SearchIO_model.HSPFragmentWithoutSeqCases)
BUILDSTDERR: Test HSPFragment.__getitem__, only hit. ... ok
BUILDSTDERR: test_getitem_only_query (test_SearchIO_model.HSPFragmentWithoutSeqCases)
BUILDSTDERR: Test HSPFragment.__getitem__, only query. ... ok
BUILDSTDERR: test_init (test_SearchIO_model.HSPFragmentWithoutSeqCases)
BUILDSTDERR: Test HSPFragment.__init__ attributes. ... ok
BUILDSTDERR: test_iter (test_SearchIO_model.HSPFragmentWithoutSeqCases)
BUILDSTDERR: Test HSP.__iter__, no alignments. ... ok
BUILDSTDERR: test_len (test_SearchIO_model.HSPFragmentWithoutSeqCases)
BUILDSTDERR: Test HSPFragment.__len__, no alignments. ... ok
BUILDSTDERR: test_repr (test_SearchIO_model.HSPFragmentWithoutSeqCases)
BUILDSTDERR: Test HSPFragment.__repr__, no alignments. ... ok
BUILDSTDERR: test_seqmodel (test_SearchIO_model.HSPFragmentWithoutSeqCases)
BUILDSTDERR: Test HSPFragment sequence attributes, no alignments. ... ok
BUILDSTDERR: test_alphabet (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP.alphabet getter. ... ok
BUILDSTDERR: test_alphabet_set (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP.alphabet setter. ... ok
BUILDSTDERR: test_contains (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP.__contains__. ... ok
BUILDSTDERR: test_delitem (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP.__delitem__. ... ok
BUILDSTDERR: test_fragments (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP.fragments property. ... ok
BUILDSTDERR: test_getitem (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP.__getitem__. ... ok
BUILDSTDERR: test_id_desc_set (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP query and hit id and description setters. ... ok
BUILDSTDERR: test_is_fragmented (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP.is_fragmented property. ... ok
BUILDSTDERR: test_len (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP.__len__. ... ok
BUILDSTDERR: test_pickle (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test pickling and unpickling of HSP. ... ok
BUILDSTDERR: test_range (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP range properties. ... ok
BUILDSTDERR: test_ranges (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP ranges properties. ... ok
BUILDSTDERR: test_seqs (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP sequence properties. ... ok
BUILDSTDERR: test_setitem_multiple (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP.__setitem__, multiple items. ... ok
BUILDSTDERR: test_setitem_single (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP.__setitem___, single item. ... ok
BUILDSTDERR: test_setters_readonly (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP read-only properties. ... ok
BUILDSTDERR: test_span (test_SearchIO_model.HSPMultipleFragmentCases)
BUILDSTDERR: Test HSP span properties. ... ok
BUILDSTDERR: test_alignment (test_SearchIO_model.HSPSingleFragmentCases)
BUILDSTDERR: Test HSP.alignment property. ... ok
BUILDSTDERR: test_aln_span (test_SearchIO_model.HSPSingleFragmentCases)
BUILDSTDERR: Test HSP.aln_span property. ... ok
BUILDSTDERR: test_fragment (test_SearchIO_model.HSPSingleFragmentCases)
BUILDSTDERR: Test HSP.fragment property. ... ok
BUILDSTDERR: test_init_no_fragment (test_SearchIO_model.HSPSingleFragmentCases)
BUILDSTDERR: Test HSP.__init__ without fragments. ... ok
BUILDSTDERR: test_is_fragmented (test_SearchIO_model.HSPSingleFragmentCases)
BUILDSTDERR: Test HSP.is_fragmented property. ... ok
BUILDSTDERR: test_len (test_SearchIO_model.HSPSingleFragmentCases)
BUILDSTDERR: Test HSP.__len__. ... ok
BUILDSTDERR: test_range (test_SearchIO_model.HSPSingleFragmentCases)
BUILDSTDERR: Test HSP range properties. ... ok
BUILDSTDERR: test_seq (test_SearchIO_model.HSPSingleFragmentCases)
BUILDSTDERR: Test HSP sequence properties. ... ok
BUILDSTDERR: test_setters_readonly (test_SearchIO_model.HSPSingleFragmentCases)
BUILDSTDERR: Test HSP read-only properties. ... ok
BUILDSTDERR: test_span (test_SearchIO_model.HSPSingleFragmentCases)
BUILDSTDERR: Test HSP span properties. ... ok
BUILDSTDERR: test_append (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.append. ... ok
BUILDSTDERR: test_delitem (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__delitem__. ... ok
BUILDSTDERR: test_desc_set (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.description setter. ... ok
BUILDSTDERR: test_desc_set_no_seqrecord (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.description setter, without HSP SeqRecords. ... ok
BUILDSTDERR: test_filter (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.filter. ... ok
BUILDSTDERR: test_filter_no_filtered (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.hit_filter, all hits filtered out. ... ok
BUILDSTDERR: test_filter_no_func (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.filter, without arguments. ... ok
BUILDSTDERR: test_fragments (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.fragments. ... ok
BUILDSTDERR: test_getitem_multiple (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__getitem__, multiple items. ... ok
BUILDSTDERR: test_getitem_single (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__getitem__, single item. ... ok
BUILDSTDERR: test_hsp_map_no_func (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.map, without arguments. ... ok
BUILDSTDERR: test_hsps (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.hsps. ... ok
BUILDSTDERR: test_id_set (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.id setter. ... ok
BUILDSTDERR: test_index (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.index. ... ok
BUILDSTDERR: test_index_not_present (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.index, when index is not present. ... ok
BUILDSTDERR: test_init_hsps_only (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__init__, with hsps only. ... ok
BUILDSTDERR: test_init_id_only (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__init__, with ID only. ... ok
BUILDSTDERR: test_init_none (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__init__, no arguments. ... ok
BUILDSTDERR: test_item_multiple (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__setitem__, multiple items. ... ok
BUILDSTDERR: test_iter (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__iter__. ... ok
BUILDSTDERR: test_len (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__len__. ... ok
BUILDSTDERR: test_map (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.hsp_map. ... ok
BUILDSTDERR: test_nonzero (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__nonzero__. ... ok
BUILDSTDERR: test_pickle (test_SearchIO_model.HitCases)
BUILDSTDERR: Test pickling and unpickling of Hit. ... ok
BUILDSTDERR: test_pop (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.pop. ... ok
BUILDSTDERR: test_repr (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__repr__. ... ok
BUILDSTDERR: test_setitem_single (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.__setitem__, single item. ... ok
BUILDSTDERR: test_sort (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.sort. ... ok
BUILDSTDERR: test_sort_not_in_place (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit.sort, not in place. ... ok
BUILDSTDERR: test_validate_hsp_ok (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit._validate_hsp. ... ok
BUILDSTDERR: test_validate_hsp_wrong_hit_id (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit._validate_hsp, wrong hit ID. ... ok
BUILDSTDERR: test_validate_hsp_wrong_query_id (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit._validate_hsp, wrong query ID. ... ok
BUILDSTDERR: test_validate_hsp_wrong_type (test_SearchIO_model.HitCases)
BUILDSTDERR: Test Hit._validate_hsp, wrong type. ... ok
BUILDSTDERR: test_absorb_hit_does_not_exist (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.absorb, hit does not exist. ... ok
BUILDSTDERR: test_absorb_hit_exists (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.absorb, hit with the same ID exists. ... ok
BUILDSTDERR: test_append_alt_id_exists (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.append, when alt ID exists. ... ok
BUILDSTDERR: test_append_alt_id_exists_alt (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.append, when alt ID exists as primary. ... ok
BUILDSTDERR: test_append_custom_hit_key_function_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.append, with custom hit key function. ... ok
BUILDSTDERR: test_append_id_exists (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.append, when ID exists. ... ok
BUILDSTDERR: test_append_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.append. ... ok
BUILDSTDERR: test_contains (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__contains__. ... ok
BUILDSTDERR: test_contains_alt (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__contains__, with alternative IDs. ... ok
BUILDSTDERR: test_delitem_alt_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__delitem__, with alt ID. ... ok
BUILDSTDERR: test_delitem_int_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__delitem__. ... ok
BUILDSTDERR: test_delitem_slice_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__delitem__, with slice. ... ok
BUILDSTDERR: test_delitem_string_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__getitem__, with string. ... ok
BUILDSTDERR: test_description_set (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.description setter. ... ok
BUILDSTDERR: test_description_set_no_seqrecord (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.description setter, without HSP SeqRecords. ... ok
BUILDSTDERR: test_fragments (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.fragments. ... ok
BUILDSTDERR: test_getitem_alt_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__getitem__, single item with alternative ID. ... ok
BUILDSTDERR: test_getitem_default_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__getitem__. ... ok
BUILDSTDERR: test_getitem_int_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__getitem__, with integer. ... ok
BUILDSTDERR: test_getitem_slice_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__getitem__, with slice. ... ok
BUILDSTDERR: test_getitm_slice_alt_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__getitem__, with slice and alt IDs. ... ok
BUILDSTDERR: test_hit_filter (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hit_filter. ... ok
BUILDSTDERR: test_hit_filter_no_filtered (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hit_filter, all hits filtered out. ... ok
BUILDSTDERR: test_hit_filter_no_func (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hit_filter, without arguments. ... ok
BUILDSTDERR: test_hit_keys (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hit_keys. ... ok
BUILDSTDERR: test_hit_map (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hit_map. ... ok
BUILDSTDERR: test_hit_map_no_func (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hit_map, without arguments. ... ok
BUILDSTDERR: test_hits (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hits. ... ok
BUILDSTDERR: test_hsp_filter (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hsp_filter. ... ok
BUILDSTDERR: test_hsp_filter_no_filtered (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hsp_filter, all hits filtered out. ... ok
BUILDSTDERR: test_hsp_filter_no_func (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hsp_filter, no arguments. ... ok
BUILDSTDERR: test_hsp_map (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hsp_map. ... ok
BUILDSTDERR: test_hsp_map_no_func (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hsp_map, without arguments. ... ok
BUILDSTDERR: test_hsps (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.hsps. ... ok
BUILDSTDERR: test_id_set (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.id setter. ... ok
BUILDSTDERR: test_index (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.index. ... ok
BUILDSTDERR: test_index_alt (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.index, with alt ID. ... ok
BUILDSTDERR: test_index_not_present (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.index, when index is not present. ... ok
BUILDSTDERR: test_init_hits_only (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__init__, with hits only. ... ok
BUILDSTDERR: test_init_id_only (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__init__, with ID only. ... ok
BUILDSTDERR: test_init_none (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__init__, no arguments. ... ok
BUILDSTDERR: test_items (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.items. ... ok
BUILDSTDERR: test_iter (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__iter__. ... ok
BUILDSTDERR: test_len (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__len__. ... ok
BUILDSTDERR: test_nonzero (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__nonzero__. ... ok
BUILDSTDERR: test_order (test_SearchIO_model.QueryResultCases) ... ok
BUILDSTDERR: test_pickle (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test pickling and unpickling of QueryResult. ... ok
BUILDSTDERR: test_pop_int_index_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.pop, with integer index. ... ok
BUILDSTDERR: test_pop_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.pop. ... ok
BUILDSTDERR: test_pop_string_alt_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.pop, with alternative ID. ... ok
BUILDSTDERR: test_pop_string_index_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.pop, with string index. ... ok
BUILDSTDERR: test_repr (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__repr__. ... ok
BUILDSTDERR: test_setitem_from_empty (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__setitem__, from empty container. ... ok
BUILDSTDERR: test_setitem_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__setitem__. ... ok
BUILDSTDERR: test_setitem_ok_alt (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__setitem__, checking alt hit IDs. ... ok
BUILDSTDERR: test_setitem_ok_alt_existing (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__setitem__, existing key. ... ok
BUILDSTDERR: test_setitem_ok_alt_ok_promote (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__setitem__, previously alt ID. ... ok
BUILDSTDERR: test_setitem_wrong_key_type (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__setitem__, wrong key type. ... ok
BUILDSTDERR: test_setitem_wrong_query_id (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__setitem__, wrong query ID. ... ok
BUILDSTDERR: test_setitem_wrong_type (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.__setitem__, wrong type. ... ok
BUILDSTDERR: test_sort_key_not_in_place_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.sort, with custom key, not in place. ... ok
BUILDSTDERR: test_sort_key_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.sort, with custom key. ... ok
BUILDSTDERR: test_sort_not_in_place_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.sort, not in place. ... ok
BUILDSTDERR: test_sort_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.sort. ... ok
BUILDSTDERR: test_sort_reverse_not_in_place_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.sort, reverse, not in place. ... ok
BUILDSTDERR: test_sort_reverse_ok (test_SearchIO_model.QueryResultCases)
BUILDSTDERR: Test QueryResult.sort, reverse. ... ok
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 14.041 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_write.py
BUILDSTDERR: test_SearchIO_write ... ok
BUILDSTDERR: test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases)
BUILDSTDERR: Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt). ... ok
BUILDSTDERR: test_write_multiple_from_blasttabc (test_SearchIO_write.BlastTabWriteCases)
BUILDSTDERR: Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt). ... ok
BUILDSTDERR: test_write_multiple_from_blasttabc_allfields (test_SearchIO_write.BlastTabWriteCases)
BUILDSTDERR: Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt). ... ok
BUILDSTDERR: test_write_single_from_blasttab (test_SearchIO_write.BlastTabWriteCases)
BUILDSTDERR: Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt). ... ok
BUILDSTDERR: test_write_single_from_blasttabc (test_SearchIO_write.BlastTabWriteCases)
BUILDSTDERR: Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt). ... ok
BUILDSTDERR: test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
BUILDSTDERR: Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml). ... ok
BUILDSTDERR: test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
BUILDSTDERR: Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml). ... ok
BUILDSTDERR: test_write_multiple_from_blatpsl (test_SearchIO_write.BlatPslWriteCases)
BUILDSTDERR: Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl). ... ok
BUILDSTDERR: test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases)
BUILDSTDERR: Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx). ... ok
BUILDSTDERR: test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases)
BUILDSTDERR: Test blat-psl writing from blat-psl, single query (psl_34_004.psl). ... ok
BUILDSTDERR: test_write_single_from_blatpsl_protein_query (test_SearchIO_write.BlatPslWriteCases)
BUILDSTDERR: Test blat-psl writing from blat-psl, single query (psl_35_002.psl). ... ok
BUILDSTDERR: test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases)
BUILDSTDERR: Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx). ... ok
BUILDSTDERR: test_write_single_from_blatpslx_protein_query (test_SearchIO_write.BlatPslWriteCases)
BUILDSTDERR: Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx). ... ok
BUILDSTDERR: test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases)
BUILDSTDERR: Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_write_single_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases)
BUILDSTDERR: Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
BUILDSTDERR: test_write_single_from_hmmsearchdomtab (test_SearchIO_write.HmmerDomtabWriteCases)
BUILDSTDERR: Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
BUILDSTDERR: test_write_multiple_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases)
BUILDSTDERR: Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok
BUILDSTDERR: test_write_single_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases)
BUILDSTDERR: Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 54.719 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqFeature.py
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: test_SeqFeature ... ok
BUILDSTDERR: test_eq_identical (test_SeqFeature.TestCompoundLocation)
BUILDSTDERR: Test two identical locations are equal. ... ok
BUILDSTDERR: test_eq_not_identical (test_SeqFeature.TestCompoundLocation)
BUILDSTDERR: Test two different locations are not equal. ... ok
BUILDSTDERR: test_eq_identical (test_SeqFeature.TestFeatureLocation)
BUILDSTDERR: Test two identical locations are equal. ... ok
BUILDSTDERR: test_eq_not_identical (test_SeqFeature.TestFeatureLocation)
BUILDSTDERR: Test two different locations are not equal. ... ok
BUILDSTDERR: test_start_before_end (test_SeqFeature.TestFeatureLocation) ... ok
BUILDSTDERR: test_fuzzy (test_SeqFeature.TestLocations)
BUILDSTDERR: Test fuzzy representations. ... ok
BUILDSTDERR: test_eq_identical (test_SeqFeature.TestReference)
BUILDSTDERR: Test two identical references eq() to True. ... ok
BUILDSTDERR: test_translation_checks_cds (test_SeqFeature.TestSeqFeature)
BUILDSTDERR: Test that a CDS feature is subject to respective checks. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 10.427 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO.py
BUILDSTDERR: test_SeqIO ... ok
BUILDSTDERR: test_abi1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_abi2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_abi3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_ace1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_ace2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_ace3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_cif_atom1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_cif_atom2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_cif_seqres1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_cif_seqres2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_clustal1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_clustal2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_clustal3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_clustal4 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl10 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl11 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl12 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl13 (test_SeqIO.TestSeqIO)
BUILDSTDERR: Test parsing embl file with wrapped locations and unspecified type. ... ok
BUILDSTDERR: test_embl14 (test_SeqIO.TestSeqIO)
BUILDSTDERR: Test parsing file with features over-indented for EMBL. ... ok
BUILDSTDERR: test_embl2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl4 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl5 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl6 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl7 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl8 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_embl9 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_emboss1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_emboss2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_emboss3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_empty_file (test_SeqIO.TestSeqIO)
BUILDSTDERR: Check parsers can cope with an empty file. ... ok
BUILDSTDERR: test_fasta1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta10 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta11 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta12 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta13 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta14 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta15 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta16 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta17 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta18 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta19 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta20 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta21 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta22 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta23 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta24 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta4 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta5 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta6 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta7 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta8 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta9 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fasta_2line1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fastq1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fastq2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fastq3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fastq4 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fastq5 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fastq_illumina1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fastq_solexa1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_fastq_solexa2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank10 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank11 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank12 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank13 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank14 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank15 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank16 (test_SeqIO.TestSeqIO)
BUILDSTDERR: Test parsing Genbank file from Vector NTI with an odd LOCUS line. ... ok
BUILDSTDERR: test_genbank17 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank18 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank19 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank20 (test_SeqIO.TestSeqIO)
BUILDSTDERR: Test parsing GenPept file with nasty bond locations. ... ok
BUILDSTDERR: test_genbank21 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank4 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank5 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank6 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank7 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank8 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_genbank9 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_ig1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_ig2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_ig3 (test_SeqIO.TestSeqIO)
BUILDSTDERR: Test parsing a MASE alignment with sequence O_ANT70 being shorter. ... ok
BUILDSTDERR: test_imgt1 (test_SeqIO.TestSeqIO)
BUILDSTDERR: Test parsing file with features over-indented for EMBL. ... ok
BUILDSTDERR: test_imgt2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_nexus1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_pdb_atom1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_pdb_atom2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_pdb_atom3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_pdb_seqres1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_pdb_seqres2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phd1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phd2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phd3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phd4 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phylip1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phylip2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phylip3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phylip4 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phylip5 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phylip6 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_phylip7 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_pir1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_pir2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_pir3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_pir4 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_pir5 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_qual1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_seqxml1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_seqxml2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_seqxml3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_sff1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_stockholm1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_stockholm2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss10 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss11 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss12 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss13 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss14 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss15 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss16 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss17 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss18 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss19 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss20 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss4 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss5 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss6 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss7 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss8 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_swiss9 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_tab1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_uniprot_xml1 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_uniprot_xml2 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_uniprot_xml3 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_uniprot_xml4 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_uniprot_xml5 (test_SeqIO.TestSeqIO) ... ok
BUILDSTDERR: test_gzip_fasta (test_SeqIO.TestZipped)
BUILDSTDERR: Testing FASTA with gzip. ... ok
BUILDSTDERR: test_gzip_fastq (test_SeqIO.TestZipped)
BUILDSTDERR: Testing FASTQ with gzip. ... ok
BUILDSTDERR: test_gzip_genbank (test_SeqIO.TestZipped)
BUILDSTDERR: Testing GenBank with gzip. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7187.687 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_AbiIO.py
BUILDSTDERR: test_SeqIO_AbiIO ... ok
BUILDSTDERR: test_file_type (test_SeqIO_AbiIO.TestAbi)
BUILDSTDERR: Test if filetype is ABIF. ... ok
BUILDSTDERR: test_no_smpl1 (test_SeqIO_AbiIO.TestAbi)
BUILDSTDERR: Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok
BUILDSTDERR: test_raw (test_SeqIO_AbiIO.TestAbi)
BUILDSTDERR: Test access to raw ABIF tags. ... ok
BUILDSTDERR: test_seqrecord (test_SeqIO_AbiIO.TestAbi)
BUILDSTDERR: Test if the extracted seqrecords data are equal to expected values. ... ok
BUILDSTDERR: test_trim (test_SeqIO_AbiIO.TestAbi)
BUILDSTDERR: Test if trim works. ... ok
BUILDSTDERR: test_file_type (test_SeqIO_AbiIO.TestAbiFake)
BUILDSTDERR: Test if error is raised if filetype is not ABIF. ... ok
BUILDSTDERR: test_nonascii_tag (test_SeqIO_AbiIO.TestAbiNonAscii)
BUILDSTDERR: Test that we can handle non-ascii tags. ... ok
BUILDSTDERR: test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode)
BUILDSTDERR: Test if exception is raised if file is not opened in 'rb' mode. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 31.702 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_FastaIO.py
BUILDSTDERR: test_SeqIO_FastaIO ... ok
BUILDSTDERR: test_edgecases_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
BUILDSTDERR: Test FastaTwoLineParser edge-cases. ... ok
BUILDSTDERR: test_edgecases_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
BUILDSTDERR: Test SimpleFastaParser edge-cases. ... ok
BUILDSTDERR: test_exceptions_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
BUILDSTDERR: Test FastaTwoLineParser exceptions. ... ok
BUILDSTDERR: test_regular_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
BUILDSTDERR: Test regular FastaTwoLineParser cases. ... ok
BUILDSTDERR: test_regular_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
BUILDSTDERR: Test regular SimpleFastaParser cases. ... ok
BUILDSTDERR: test_mutli_dna_Quality/example (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking multi DNA file Quality/example.fasta ... ok
BUILDSTDERR: test_mutli_pro_Fasta/f002 (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking multi protein file Fasta/f002 ... ok
BUILDSTDERR: test_mutli_pro_Fasta/fa01 (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking multi protein file Fasta/fa01 ... ok
BUILDSTDERR: test_no_name (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Test FASTA record with no identifier. ... ok
BUILDSTDERR: test_nuc_Fasta/centaurea (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking nucleotide file Fasta/centaurea.nu ... ok
BUILDSTDERR: test_nuc_Fasta/elderberry (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking nucleotide file Fasta/elderberry.nu ... ok
BUILDSTDERR: test_nuc_Fasta/f001 (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking nucleotide file Fasta/f001 ... ok
BUILDSTDERR: test_nuc_Fasta/lavender (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking nucleotide file Fasta/lavender.nu ... ok
BUILDSTDERR: test_nuc_Fasta/lupine (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking nucleotide file Fasta/lupine.nu ... ok
BUILDSTDERR: test_nuc_Fasta/phlox (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking nucleotide file Fasta/phlox.nu ... ok
BUILDSTDERR: test_nuc_Fasta/sweetpea (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking nucleotide file Fasta/sweetpea.nu ... ok
BUILDSTDERR: test_nuc_Fasta/wisteria (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking nucleotide file Fasta/wisteria.nu ... ok
BUILDSTDERR: test_pro_Fasta/aster (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking protein file Fasta/aster.pro ... ok
BUILDSTDERR: test_pro_Fasta/loveliesbleeding (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking protein file Fasta/loveliesbleeding.pro ... ok
BUILDSTDERR: test_pro_Fasta/rose (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking protein file Fasta/rose.pro ... ok
BUILDSTDERR: test_pro_Fasta/rosemary (test_SeqIO_FastaIO.TitleFunctions)
BUILDSTDERR: Checking protein file Fasta/rosemary.pro ... ok
BUILDSTDERR: test_fails (test_SeqIO_FastaIO.Wrapping)
BUILDSTDERR: Test case which should fail. ... ok
BUILDSTDERR: test_passes (test_SeqIO_FastaIO.Wrapping)
BUILDSTDERR: Test case which should pass. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 10.534 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Insdc.py
BUILDSTDERR: test_SeqIO_Insdc ... /builddir/build/BUILD/python-biopython-1.74/python3/build/lib.linux-riscv64-3.7/Bio/GenBank/Scanner.py:291: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
BUILDSTDERR:   BiopythonParserWarning)
BUILDSTDERR: ok
BUILDSTDERR: test_annotation1 (test_SeqIO_Insdc.TestEmbl)
BUILDSTDERR: Check parsing of annotation from EMBL files (1). ... ok
BUILDSTDERR: test_annotation2 (test_SeqIO_Insdc.TestEmbl)
BUILDSTDERR: Check parsing of annotation from EMBL files (2). ... ok
BUILDSTDERR: test_annotation3 (test_SeqIO_Insdc.TestEmbl)
BUILDSTDERR: Check parsing of annotation from EMBL files (3). ... ok
BUILDSTDERR: test_annotation4 (test_SeqIO_Insdc.TestEmbl)
BUILDSTDERR: Check parsing of annotation from EMBL files (4). ... ok
BUILDSTDERR: test_writing_empty_qualifiers (test_SeqIO_Insdc.TestEmbl) ... ok
BUILDSTDERR: test_annotation1 (test_SeqIO_Insdc.TestEmblRewrite)
BUILDSTDERR: Check writing-and-parsing EMBL file (1). ... ok
BUILDSTDERR: test_annotation2 (test_SeqIO_Insdc.TestEmblRewrite)
BUILDSTDERR: Check writing-and-parsing EMBL file (2). ... ok
BUILDSTDERR: test_annotation3 (test_SeqIO_Insdc.TestEmblRewrite)
BUILDSTDERR: Check writing-and-parsing EMBL file (3). ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 12.447 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_NibIO.py
BUILDSTDERR: test_SeqIO_NibIO ... ok
BUILDSTDERR: test_read_bigendian (test_SeqIO_NibIO.TestNibReaderWriter) ... ok
BUILDSTDERR: test_read_littleendian (test_SeqIO_NibIO.TestNibReaderWriter) ... ok
BUILDSTDERR: test_write_and_read (test_SeqIO_NibIO.TestNibReaderWriter) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.923 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_PdbIO.py
BUILDSTDERR: test_SeqIO_PdbIO ... ok
BUILDSTDERR: test_atom_parse (test_SeqIO_PdbIO.TestCifAtom)
BUILDSTDERR: Parse a multi-chain structure by ATOM entries. ... ok
BUILDSTDERR: test_atom_read (test_SeqIO_PdbIO.TestCifAtom)
BUILDSTDERR: Read a single-chain structure by ATOM entries. ... ok
BUILDSTDERR: test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom)
BUILDSTDERR: Read a single-chain CIF without a header by ATOM entries. ... ok
BUILDSTDERR: test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres)
BUILDSTDERR: Parse a PDB with no SEQRES entries. ... ok
BUILDSTDERR: test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres)
BUILDSTDERR: Parse a multi-chain PDB by SEQRES entries. ... ok
BUILDSTDERR: test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres)
BUILDSTDERR: Read a single-chain structure by sequence entries. ... ok
BUILDSTDERR: test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom)
BUILDSTDERR: Parse a PDB with no HEADER line. ... ok
BUILDSTDERR: test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom)
BUILDSTDERR: Parse a multi-chain structure by ATOM entries. ... ok
BUILDSTDERR: test_atom_read (test_SeqIO_PdbIO.TestPdbAtom)
BUILDSTDERR: Read a single-chain structure by ATOM entries. ... ok
BUILDSTDERR: test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom)
BUILDSTDERR: Read a single-chain PDB without a header by ATOM entries. ... ok
BUILDSTDERR: test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres)
BUILDSTDERR: Parse a PDB with no SEQRES entries. ... ok
BUILDSTDERR: test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres)
BUILDSTDERR: Parse a multi-chain PDB by SEQRES entries. ... ok
BUILDSTDERR: test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres)
BUILDSTDERR: Read a single-chain structure by sequence entries. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 966.378 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_QualityIO.py
BUILDSTDERR: test_SeqIO_QualityIO ... ok
BUILDSTDERR: test_illumina_to_sanger (test_SeqIO_QualityIO.MappingTests)
BUILDSTDERR: Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62). ... ok
BUILDSTDERR: test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests)
BUILDSTDERR: Mapping check for function phred_quality_from_solexa. ... ok
BUILDSTDERR: test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests)
BUILDSTDERR: Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62). ... ok
BUILDSTDERR: test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests)
BUILDSTDERR: Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62). ... ok
BUILDSTDERR: test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests)
BUILDSTDERR: Mapping check for function solexa_quality_from_phred. ... ok
BUILDSTDERR: test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests)
BUILDSTDERR: Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62). ... ok
BUILDSTDERR: test_fasta_as_fastq (test_SeqIO_QualityIO.NonFastqTests) ... ok
BUILDSTDERR: test_sff_as_fastq (test_SeqIO_QualityIO.NonFastqTests) ... ok
BUILDSTDERR: test_diff_ids (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with diff ids ... ok
BUILDSTDERR: test_double_qual (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with double qual ... ok
BUILDSTDERR: test_double_seq (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with double seq ... ok
BUILDSTDERR: test_long_qual (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with long qual ... ok
BUILDSTDERR: test_no_qual (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with no qual ... ok
BUILDSTDERR: test_qual_del (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with del in quality ... ok
BUILDSTDERR: test_qual_escape (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with escape in quality ... ok
BUILDSTDERR: test_qual_null (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with null in quality ... ok
BUILDSTDERR: test_qual_space (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with space in quality ... ok
BUILDSTDERR: test_qual_tab (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with tab in quality ... ok
BUILDSTDERR: test_qual_unit_sep (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with unit sep in quality ... ok
BUILDSTDERR: test_qual_vtab (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with vtab in quality ... ok
BUILDSTDERR: test_short_qual (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with short qual ... ok
BUILDSTDERR: test_spaces (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with spaces ... ok
BUILDSTDERR: test_tabs (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with tabs ... ok
BUILDSTDERR: test_trunc_at_plus (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with trunc at plus ... ok
BUILDSTDERR: test_trunc_at_qual (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with trunc at qual ... ok
BUILDSTDERR: test_trunc_at_seq (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with trunc at seq ... ok
BUILDSTDERR: test_trunc_in_plus (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with trunc in plus ... ok
BUILDSTDERR: test_trunc_in_qual (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with trunc in qual ... ok
BUILDSTDERR: test_trunc_in_seq (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with trunc in seq ... ok
BUILDSTDERR: test_trunc_in_title (test_SeqIO_QualityIO.TestFastqErrors)
BUILDSTDERR: Reject FASTQ with trunc in title ... ok
BUILDSTDERR: test_fasta (test_SeqIO_QualityIO.TestQual)
BUILDSTDERR: Check FASTQ parsing matches FASTA parsing. ... ok
BUILDSTDERR: test_fasta_out (test_SeqIO_QualityIO.TestQual)
BUILDSTDERR: Check FASTQ to FASTA output. ... ok
BUILDSTDERR: test_paired (test_SeqIO_QualityIO.TestQual)
BUILDSTDERR: Check FASTQ parsing matches FASTA+QUAL parsing. ... ok
BUILDSTDERR: test_qual (test_SeqIO_QualityIO.TestQual)
BUILDSTDERR: Check FASTQ parsing matches QUAL parsing. ... ok
BUILDSTDERR: test_qual_negative (test_SeqIO_QualityIO.TestQual)
BUILDSTDERR: Check QUAL negative scores mapped to PHRED zero. ... ok
BUILDSTDERR: test_qual_out (test_SeqIO_QualityIO.TestQual)
BUILDSTDERR: Check FASTQ to QUAL output. ... ok
BUILDSTDERR: test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite)
BUILDSTDERR: Read and write back simple example with mixed case 1000bp read. ... ok
BUILDSTDERR: test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite)
BUILDSTDERR: Read and write back simple example with upper case 2000bp read. ... ok
BUILDSTDERR: test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite)
BUILDSTDERR: Read and write back simple example with ambiguous DNA. ... ok
BUILDSTDERR: test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite)
BUILDSTDERR: Read and write back simple example with ambiguous RNA. ... ok
BUILDSTDERR: test_illumina_full_range_illumina (test_SeqIO_QualityIO.TestReferenceFastqConversions)
BUILDSTDERR: Reference conversions of illumina file illumina_full_range ... ok
BUILDSTDERR: test_longreads_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
BUILDSTDERR: Reference conversions of sanger file longreads ... ok
BUILDSTDERR: test_misc_dna_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
BUILDSTDERR: Reference conversions of sanger file misc_dna ... ok
BUILDSTDERR: test_misc_rna_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
BUILDSTDERR: Reference conversions of sanger file misc_rna ... ok
BUILDSTDERR: test_sanger_full_range_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
BUILDSTDERR: Reference conversions of sanger file sanger_full_range ... ok
BUILDSTDERR: test_solexa_full_range_solexa (test_SeqIO_QualityIO.TestReferenceFastqConversions)
BUILDSTDERR: Reference conversions of solexa file solexa_full_range ... ok
BUILDSTDERR: test_wrapping_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
BUILDSTDERR: Reference conversions of sanger file wrapping ... ok
BUILDSTDERR: test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions)
BUILDSTDERR: Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL. ... ok
BUILDSTDERR: test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions)
BUILDSTDERR: Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL. ... ok
BUILDSTDERR: test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions)
BUILDSTDERR: Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL. ... ok
BUILDSTDERR: test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions)
BUILDSTDERR: Test converting E3MFGYR02_index_in_middle into FASTA+QUAL. ... ok
BUILDSTDERR: test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions)
BUILDSTDERR: Test converting E3MFGYR02_index_at_start into FASTA+QUAL. ... ok
BUILDSTDERR: test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions)
BUILDSTDERR: Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL. ... ok
BUILDSTDERR: test_original (test_SeqIO_QualityIO.TestReferenceSffConversions)
BUILDSTDERR: Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL. ... ok
BUILDSTDERR: test_negative_clip (test_SeqIO_QualityIO.TestSFF) ... ok
BUILDSTDERR: test_overlapping_clip (test_SeqIO_QualityIO.TestSFF) ... ok
BUILDSTDERR: test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back E3MFGYR02_random_10_reads.sff. ... ok
BUILDSTDERR: test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back E3MFGYR02_alt_index_at_end.sff. ... ok
BUILDSTDERR: test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back E3MFGYR02_alt_index_at_start.sff. ... ok
BUILDSTDERR: test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back E3MFGYR02_alt_index_in_middle.sff. ... ok
BUILDSTDERR: test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back E3MFGYR02_index_at_start.sff. ... ok
BUILDSTDERR: test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back E3MFGYR02_index_in_middle.sff. ... ok
BUILDSTDERR: test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back E3MFGYR02_no_manifest.sff. ... ok
BUILDSTDERR: test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back E3MFGYR02_random_10_reads.sff (trimmed). ... ok
BUILDSTDERR: test_example_fasta (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back example.fasta. ... ok
BUILDSTDERR: test_example_fastq (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back example.fastq. ... ok
BUILDSTDERR: test_example_qual (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back example.qual. ... ok
BUILDSTDERR: test_generated (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back odd SeqRecord objects. ... ok
BUILDSTDERR: test_greek_sff (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back greek.sff. ... ok
BUILDSTDERR: test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back illumina_faked.fastq. ... ok
BUILDSTDERR: test_paired_sff (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back paired.sff. ... ok
BUILDSTDERR: test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back sanger_93.fastq. ... ok
BUILDSTDERR: test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back sanger_faked.fastq. ... ok
BUILDSTDERR: test_solexa_example (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back solexa_example.fastq. ... ok
BUILDSTDERR: test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back solexa_faked.fastq. ... ok
BUILDSTDERR: test_tricky (test_SeqIO_QualityIO.TestWriteRead)
BUILDSTDERR: Write and read back tricky.fastq. ... ok
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 82.031 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SeqXML.py
BUILDSTDERR: test_SeqIO_SeqXML ... ok
BUILDSTDERR: test_duplicated_dbxref (test_SeqIO_SeqXML.TestDetailedRead)
BUILDSTDERR: Read multiple cross references to a single source. ... ok
BUILDSTDERR: test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead)
BUILDSTDERR: Read property with multiple values. ... ok
BUILDSTDERR: test_empty_description (test_SeqIO_SeqXML.TestDetailedRead)
BUILDSTDERR: Check empty description. ... ok
BUILDSTDERR: test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead)
BUILDSTDERR: Read full characters set for each type. ... ok
BUILDSTDERR: test_global_species (test_SeqIO_SeqXML.TestDetailedRead)
BUILDSTDERR: Check global species. ... ok
BUILDSTDERR: test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead)
BUILDSTDERR: Check local source. ... ok
BUILDSTDERR: test_local_species (test_SeqIO_SeqXML.TestDetailedRead)
BUILDSTDERR: Check local species. ... ok
BUILDSTDERR: test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead)
BUILDSTDERR: Check minimal record. ... ok
BUILDSTDERR: test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead)
BUILDSTDERR: Read special XML characters in description. ... ok
BUILDSTDERR: test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead)
BUILDSTDERR: Test special unicode characters in the description. ... ok
BUILDSTDERR: test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite)
BUILDSTDERR: Read and write DNA. ... ok
BUILDSTDERR: test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite)
BUILDSTDERR: Read and write global species. ... ok
BUILDSTDERR: test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite)
BUILDSTDERR: Read and write protein. ... ok
BUILDSTDERR: test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite)
BUILDSTDERR: Read and write RNA. ... ok
BUILDSTDERR: test_write_species (test_SeqIO_SeqXML.TestReadAndWrite)
BUILDSTDERR: Test writing species from annotation tags. ... ok
BUILDSTDERR: test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles)
BUILDSTDERR: Handling of corrupt files. ... ok
BUILDSTDERR: test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead)
BUILDSTDERR: Files readable using parser via SeqIO. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 16.685 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_convert.py
BUILDSTDERR: test_SeqIO_convert ... ok
BUILDSTDERR: test_EMBL_TRBG361_embl_embl_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert EMBL/TRBG361.embl from embl to fasta ... ok
BUILDSTDERR: test_EMBL_U87107_embl_embl_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert EMBL/U87107.embl from embl to fasta ... ok
BUILDSTDERR: test_GenBank_NC_005816_gb_gb_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert GenBank/NC_005816.gb from gb to fasta ... ok
BUILDSTDERR: test_GenBank_cor6_6_gb_genbank_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert GenBank/cor6_6.gb from genbank to fasta ... ok
BUILDSTDERR: test_Quality_error_diff_ids_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_diff_ids.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_diff_ids_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_diff_ids.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_diff_ids_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_diff_ids.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_diff_ids_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_diff_ids.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_diff_ids_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_diff_ids.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_diff_ids_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_diff_ids.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_diff_ids_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_diff_ids.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_double_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_qual.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_double_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_qual.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_double_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_qual.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_double_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_qual.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_double_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_qual.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_double_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_qual.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_double_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_qual.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_double_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_seq.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_double_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_seq.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_double_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_seq.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_double_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_seq.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_double_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_seq.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_double_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_seq.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_double_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_double_seq.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_long_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_long_qual.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_long_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_long_qual.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_long_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_long_qual.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_long_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_long_qual.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_long_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_long_qual.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_long_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_long_qual.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_long_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_long_qual.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_no_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_no_qual.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_no_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_no_qual.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_no_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_no_qual.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_no_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_no_qual.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_no_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_no_qual.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_no_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_no_qual.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_no_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_no_qual.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_qual_del_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_del.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_qual_del_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_del.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_qual_del_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_del.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_qual_del_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_del.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_qual_del_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_del.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_qual_escape_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_escape.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_qual_escape_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_escape.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_qual_escape_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_escape.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_qual_escape_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_escape.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_qual_escape_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_escape.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_qual_null_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_null.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_qual_null_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_null.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_qual_null_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_null.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_qual_null_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_null.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_qual_null_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_null.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_qual_space_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_space.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_qual_space_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_space.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_qual_space_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_space.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_qual_space_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_space.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_qual_space_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_space.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_qual_tab_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_tab.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_qual_tab_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_tab.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_qual_tab_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_tab.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_qual_tab_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_tab.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_qual_tab_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_tab.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_unit_sep.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_qual_unit_sep_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_unit_sep.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_qual_vtab_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_vtab.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_qual_vtab_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_vtab.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_qual_vtab_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_vtab.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_qual_vtab_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_vtab.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_qual_vtab_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_qual_vtab.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_short_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_short_qual.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_short_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_short_qual.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_short_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_short_qual.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_short_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_short_qual.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_short_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_short_qual.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_short_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_short_qual.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_short_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_short_qual.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_spaces_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_spaces.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_spaces_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_spaces.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_spaces_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_spaces.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_spaces_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_spaces.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_spaces_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_spaces.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_spaces_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_spaces.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_spaces_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_spaces.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_tabs_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_tabs.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_tabs_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_tabs.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_tabs_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_tabs.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_tabs_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_tabs.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_tabs_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_tabs.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_tabs_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_tabs.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_tabs_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_tabs.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_trunc_at_plus_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_plus.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_plus.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_trunc_at_plus_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_plus.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_trunc_at_plus_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_plus.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_trunc_at_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_qual.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_qual.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_trunc_at_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_qual.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_trunc_at_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_qual.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_trunc_at_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_seq.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_seq.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_trunc_at_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_seq.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_trunc_at_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_at_seq.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_trunc_in_plus_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_plus.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_plus.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_trunc_in_plus_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_plus.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_trunc_in_plus_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_plus.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_trunc_in_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_qual.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_qual.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_trunc_in_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_qual.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_trunc_in_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_qual.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_trunc_in_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_seq.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_seq.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_trunc_in_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_seq.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_trunc_in_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_seq.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_error_trunc_in_title_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_title.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_error_trunc_in_title_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_title.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_title.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_title.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_title.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_error_trunc_in_title_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_title.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_error_trunc_in_title_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/error_trunc_in_title.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to fasta ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to fastq ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to fastq-illumina ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to fastq-sanger ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to fastq-solexa ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to qual ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq-sanger to tab ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_example_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/example.fastq from fastq to tab ... ok
BUILDSTDERR: test_Quality_illumina_faked_fastq_fastq-illumina_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/illumina_faked.fastq from fastq-illumina to fasta ... ok
BUILDSTDERR: test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/illumina_faked.fastq from fastq-illumina to fastq ... ok
BUILDSTDERR: test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-illumina ... ok
BUILDSTDERR: test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-sanger ... ok
BUILDSTDERR: test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-solexa ... ok
BUILDSTDERR: test_Quality_illumina_faked_fastq_fastq-illumina_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/illumina_faked.fastq from fastq-illumina to qual ... ok
BUILDSTDERR: test_Quality_illumina_faked_fastq_fastq-illumina_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/illumina_faked.fastq from fastq-illumina to tab ... ok
BUILDSTDERR: test_Quality_sanger_93_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_93.fastq from fastq-sanger to fasta ... ok
BUILDSTDERR: test_Quality_sanger_93_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_93.fastq from fastq-sanger to fastq ... ok
BUILDSTDERR: test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_93.fastq from fastq-sanger to fastq-illumina ... ok
BUILDSTDERR: test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_93.fastq from fastq-sanger to fastq-sanger ... ok
BUILDSTDERR: test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_93.fastq from fastq-sanger to fastq-solexa ... ok
BUILDSTDERR: test_Quality_sanger_93_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_93.fastq from fastq-sanger to qual ... ok
BUILDSTDERR: test_Quality_sanger_93_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_93.fastq from fastq-sanger to tab ... ok
BUILDSTDERR: test_Quality_sanger_faked_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_faked.fastq from fastq-sanger to fasta ... ok
BUILDSTDERR: test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_faked.fastq from fastq-sanger to fastq ... ok
BUILDSTDERR: test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-illumina ... ok
BUILDSTDERR: test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-sanger ... ok
BUILDSTDERR: test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-solexa ... ok
BUILDSTDERR: test_Quality_sanger_faked_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_faked.fastq from fastq-sanger to qual ... ok
BUILDSTDERR: test_Quality_sanger_faked_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/sanger_faked.fastq from fastq-sanger to tab ... ok
BUILDSTDERR: test_Quality_solexa_faked_fastq_fastq-solexa_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/solexa_faked.fastq from fastq-solexa to fasta ... ok
BUILDSTDERR: test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/solexa_faked.fastq from fastq-solexa to fastq ... ok
BUILDSTDERR: test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-illumina ... ok
BUILDSTDERR: test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-sanger ... ok
BUILDSTDERR: test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-solexa ... ok
BUILDSTDERR: test_Quality_solexa_faked_fastq_fastq-solexa_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/solexa_faked.fastq from fastq-solexa to qual ... ok
BUILDSTDERR: test_Quality_solexa_faked_fastq_fastq-solexa_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/solexa_faked.fastq from fastq-solexa to tab ... ok
BUILDSTDERR: test_Quality_tricky_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/tricky.fastq from fastq to fasta ... ok
BUILDSTDERR: test_Quality_tricky_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/tricky.fastq from fastq to fastq ... ok
BUILDSTDERR: test_Quality_tricky_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/tricky.fastq from fastq to fastq-illumina ... ok
BUILDSTDERR: test_Quality_tricky_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/tricky.fastq from fastq to fastq-sanger ... ok
BUILDSTDERR: test_Quality_tricky_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/tricky.fastq from fastq to fastq-solexa ... ok
BUILDSTDERR: test_Quality_tricky_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/tricky.fastq from fastq to qual ... ok
BUILDSTDERR: test_Quality_tricky_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
BUILDSTDERR: Convert Quality/tricky.fastq from fastq to tab ... ok
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 19.477 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_features.py
BUILDSTDERR: test_SeqIO_features ... ok
BUILDSTDERR: test_after (test_SeqIO_features.FeatureWriting)
BUILDSTDERR: Features: write/read simple after locations. ... ok
BUILDSTDERR: test_before (test_SeqIO_features.FeatureWriting)
BUILDSTDERR: Features: write/read simple before locations. ... ok
BUILDSTDERR: test_between (test_SeqIO_features.FeatureWriting)
BUILDSTDERR: GenBank/EMBL write/read simple between locations. ... ok
BUILDSTDERR: test_exact (test_SeqIO_features.FeatureWriting)
BUILDSTDERR: GenBank/EMBL write/read simple exact locations. ... ok
BUILDSTDERR: test_fuzzy_join (test_SeqIO_features.FeatureWriting)
BUILDSTDERR: Features: write/read fuzzy join locations. ... ok
BUILDSTDERR: test_join (test_SeqIO_features.FeatureWriting)
BUILDSTDERR: GenBank/EMBL write/read simple join locations. ... ok
BUILDSTDERR: test_oneof (test_SeqIO_features.FeatureWriting)
BUILDSTDERR: Features: write/read simple one-of locations. ... ok
BUILDSTDERR: test_unknown (test_SeqIO_features.FeatureWriting)
BUILDSTDERR: GenBank/EMBL write/read with unknown end points. ... ok
BUILDSTDERR: test_within (test_SeqIO_features.FeatureWriting)
BUILDSTDERR: Features: write/read simple within locations. ... ok
BUILDSTDERR: test_mixed_strand (test_SeqIO_features.GenBankLocations) ... ok
BUILDSTDERR: test_rev_comp_styles (test_SeqIO_features.GenBankLocations) ... ok
BUILDSTDERR: test_CDS (test_SeqIO_features.NC_000932)
BUILDSTDERR: Checking GenBank CDS translations vs FASTA faa file. ... ok
BUILDSTDERR: test_CDS (test_SeqIO_features.NC_005816)
BUILDSTDERR: Checking GenBank CDS translations vs FASTA faa file. ... ok
BUILDSTDERR: test_Features (test_SeqIO_features.NC_005816)
BUILDSTDERR: Checking GenBank features sequences vs FASTA ffn file. ... ok
BUILDSTDERR: test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816) ... ok
BUILDSTDERR: test_Genome (test_SeqIO_features.NC_005816)
BUILDSTDERR: Checking GenBank sequence vs FASTA fna file. ... ok
BUILDSTDERR: test_Translations (test_SeqIO_features.NC_005816)
BUILDSTDERR: Checking translation of FASTA features (faa vs ffn). ... ok
BUILDSTDERR: test_qualifiers (test_SeqIO_features.SeqFeatureCreation)
BUILDSTDERR: Pass in qualifiers to SeqFeatures. ... ok
BUILDSTDERR: test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (join, mixed strand). ... ok
BUILDSTDERR: test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (multi-join, mixed strand). ... ok
BUILDSTDERR: test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on protein (between location, zero length). ... ok
BUILDSTDERR: test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on protein (join). ... ok
BUILDSTDERR: test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on protein (fuzzy join). ... ok
BUILDSTDERR: test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on protein (multi-join). ... ok
BUILDSTDERR: test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on protein (one-of positions). ... ok
BUILDSTDERR: test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on protein (simple). ... ok
BUILDSTDERR: test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (simple, default strand). ... ok
BUILDSTDERR: test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (join, strand +1). ... ok
BUILDSTDERR: test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (join, strand -1, after position). ... ok
BUILDSTDERR: test_simple_dna_join_before (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (join, strand -1, before position). ... ok
BUILDSTDERR: test_simple_dna_join_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (join, strand -1). ... ok
BUILDSTDERR: test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (simple, strand 0). ... ok
BUILDSTDERR: test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (simple, strand +1). ... ok
BUILDSTDERR: test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (simple, strand -1). ... ok
BUILDSTDERR: test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (simple, strand None). ... ok
BUILDSTDERR: test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on RNA (simple, default strand). ... ok
BUILDSTDERR: test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (single letter, default strand). ... ok
BUILDSTDERR: test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (between location, zero length, default strand). ... ok
BUILDSTDERR: test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading)
BUILDSTDERR: Feature on DNA (between location at end, zero length, default strand). ... ok
BUILDSTDERR: test_AAA03323 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back AAA03323.embl. ... ok
BUILDSTDERR: test_AE017046 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back AE017046.embl. ... ok
BUILDSTDERR: test_DD231055_edited (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back DD231055_edited.embl. ... ok
BUILDSTDERR: test_Human_contigs (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back Human_contigs.embl. ... ok
BUILDSTDERR: test_NC_000932 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back NC_000932.gb. ... ok
BUILDSTDERR: test_NC_005816 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back NC_005816.gb. ... ok
BUILDSTDERR: test_NT_019265 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back NT_019265.gb. ... ok
BUILDSTDERR: test_SC10H5 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back SC10H5.embl. ... ok
BUILDSTDERR: test_TRBG361 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back TRBG361.embl. ... ok
BUILDSTDERR: test_U87107 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back U87107.embl. ... ok
BUILDSTDERR: test_arab1 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back arab1.gb. ... ok
BUILDSTDERR: test_blank_seq (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back blank_seq.gb. ... ok
BUILDSTDERR: test_cor6 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back cor6_6.gb. ... ok
BUILDSTDERR: test_dbsource_wrap (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back dbsource_wrap.gb. ... ok
BUILDSTDERR: test_extra_keywords (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back extra_keywords.gb. ... ok
BUILDSTDERR: test_gbvrl1_start (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back gbvrl1_start.seq. ... ok
BUILDSTDERR: test_noref (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back noref.gb. ... ok
BUILDSTDERR: test_one_of (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back of_one.gb. ... ok
BUILDSTDERR: test_origin_line (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back origin_line.gb. ... ok
BUILDSTDERR: test_pri1 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back pri1.gb. ... ok
BUILDSTDERR: test_protein_refseq (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back protein_refseq.gb. ... ok
BUILDSTDERR: test_protein_refseq2 (test_SeqIO_features.TestWriteRead)
BUILDSTDERR: Write and read back protein_refseq2.gb. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 110.927 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_index.py
BUILDSTDERR: test_SeqIO_index ... ok
BUILDSTDERR: test_ace_Ace_consed_sample_ace_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ace file Ace/consed_sample.ace get_raw ... ok
BUILDSTDERR: test_ace_Ace_consed_sample_ace_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ace file Ace/consed_sample.ace with key function ... ok
BUILDSTDERR: test_ace_Ace_consed_sample_ace_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ace file Ace/consed_sample.ace defaults ... ok
BUILDSTDERR: test_ace_Ace_contig1_ace_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ace file Ace/contig1.ace get_raw ... ok
BUILDSTDERR: test_ace_Ace_contig1_ace_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ace file Ace/contig1.ace with key function ... ok
BUILDSTDERR: test_ace_Ace_contig1_ace_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ace file Ace/contig1.ace defaults ... ok
BUILDSTDERR: test_ace_Ace_seq_cap_ace_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ace file Ace/seq.cap.ace get_raw ... ok
BUILDSTDERR: test_ace_Ace_seq_cap_ace_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ace file Ace/seq.cap.ace with key function ... ok
BUILDSTDERR: test_ace_Ace_seq_cap_ace_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ace file Ace/seq.cap.ace defaults ... ok
BUILDSTDERR: test_duplicates_index (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index file with duplicate identifiers with Bio.SeqIO.index(). ... ok
BUILDSTDERR: test_duplicates_index_db (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index file with duplicate identifiers with Bio.SeqIO.index_db(). ... ok
BUILDSTDERR: test_duplicates_to_dict (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index file with duplicate identifiers with Bio.SeqIO.to_dict(). ... ok
BUILDSTDERR: test_embl_EMBL_A04195_imgt_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/A04195.imgt get_raw ... ok
BUILDSTDERR: test_embl_EMBL_A04195_imgt_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/A04195.imgt with key function ... ok
BUILDSTDERR: test_embl_EMBL_A04195_imgt_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/A04195.imgt defaults ... ok
BUILDSTDERR: test_embl_EMBL_AAA03323_embl_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/AAA03323.embl get_raw ... ok
BUILDSTDERR: test_embl_EMBL_AAA03323_embl_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/AAA03323.embl with key function ... ok
BUILDSTDERR: test_embl_EMBL_AAA03323_embl_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/AAA03323.embl defaults ... ok
BUILDSTDERR: test_embl_EMBL_TRBG361_embl_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/TRBG361.embl get_raw ... ok
BUILDSTDERR: test_embl_EMBL_TRBG361_embl_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/TRBG361.embl with key function ... ok
BUILDSTDERR: test_embl_EMBL_TRBG361_embl_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/TRBG361.embl defaults ... ok
BUILDSTDERR: test_embl_EMBL_U87107_embl_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/U87107.embl get_raw ... ok
BUILDSTDERR: test_embl_EMBL_U87107_embl_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/U87107.embl with key function ... ok
BUILDSTDERR: test_embl_EMBL_U87107_embl_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/U87107.embl defaults ... ok
BUILDSTDERR: test_embl_EMBL_epo_prt_selection_embl_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/epo_prt_selection.embl get_raw ... ok
BUILDSTDERR: test_embl_EMBL_epo_prt_selection_embl_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/epo_prt_selection.embl with key function ... ok
BUILDSTDERR: test_embl_EMBL_epo_prt_selection_embl_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/epo_prt_selection.embl defaults ... ok
BUILDSTDERR: test_embl_EMBL_kipo_prt_sample_embl_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/kipo_prt_sample.embl get_raw ... ok
BUILDSTDERR: test_embl_EMBL_kipo_prt_sample_embl_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/kipo_prt_sample.embl with key function ... ok
BUILDSTDERR: test_embl_EMBL_kipo_prt_sample_embl_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/kipo_prt_sample.embl defaults ... ok
BUILDSTDERR: test_embl_EMBL_patents_embl_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/patents.embl get_raw ... ok
BUILDSTDERR: test_embl_EMBL_patents_embl_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/patents.embl with key function ... ok
BUILDSTDERR: test_embl_EMBL_patents_embl_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index embl file EMBL/patents.embl defaults ... ok
BUILDSTDERR: test_fasta_GenBank_NC_000932_faa_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_000932.faa get_raw ... ok
BUILDSTDERR: test_fasta_GenBank_NC_000932_faa_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_000932.faa with key function ... ok
BUILDSTDERR: test_fasta_GenBank_NC_000932_faa_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_000932.faa defaults ... ok
BUILDSTDERR: test_fasta_GenBank_NC_005816_faa_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_005816.faa get_raw ... ok
BUILDSTDERR: test_fasta_GenBank_NC_005816_faa_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_005816.faa with key function ... ok
BUILDSTDERR: test_fasta_GenBank_NC_005816_faa_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_005816.faa defaults ... ok
BUILDSTDERR: test_fasta_GenBank_NC_005816_ffn_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_005816.ffn get_raw ... ok
BUILDSTDERR: test_fasta_GenBank_NC_005816_ffn_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_005816.ffn with key function ... ok
BUILDSTDERR: test_fasta_GenBank_NC_005816_ffn_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_005816.ffn defaults ... ok
BUILDSTDERR: test_fasta_GenBank_NC_005816_fna_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_005816.fna get_raw ... ok
BUILDSTDERR: test_fasta_GenBank_NC_005816_fna_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_005816.fna with key function ... ok
BUILDSTDERR: test_fasta_GenBank_NC_005816_fna_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file GenBank/NC_005816.fna defaults ... ok
BUILDSTDERR: test_fasta_SwissProt_multi_ex_fasta_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file SwissProt/multi_ex.fasta get_raw ... ok
BUILDSTDERR: test_fasta_SwissProt_multi_ex_fasta_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file SwissProt/multi_ex.fasta with key function ... ok
BUILDSTDERR: test_fasta_SwissProt_multi_ex_fasta_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fasta file SwissProt/multi_ex.fasta defaults ... ok
BUILDSTDERR: test_fastq-illumina_Quality_illumina_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-illumina file Quality/illumina_faked.fastq get_raw ... ok
BUILDSTDERR: test_fastq-illumina_Quality_illumina_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-illumina file Quality/illumina_faked.fastq with key function ... ok
BUILDSTDERR: test_fastq-illumina_Quality_illumina_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-illumina file Quality/illumina_faked.fastq defaults ... ok
BUILDSTDERR: test_fastq-sanger_Quality_example_fastq_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-sanger file Quality/example.fastq get_raw ... ok
BUILDSTDERR: test_fastq-sanger_Quality_example_fastq_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-sanger file Quality/example.fastq with key function ... ok
BUILDSTDERR: test_fastq-sanger_Quality_example_fastq_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-sanger file Quality/example.fastq defaults ... ok
BUILDSTDERR: test_fastq-sanger_Quality_sanger_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-sanger file Quality/sanger_faked.fastq get_raw ... ok
BUILDSTDERR: test_fastq-sanger_Quality_sanger_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-sanger file Quality/sanger_faked.fastq with key function ... ok
BUILDSTDERR: test_fastq-sanger_Quality_sanger_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-sanger file Quality/sanger_faked.fastq defaults ... ok
BUILDSTDERR: test_fastq-solexa_Quality_solexa_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-solexa file Quality/solexa_faked.fastq get_raw ... ok
BUILDSTDERR: test_fastq-solexa_Quality_solexa_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-solexa file Quality/solexa_faked.fastq with key function ... ok
BUILDSTDERR: test_fastq-solexa_Quality_solexa_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq-solexa file Quality/solexa_faked.fastq defaults ... ok
BUILDSTDERR: test_fastq_Quality_example_dos_fastq_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/example_dos.fastq get_raw ... ok
BUILDSTDERR: test_fastq_Quality_example_dos_fastq_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/example_dos.fastq with key function ... ok
BUILDSTDERR: test_fastq_Quality_example_dos_fastq_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/example_dos.fastq defaults ... ok
BUILDSTDERR: test_fastq_Quality_example_fastq_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/example.fastq get_raw ... ok
BUILDSTDERR: test_fastq_Quality_example_fastq_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/example.fastq with key function ... ok
BUILDSTDERR: test_fastq_Quality_example_fastq_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/example.fastq defaults ... ok
BUILDSTDERR: test_fastq_Quality_tricky_fastq_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/tricky.fastq get_raw ... ok
BUILDSTDERR: test_fastq_Quality_tricky_fastq_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/tricky.fastq with key function ... ok
BUILDSTDERR: test_fastq_Quality_tricky_fastq_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/tricky.fastq defaults ... ok
BUILDSTDERR: test_fastq_Quality_wrapping_original_sanger_fastq_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/wrapping_original_sanger.fastq get_raw ... ok
BUILDSTDERR: test_fastq_Quality_wrapping_original_sanger_fastq_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/wrapping_original_sanger.fastq with key function ... ok
BUILDSTDERR: test_fastq_Quality_wrapping_original_sanger_fastq_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/wrapping_original_sanger.fastq defaults ... ok
BUILDSTDERR: test_fastq_Quality_zero_length_fastq_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/zero_length.fastq get_raw ... ok
BUILDSTDERR: test_fastq_Quality_zero_length_fastq_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/zero_length.fastq with key function ... ok
BUILDSTDERR: test_fastq_Quality_zero_length_fastq_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index fastq file Quality/zero_length.fastq defaults ... ok
BUILDSTDERR: test_gb_GenBank_NC_005816_gb_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index gb file GenBank/NC_005816.gb get_raw ... ok
BUILDSTDERR: test_gb_GenBank_NC_005816_gb_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index gb file GenBank/NC_005816.gb with key function ... ok
BUILDSTDERR: test_gb_GenBank_NC_005816_gb_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index gb file GenBank/NC_005816.gb defaults ... ok
BUILDSTDERR: test_gb_GenBank_empty_accession_gbk_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index gb file GenBank/empty_accession.gbk get_raw ... ok
BUILDSTDERR: test_gb_GenBank_empty_accession_gbk_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index gb file GenBank/empty_accession.gbk with key function ... ok
BUILDSTDERR: test_gb_GenBank_empty_accession_gbk_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index gb file GenBank/empty_accession.gbk defaults ... ok
BUILDSTDERR: test_gb_GenBank_empty_version_gbk_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index gb file GenBank/empty_version.gbk get_raw ... ok
BUILDSTDERR: test_gb_GenBank_empty_version_gbk_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index gb file GenBank/empty_version.gbk with key function ... ok
BUILDSTDERR: test_gb_GenBank_empty_version_gbk_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index gb file GenBank/empty_version.gbk defaults ... ok
BUILDSTDERR: test_genbank_GenBank_cor6_6_gb_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index genbank file GenBank/cor6_6.gb get_raw ... ok
BUILDSTDERR: test_genbank_GenBank_cor6_6_gb_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index genbank file GenBank/cor6_6.gb with key function ... ok
BUILDSTDERR: test_genbank_GenBank_cor6_6_gb_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index genbank file GenBank/cor6_6.gb defaults ... ok
BUILDSTDERR: test_ig_IntelliGenetics_TAT_mase_nuc_txt_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ig file IntelliGenetics/TAT_mase_nuc.txt get_raw ... ok
BUILDSTDERR: test_ig_IntelliGenetics_TAT_mase_nuc_txt_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ig file IntelliGenetics/TAT_mase_nuc.txt with key function ... ok
BUILDSTDERR: test_ig_IntelliGenetics_TAT_mase_nuc_txt_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ig file IntelliGenetics/TAT_mase_nuc.txt defaults ... ok
BUILDSTDERR: test_ig_IntelliGenetics_VIF_mase-pro_txt_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ig file IntelliGenetics/VIF_mase-pro.txt get_raw ... ok
BUILDSTDERR: test_ig_IntelliGenetics_VIF_mase-pro_txt_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ig file IntelliGenetics/VIF_mase-pro.txt with key function ... ok
BUILDSTDERR: test_ig_IntelliGenetics_VIF_mase-pro_txt_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ig file IntelliGenetics/VIF_mase-pro.txt defaults ... ok
BUILDSTDERR: test_ig_IntelliGenetics_vpu_nucaligned_txt_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ig file IntelliGenetics/vpu_nucaligned.txt get_raw ... ok
BUILDSTDERR: test_ig_IntelliGenetics_vpu_nucaligned_txt_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ig file IntelliGenetics/vpu_nucaligned.txt with key function ... ok
BUILDSTDERR: test_ig_IntelliGenetics_vpu_nucaligned_txt_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index ig file IntelliGenetics/vpu_nucaligned.txt defaults ... ok
BUILDSTDERR: test_imgt_EMBL_A04195_imgt_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index imgt file EMBL/A04195.imgt get_raw ... ok
BUILDSTDERR: test_imgt_EMBL_A04195_imgt_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index imgt file EMBL/A04195.imgt with key function ... ok
BUILDSTDERR: test_imgt_EMBL_A04195_imgt_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index imgt file EMBL/A04195.imgt defaults ... ok
BUILDSTDERR: test_imgt_EMBL_hla_3260_sample_imgt_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index imgt file EMBL/hla_3260_sample.imgt get_raw ... ok
BUILDSTDERR: test_imgt_EMBL_hla_3260_sample_imgt_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index imgt file EMBL/hla_3260_sample.imgt with key function ... ok
BUILDSTDERR: test_imgt_EMBL_hla_3260_sample_imgt_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index imgt file EMBL/hla_3260_sample.imgt defaults ... ok
BUILDSTDERR: test_phd_Phd_phd1_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd1 get_raw ... ok
BUILDSTDERR: test_phd_Phd_phd1_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd1 with key function ... ok
BUILDSTDERR: test_phd_Phd_phd1_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd1 defaults ... ok
BUILDSTDERR: test_phd_Phd_phd2_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd2 get_raw ... ok
BUILDSTDERR: test_phd_Phd_phd2_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd2 with key function ... ok
BUILDSTDERR: test_phd_Phd_phd2_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd2 defaults ... ok
BUILDSTDERR: test_phd_Phd_phd_454_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd_454 get_raw ... ok
BUILDSTDERR: test_phd_Phd_phd_454_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd_454 with key function ... ok
BUILDSTDERR: test_phd_Phd_phd_454_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd_454 defaults ... ok
BUILDSTDERR: test_phd_Phd_phd_solexa_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd_solexa get_raw ... ok
BUILDSTDERR: test_phd_Phd_phd_solexa_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd_solexa with key function ... ok
BUILDSTDERR: test_phd_Phd_phd_solexa_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index phd file Phd/phd_solexa defaults ... ok
BUILDSTDERR: test_pir_NBRF_B_nuc_pir_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index pir file NBRF/B_nuc.pir get_raw ... ok
BUILDSTDERR: test_pir_NBRF_B_nuc_pir_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index pir file NBRF/B_nuc.pir with key function ... ok
BUILDSTDERR: test_pir_NBRF_B_nuc_pir_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index pir file NBRF/B_nuc.pir defaults ... ok
BUILDSTDERR: test_pir_NBRF_Cw_prot_pir_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index pir file NBRF/Cw_prot.pir get_raw ... ok
BUILDSTDERR: test_pir_NBRF_Cw_prot_pir_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index pir file NBRF/Cw_prot.pir with key function ... ok
BUILDSTDERR: test_pir_NBRF_Cw_prot_pir_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index pir file NBRF/Cw_prot.pir defaults ... ok
BUILDSTDERR: test_pir_NBRF_clustalw_pir_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index pir file NBRF/clustalw.pir get_raw ... ok
BUILDSTDERR: test_pir_NBRF_clustalw_pir_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index pir file NBRF/clustalw.pir with key function ... ok
BUILDSTDERR: test_pir_NBRF_clustalw_pir_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index pir file NBRF/clustalw.pir defaults ... ok
BUILDSTDERR: test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff get_raw ... ok
BUILDSTDERR: test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff with key function ... ok
BUILDSTDERR: test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff defaults ... ok
BUILDSTDERR: test_sff-trim_Roche_greek_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff-trim file Roche/greek.sff get_raw ... ok
BUILDSTDERR: test_sff-trim_Roche_greek_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff-trim file Roche/greek.sff with key function ... ok
BUILDSTDERR: test_sff-trim_Roche_greek_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff-trim file Roche/greek.sff defaults ... ok
BUILDSTDERR: test_sff-trim_Roche_paired_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff-trim file Roche/paired.sff get_raw ... ok
BUILDSTDERR: test_sff-trim_Roche_paired_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff-trim file Roche/paired.sff with key function ... ok
BUILDSTDERR: test_sff-trim_Roche_paired_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff-trim file Roche/paired.sff defaults ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_alt_index_at_end.sff get_raw ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_alt_index_at_end.sff with key function ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_alt_index_at_end.sff defaults ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_alt_index_at_start.sff get_raw ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_alt_index_at_start.sff with key function ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_alt_index_at_start.sff defaults ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff get_raw ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff with key function ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff defaults ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_index_at_start_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_index_at_start.sff get_raw ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_index_at_start_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_index_at_start.sff with key function ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_index_at_start_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_index_at_start.sff defaults ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_index_in_middle_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_index_in_middle.sff get_raw ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_index_in_middle_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_index_in_middle.sff with key function ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_index_in_middle_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_index_in_middle.sff defaults ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_no_manifest_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_no_manifest.sff get_raw ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_no_manifest_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_no_manifest.sff with key function ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_no_manifest_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_no_manifest.sff defaults ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_random_10_reads_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_random_10_reads.sff get_raw ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_random_10_reads_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_random_10_reads.sff with key function ... ok
BUILDSTDERR: test_sff_Roche_E3MFGYR02_random_10_reads_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/E3MFGYR02_random_10_reads.sff defaults ... ok
BUILDSTDERR: test_sff_Roche_greek_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/greek.sff get_raw ... ok
BUILDSTDERR: test_sff_Roche_greek_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/greek.sff with key function ... ok
BUILDSTDERR: test_sff_Roche_greek_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/greek.sff defaults ... ok
BUILDSTDERR: test_sff_Roche_paired_sff_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/paired.sff get_raw ... ok
BUILDSTDERR: test_sff_Roche_paired_sff_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/paired.sff with key function ... ok
BUILDSTDERR: test_sff_Roche_paired_sff_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index sff file Roche/paired.sff defaults ... ok
BUILDSTDERR: test_swiss_SwissProt_multi_ex_txt_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/multi_ex.txt get_raw ... ok
BUILDSTDERR: test_swiss_SwissProt_multi_ex_txt_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/multi_ex.txt with key function ... ok
BUILDSTDERR: test_swiss_SwissProt_multi_ex_txt_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/multi_ex.txt defaults ... ok
BUILDSTDERR: test_swiss_SwissProt_sp001_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/sp001 get_raw ... ok
BUILDSTDERR: test_swiss_SwissProt_sp001_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/sp001 with key function ... ok
BUILDSTDERR: test_swiss_SwissProt_sp001_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/sp001 defaults ... ok
BUILDSTDERR: test_swiss_SwissProt_sp010_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/sp010 get_raw ... ok
BUILDSTDERR: test_swiss_SwissProt_sp010_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/sp010 with key function ... ok
BUILDSTDERR: test_swiss_SwissProt_sp010_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/sp010 defaults ... ok
BUILDSTDERR: test_swiss_SwissProt_sp016_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/sp016 get_raw ... ok
BUILDSTDERR: test_swiss_SwissProt_sp016_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/sp016 with key function ... ok
BUILDSTDERR: test_swiss_SwissProt_sp016_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index swiss file SwissProt/sp016 defaults ... ok
BUILDSTDERR: test_tab_GenBank_NC_005816_tsv_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index tab file GenBank/NC_005816.tsv get_raw ... ok
BUILDSTDERR: test_tab_GenBank_NC_005816_tsv_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index tab file GenBank/NC_005816.tsv with key function ... ok
BUILDSTDERR: test_tab_GenBank_NC_005816_tsv_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index tab file GenBank/NC_005816.tsv defaults ... ok
BUILDSTDERR: test_uniprot-xml_SwissProt_multi_ex_xml_get_raw (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index uniprot-xml file SwissProt/multi_ex.xml get_raw ... ok
BUILDSTDERR: test_uniprot-xml_SwissProt_multi_ex_xml_keyf (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index uniprot-xml file SwissProt/multi_ex.xml with key function ... ok
BUILDSTDERR: test_uniprot-xml_SwissProt_multi_ex_xml_simple (test_SeqIO_index.IndexDictTests)
BUILDSTDERR: Index uniprot-xml file SwissProt/multi_ex.xml defaults ... ok
BUILDSTDERR: test_order_index_db (test_SeqIO_index.IndexOrderingManyFiles)
BUILDSTDERR: Check index_db preserves order in multiple indexed files. ... ok
BUILDSTDERR: test_order_index (test_SeqIO_index.IndexOrderingSingleFile)
BUILDSTDERR: Check index preserves order in indexed file. ... ok
BUILDSTDERR: test_order_index_db (test_SeqIO_index.IndexOrderingSingleFile)
BUILDSTDERR: Check index_db preserves ordering indexed file. ... ok
BUILDSTDERR: test_order_to_dict (test_SeqIO_index.IndexOrderingSingleFile)
BUILDSTDERR: Check to_dict preserves order in indexed file. ... ok
BUILDSTDERR: test_child_folder_rel (test_SeqIO_index.NewIndexTest)
BUILDSTDERR: Check relative links to child folder. ... ok
BUILDSTDERR: test_same_folder (test_SeqIO_index.NewIndexTest)
BUILDSTDERR: Check relative links in same folder. ... ok
BUILDSTDERR: test_some_abs (test_SeqIO_index.NewIndexTest)
BUILDSTDERR: Check absolute filenames in index. ... ok
BUILDSTDERR: test_old (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Load existing index with no options (from parent directory). ... ok
BUILDSTDERR: test_old_contents (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Check actual filenames in existing indexes. ... ok
BUILDSTDERR: test_old_files (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Load existing index with correct files (from parent directory). ... ok
BUILDSTDERR: test_old_files_same_dir (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Load existing index with correct files (from same directory). ... ok
BUILDSTDERR: test_old_files_wrong (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Load existing index with wrong files. ... ok
BUILDSTDERR: test_old_files_wrong2 (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Load existing index with wrong number of files. ... ok
BUILDSTDERR: test_old_format (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Load existing index with correct format. ... ok
BUILDSTDERR: test_old_format_wrong (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Load existing index with wrong format. ... ok
BUILDSTDERR: test_old_rel (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Load existing index (with relative paths) with no options (from parent directory). ... ok
BUILDSTDERR: test_old_same_dir (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Load existing index with no options (from same directory). ... ok
BUILDSTDERR: test_old_same_dir_rel (test_SeqIO_index.OldIndexTest)
BUILDSTDERR: Load existing index (with relative paths) with no options (from same directory). ... ok
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1682.388 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_online.py
BUILDSTDERR: test_SeqIO_online ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.648 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_write.py
BUILDSTDERR: test_SeqIO_write ... ok
BUILDSTDERR: test_bad_handle (test_SeqIO_write.WriterTests) ... ok
BUILDSTDERR: test_clustal_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: clustal for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_clustal_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: clustal for alignment with repeated record ... ok
BUILDSTDERR: test_clustal_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: clustal for three DNA sequence alignment ... ok
BUILDSTDERR: test_clustal_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: clustal for three peptides of different lengths ... ok
BUILDSTDERR: test_clustal_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: clustal for three proteins alignment ... ok
BUILDSTDERR: test_clustal_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: clustal for zero records ... ok
BUILDSTDERR: test_embl_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: embl for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_embl_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: embl for alignment with repeated record ... ok
BUILDSTDERR: test_embl_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: embl for three DNA sequence alignment ... ok
BUILDSTDERR: test_embl_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: embl for three peptides of different lengths ... ok
BUILDSTDERR: test_embl_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: embl for three proteins alignment ... ok
BUILDSTDERR: test_embl_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: embl for zero records ... ok
BUILDSTDERR: test_fasta-2line_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta-2line for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_fasta-2line_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta-2line for alignment with repeated record ... ok
BUILDSTDERR: test_fasta-2line_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta-2line for three DNA sequence alignment ... ok
BUILDSTDERR: test_fasta-2line_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta-2line for three peptides of different lengths ... ok
BUILDSTDERR: test_fasta-2line_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta-2line for three proteins alignment ... ok
BUILDSTDERR: test_fasta-2line_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta-2line for zero records ... ok
BUILDSTDERR: test_fasta_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_fasta_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta for alignment with repeated record ... ok
BUILDSTDERR: test_fasta_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta for three DNA sequence alignment ... ok
BUILDSTDERR: test_fasta_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta for three peptides of different lengths ... ok
BUILDSTDERR: test_fasta_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta for three proteins alignment ... ok
BUILDSTDERR: test_fasta_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: fasta for zero records ... ok
BUILDSTDERR: test_fastq-illumina_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-illumina for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_fastq-illumina_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-illumina for alignment with repeated record ... ok
BUILDSTDERR: test_fastq-illumina_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-illumina for three DNA sequence alignment ... ok
BUILDSTDERR: test_fastq-illumina_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-illumina for three peptides of different lengths ... ok
BUILDSTDERR: test_fastq-illumina_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-illumina for three proteins alignment ... ok
BUILDSTDERR: test_fastq-illumina_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-illumina for zero records ... ok
BUILDSTDERR: test_fastq-solexa_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-solexa for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_fastq-solexa_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-solexa for alignment with repeated record ... ok
BUILDSTDERR: test_fastq-solexa_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-solexa for three DNA sequence alignment ... ok
BUILDSTDERR: test_fastq-solexa_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-solexa for three peptides of different lengths ... ok
BUILDSTDERR: test_fastq-solexa_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-solexa for three proteins alignment ... ok
BUILDSTDERR: test_fastq-solexa_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq-solexa for zero records ... ok
BUILDSTDERR: test_fastq_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_fastq_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq for alignment with repeated record ... ok
BUILDSTDERR: test_fastq_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq for three DNA sequence alignment ... ok
BUILDSTDERR: test_fastq_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq for three peptides of different lengths ... ok
BUILDSTDERR: test_fastq_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq for three proteins alignment ... ok
BUILDSTDERR: test_fastq_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: fastq for zero records ... ok
BUILDSTDERR: test_genbank_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: genbank for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_genbank_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: genbank for alignment with repeated record ... ok
BUILDSTDERR: test_genbank_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: genbank for three DNA sequence alignment ... ok
BUILDSTDERR: test_genbank_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: genbank for three peptides of different lengths ... ok
BUILDSTDERR: test_genbank_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: genbank for three proteins alignment ... ok
BUILDSTDERR: test_genbank_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: genbank for zero records ... ok
BUILDSTDERR: test_imgt_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: imgt for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_imgt_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: imgt for alignment with repeated record ... ok
BUILDSTDERR: test_imgt_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: imgt for three DNA sequence alignment ... ok
BUILDSTDERR: test_imgt_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: imgt for three peptides of different lengths ... ok
BUILDSTDERR: test_imgt_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: imgt for three proteins alignment ... ok
BUILDSTDERR: test_imgt_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: imgt for zero records ... ok
BUILDSTDERR: test_maf_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: maf for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_maf_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: maf for alignment with repeated record ... ok
BUILDSTDERR: test_maf_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: maf for three DNA sequence alignment ... ok
BUILDSTDERR: test_maf_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: maf for three peptides of different lengths ... ok
BUILDSTDERR: test_maf_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: maf for three proteins alignment ... ok
BUILDSTDERR: test_maf_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: maf for zero records ... ok
BUILDSTDERR: test_mauve_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: mauve for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_mauve_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: mauve for alignment with repeated record ... ok
BUILDSTDERR: test_mauve_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: mauve for three DNA sequence alignment ... ok
BUILDSTDERR: test_mauve_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: mauve for three peptides of different lengths ... ok
BUILDSTDERR: test_mauve_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: mauve for three proteins alignment ... ok
BUILDSTDERR: test_mauve_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: mauve for zero records ... ok
BUILDSTDERR: test_nexus_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: nexus for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_nexus_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: nexus for alignment with repeated record ... ok
BUILDSTDERR: test_nexus_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: nexus for three DNA sequence alignment ... ok
BUILDSTDERR: test_nexus_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: nexus for three peptides of different lengths ... ok
BUILDSTDERR: test_nexus_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: nexus for three proteins alignment ... ok
BUILDSTDERR: test_nexus_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: nexus for zero records ... ok
BUILDSTDERR: test_nib_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: nib for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_nib_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: nib for alignment with repeated record ... ok
BUILDSTDERR: test_nib_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: nib for three DNA sequence alignment ... ok
BUILDSTDERR: test_nib_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: nib for three peptides of different lengths ... ok
BUILDSTDERR: test_nib_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: nib for three proteins alignment ... ok
BUILDSTDERR: test_nib_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: nib for zero records ... ok
BUILDSTDERR: test_phd_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: phd for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_phd_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: phd for alignment with repeated record ... ok
BUILDSTDERR: test_phd_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: phd for three DNA sequence alignment ... ok
BUILDSTDERR: test_phd_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: phd for three peptides of different lengths ... ok
BUILDSTDERR: test_phd_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: phd for three proteins alignment ... ok
BUILDSTDERR: test_phd_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: phd for zero records ... ok
BUILDSTDERR: test_phylip-relaxed_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-relaxed for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_phylip-relaxed_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-relaxed for alignment with repeated record ... ok
BUILDSTDERR: test_phylip-relaxed_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-relaxed for three DNA sequence alignment ... ok
BUILDSTDERR: test_phylip-relaxed_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-relaxed for three peptides of different lengths ... ok
BUILDSTDERR: test_phylip-relaxed_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-relaxed for three proteins alignment ... ok
BUILDSTDERR: test_phylip-relaxed_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-relaxed for zero records ... ok
BUILDSTDERR: test_phylip-sequential_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-sequential for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_phylip-sequential_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-sequential for alignment with repeated record ... ok
BUILDSTDERR: test_phylip-sequential_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-sequential for three DNA sequence alignment ... ok
BUILDSTDERR: test_phylip-sequential_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-sequential for three peptides of different lengths ... ok
BUILDSTDERR: test_phylip-sequential_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-sequential for three proteins alignment ... ok
BUILDSTDERR: test_phylip-sequential_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip-sequential for zero records ... ok
BUILDSTDERR: test_phylip_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_phylip_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip for alignment with repeated record ... ok
BUILDSTDERR: test_phylip_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip for three DNA sequence alignment ... ok
BUILDSTDERR: test_phylip_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip for three peptides of different lengths ... ok
BUILDSTDERR: test_phylip_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip for three proteins alignment ... ok
BUILDSTDERR: test_phylip_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: phylip for zero records ... ok
BUILDSTDERR: test_pir_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: pir for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_pir_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: pir for alignment with repeated record ... ok
BUILDSTDERR: test_pir_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: pir for three DNA sequence alignment ... ok
BUILDSTDERR: test_pir_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: pir for three peptides of different lengths ... ok
BUILDSTDERR: test_pir_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: pir for three proteins alignment ... ok
BUILDSTDERR: test_pir_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: pir for zero records ... ok
BUILDSTDERR: test_qual_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: qual for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_qual_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: qual for alignment with repeated record ... ok
BUILDSTDERR: test_qual_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: qual for three DNA sequence alignment ... ok
BUILDSTDERR: test_qual_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: qual for three peptides of different lengths ... ok
BUILDSTDERR: test_qual_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: qual for three proteins alignment ... ok
BUILDSTDERR: test_qual_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: qual for zero records ... ok
BUILDSTDERR: test_seqxml_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: seqxml for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_seqxml_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: seqxml for alignment with repeated record ... ok
BUILDSTDERR: test_seqxml_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: seqxml for three DNA sequence alignment ... ok
BUILDSTDERR: test_seqxml_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: seqxml for three peptides of different lengths ... ok
BUILDSTDERR: test_seqxml_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: seqxml for three proteins alignment ... ok
BUILDSTDERR: test_seqxml_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: seqxml for zero records ... ok
BUILDSTDERR: test_sff_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: sff for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_sff_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: sff for alignment with repeated record ... ok
BUILDSTDERR: test_sff_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: sff for three DNA sequence alignment ... ok
BUILDSTDERR: test_sff_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: sff for three peptides of different lengths ... ok
BUILDSTDERR: test_sff_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: sff for three proteins alignment ... ok
BUILDSTDERR: test_sff_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: sff for zero records ... ok
BUILDSTDERR: test_stockholm_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: stockholm for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_stockholm_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: stockholm for alignment with repeated record ... ok
BUILDSTDERR: test_stockholm_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: stockholm for three DNA sequence alignment ... ok
BUILDSTDERR: test_stockholm_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: stockholm for three peptides of different lengths ... ok
BUILDSTDERR: test_stockholm_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: stockholm for three proteins alignment ... ok
BUILDSTDERR: test_stockholm_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: stockholm for zero records ... ok
BUILDSTDERR: test_tab_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
BUILDSTDERR: tab for 3 DNA seq alignment with CR/LF in name/descr ... ok
BUILDSTDERR: test_tab_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
BUILDSTDERR: tab for alignment with repeated record ... ok
BUILDSTDERR: test_tab_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: tab for three DNA sequence alignment ... ok
BUILDSTDERR: test_tab_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
BUILDSTDERR: tab for three peptides of different lengths ... ok
BUILDSTDERR: test_tab_three_proteins_alignment (test_SeqIO_write.WriterTests)
BUILDSTDERR: tab for three proteins alignment ... ok
BUILDSTDERR: test_tab_zero_records (test_SeqIO_write.WriterTests)
BUILDSTDERR: tab for zero records ... ok
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 15.404 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqRecord.py
BUILDSTDERR: test_SeqRecord ... ok
BUILDSTDERR: test_annotations (test_SeqRecord.SeqRecordCreation)
BUILDSTDERR: Pass in annotations to SeqRecords. ... ok
BUILDSTDERR: test_letter_annotations (test_SeqRecord.SeqRecordCreation)
BUILDSTDERR: Pass in letter annotations to SeqRecords. ... ok
BUILDSTDERR: test_replacing_seq (test_SeqRecord.SeqRecordCreation)
BUILDSTDERR: Replacing .seq if .letter_annotation present. ... ok
BUILDSTDERR: test_valid_annotations (test_SeqRecord.SeqRecordCreation) ... ok
BUILDSTDERR: test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation) ... ok
BUILDSTDERR: test_valid_description (test_SeqRecord.SeqRecordCreation) ... ok
BUILDSTDERR: test_valid_features (test_SeqRecord.SeqRecordCreation) ... ok
BUILDSTDERR: test_valid_id (test_SeqRecord.SeqRecordCreation) ... ok
BUILDSTDERR: test_valid_name (test_SeqRecord.SeqRecordCreation) ... ok
BUILDSTDERR: test_add_seq (test_SeqRecord.SeqRecordMethods)
BUILDSTDERR: Simple addition of Seq or string. ... ok
BUILDSTDERR: test_add_seq_left (test_SeqRecord.SeqRecordMethods)
BUILDSTDERR: Simple left addition of Seq or string. ... ok
BUILDSTDERR: test_add_seqrecord (test_SeqRecord.SeqRecordMethods)
BUILDSTDERR: Simple left addition of SeqRecord from genbank file. ... ok
BUILDSTDERR: test_add_simple (test_SeqRecord.SeqRecordMethods)
BUILDSTDERR: Simple addition. ... ok
BUILDSTDERR: test_contains (test_SeqRecord.SeqRecordMethods) ... ok
BUILDSTDERR: test_format (test_SeqRecord.SeqRecordMethods) ... ok
BUILDSTDERR: test_iter (test_SeqRecord.SeqRecordMethods) ... ok
BUILDSTDERR: test_lower (test_SeqRecord.SeqRecordMethods) ... ok
BUILDSTDERR: test_repr (test_SeqRecord.SeqRecordMethods) ... ok
BUILDSTDERR: test_slice_add_shift (test_SeqRecord.SeqRecordMethods)
BUILDSTDERR: Simple slice and add to shift. ... ok
BUILDSTDERR: test_slice_add_simple (test_SeqRecord.SeqRecordMethods)
BUILDSTDERR: Simple slice and add. ... ok
BUILDSTDERR: test_slice_simple (test_SeqRecord.SeqRecordMethods)
BUILDSTDERR: Simple slice. ... ok
BUILDSTDERR: test_slice_variants (test_SeqRecord.SeqRecordMethods)
BUILDSTDERR: Simple slices using different start/end values. ... ok
BUILDSTDERR: test_slice_zero (test_SeqRecord.SeqRecordMethods)
BUILDSTDERR: Zero slice. ... ok
BUILDSTDERR: test_slicing (test_SeqRecord.SeqRecordMethods) ... ok
BUILDSTDERR: test_str (test_SeqRecord.SeqRecordMethods) ... ok
BUILDSTDERR: test_upper (test_SeqRecord.SeqRecordMethods) ... ok
BUILDSTDERR: test_eq_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
BUILDSTDERR: test_ge_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
BUILDSTDERR: test_gt_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
BUILDSTDERR: test_hash_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
BUILDSTDERR: test_le_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
BUILDSTDERR: test_lt_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
BUILDSTDERR: test_ne_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
BUILDSTDERR: test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethodsMore) ... ok
BUILDSTDERR: test_reverse_complement_seq (test_SeqRecord.SeqRecordMethodsMore) ... ok
BUILDSTDERR: test_translate (test_SeqRecord.SeqRecordMethodsMore) ... ok
BUILDSTDERR: test_defaults (test_SeqRecord.TestTranslation) ... ok
BUILDSTDERR: test_new_annot (test_SeqRecord.TestTranslation) ... ok
BUILDSTDERR: test_preserve (test_SeqRecord.TestTranslation) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 29.510 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqUtils.py
BUILDSTDERR: test_SeqUtils ... ok
BUILDSTDERR: test_GC (test_SeqUtils.SeqUtilsTests) ... ok
BUILDSTDERR: test_GC_skew (test_SeqUtils.SeqUtilsTests) ... ok
BUILDSTDERR: test_checksum1 (test_SeqUtils.SeqUtilsTests) ... ok
BUILDSTDERR: test_checksum2 (test_SeqUtils.SeqUtilsTests) ... ok
BUILDSTDERR: test_checksum3 (test_SeqUtils.SeqUtilsTests) ... ok
BUILDSTDERR: test_codon_adaptation_index (test_SeqUtils.SeqUtilsTests) ... ok
BUILDSTDERR: test_codon_usage_custom (test_SeqUtils.SeqUtilsTests)
BUILDSTDERR: Test Codon Adaptation Index (CAI) using FASTA file for background. ... ok
BUILDSTDERR: test_codon_usage_ecoli (test_SeqUtils.SeqUtilsTests)
BUILDSTDERR: Test Codon Adaptation Index (CAI) using default E. coli data. ... ok
BUILDSTDERR: test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests) ... ok
BUILDSTDERR: test_index (test_SeqUtils.SeqUtilsTests) ... ok
BUILDSTDERR: test_seq1_seq3 (test_SeqUtils.SeqUtilsTests) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 13.420 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Seq_objs.py
BUILDSTDERR: test_Seq_objs ... ok
BUILDSTDERR: test_unknown_seq_ungap (test_Seq_objs.FileBasedTests)
BUILDSTDERR: Test ungap() works properly on UnknownSeq instances. ... ok
BUILDSTDERR: test_MutableSeq_init_typeerror (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check MutableSeq __init__ gives TypeError exceptions. ... ok
BUILDSTDERR: test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check our count_overlap method using GG with variable ends and starts. ... ok
BUILDSTDERR: test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check our count_overlap method using NN with variable ends and starts. ... ok
BUILDSTDERR: test_init_typeerror (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check Seq __init__ gives TypeError exceptions. ... ok
BUILDSTDERR: test_join_MutableSeq (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok
BUILDSTDERR: test_join_MutableSeq_TypeError (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks that a TypeError is thrown for incompatible alphabets. ... ok
BUILDSTDERR: test_join_MutableSeq_ValueError (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks that a ValueError is thrown for all non-iterable types. ... ok
BUILDSTDERR: test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok
BUILDSTDERR: test_join_Seq (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks if Seq join correctly concatenates sequence with the spacer. ... ok
BUILDSTDERR: test_join_Seq_TypeError (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks that a TypeError is thrown for incompatible alphabets. ... ok
BUILDSTDERR: test_join_Seq_ValueError (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks that a ValueError is thrown for all non-iterable types. ... ok
BUILDSTDERR: test_join_Seq_with_file (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok
BUILDSTDERR: test_join_UnknownSeq (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks if UnknownSeq join correctly concatenates sequence with the spacer. ... ok
BUILDSTDERR: test_join_UnknownSeq_TypeError (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks that a TypeError is thrown for incompatible alphabets. ... ok
BUILDSTDERR: test_join_UnknownSeq_ValueError (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks that a ValueError is thrown for all non-iterable types. ... ok
BUILDSTDERR: test_join_UnknownSeq_with_file (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Checks if UnknownSeq join correctly concatenates sequence from a file with the spacer. ... ok
BUILDSTDERR: test_str_comparison (test_Seq_objs.StringMethodTests) ... ok
BUILDSTDERR: test_str_count (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string count method. ... ok
BUILDSTDERR: test_str_count_overlap_GG (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check our count_overlap method using GG. ... ok
BUILDSTDERR: test_str_count_overlap_NN (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check our count_overlap method using NN. ... ok
BUILDSTDERR: test_str_endswith (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string endswith method. ... ok
BUILDSTDERR: test_str_find (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string find method. ... ok
BUILDSTDERR: test_str_getitem (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check slicing and indexing works like a string. ... ok
BUILDSTDERR: test_str_hash (test_Seq_objs.StringMethodTests) ... ok
BUILDSTDERR: test_str_length (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string __len__ method. ... ok
BUILDSTDERR: test_str_lower (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string lower method. ... ok
BUILDSTDERR: test_str_lsplit (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string rstrip method. ... ok
BUILDSTDERR: test_str_rfind (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string rfind method. ... ok
BUILDSTDERR: test_str_rsplit (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string rstrip method. ... ok
BUILDSTDERR: test_str_rstrip (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string rstrip method. ... ok
BUILDSTDERR: test_str_split (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string rstrip method. ... ok
BUILDSTDERR: test_str_startswith (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string startswith method. ... ok
BUILDSTDERR: test_str_strip (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string strip method. ... ok
BUILDSTDERR: test_str_upper (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check matches the python string upper method. ... ok
BUILDSTDERR: test_the_back_transcription (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check obj.back_transcribe() method. ... ok
BUILDSTDERR: test_the_complement (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check obj.complement() method. ... ok
BUILDSTDERR: test_the_reverse_complement (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check obj.reverse_complement() method. ... ok
BUILDSTDERR: test_the_transcription (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check obj.transcribe() method. ... ok
BUILDSTDERR: test_the_translate (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check obj.translate() method. ... ok
BUILDSTDERR: test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check obj.translate() method with ambiguous codons. ... ok
BUILDSTDERR: test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check obj.translate() method with invalid codons. ... ok
BUILDSTDERR: test_the_translation_of_stops (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check obj.translate() method with stop codons. ... ok
BUILDSTDERR: test_tomutable (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check obj.tomutable() method. ... ok
BUILDSTDERR: test_toseq (test_Seq_objs.StringMethodTests)
BUILDSTDERR: Check obj.toseq() method. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 541.394 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SffIO.py
BUILDSTDERR: test_SffIO ... ok
BUILDSTDERR: test_alt_index_at_end (test_SffIO.TestAlternativeIndexes) ... ok
BUILDSTDERR: test_alt_index_at_start (test_SffIO.TestAlternativeIndexes) ... ok
BUILDSTDERR: test_alt_index_in_middle (test_SffIO.TestAlternativeIndexes) ... ok
BUILDSTDERR: test_index_at_start (test_SffIO.TestAlternativeIndexes) ... ok
BUILDSTDERR: test_index_in_middle (test_SffIO.TestAlternativeIndexes) ... ok
BUILDSTDERR: test_trim (test_SffIO.TestAlternativeIndexes) ... ok
BUILDSTDERR: test_index1 (test_SffIO.TestConcatenated) ... ok
BUILDSTDERR: test_index2 (test_SffIO.TestConcatenated) ... ok
BUILDSTDERR: test_parse1 (test_SffIO.TestConcatenated) ... ok
BUILDSTDERR: test_parse2 (test_SffIO.TestConcatenated) ... ok
BUILDSTDERR: test_parses_gzipped_stream (test_SffIO.TestConcatenated) ... ok
BUILDSTDERR: test_30bytes (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_31bytes (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_31bytes_bad_flowgram (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_31bytes_bad_ver (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_31bytes_index_header (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_bad_index_eof (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_bad_index_length (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_bad_index_offset (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_empty (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_index_lengths (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_index_mft_data_size (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_index_mft_version (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_index_name_no_null (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_no_index (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_no_manifest_xml (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_premature_end_of_index (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_unknown_index (test_SffIO.TestErrors) ... ok
BUILDSTDERR: test_both_ways (test_SffIO.TestIndex) ... ok
BUILDSTDERR: test_manifest (test_SffIO.TestIndex) ... ok
BUILDSTDERR: test_index (test_SffIO.TestSelf) ... ok
BUILDSTDERR: test_read (test_SffIO.TestSelf) ... ok
BUILDSTDERR: test_read_wrong (test_SffIO.TestSelf) ... ok
BUILDSTDERR: test_write (test_SffIO.TestSelf) ... ok
BUILDSTDERR: test_coords (test_SffIO.TestUAN) ... ok
BUILDSTDERR: test_region (test_SffIO.TestUAN) ... ok
BUILDSTDERR: test_time (test_SffIO.TestUAN) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 13.329 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SubsMat.py
BUILDSTDERR: test_SubsMat ... ok
BUILDSTDERR: test_freqtable (test_SubsMat.TestGeo) ... ok
BUILDSTDERR: test_log_odds_matris (test_SubsMat.TestGeo) ... ok
BUILDSTDERR: test_matrices (test_SubsMat.TestGeo) ... ok
BUILDSTDERR: test_matrix_correlations (test_SubsMat.TestGeo) ... ok
BUILDSTDERR: test_obs_freq_mat (test_SubsMat.TestGeo) ... ok
BUILDSTDERR: test_obs_freq_mat_sum (test_SubsMat.TestGeo) ... ok
BUILDSTDERR: test_protein_freq (test_SubsMat.TestGeo) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 4.388 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SwissProt.py
BUILDSTDERR: test_SwissProt ... ok
BUILDSTDERR: test_sp001 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp001. ... ok
BUILDSTDERR: test_sp002 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp002. ... ok
BUILDSTDERR: test_sp003 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp003. ... ok
BUILDSTDERR: test_sp004 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp004. ... ok
BUILDSTDERR: test_sp005 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp005. ... ok
BUILDSTDERR: test_sp006 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp006. ... ok
BUILDSTDERR: test_sp007 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp007. ... ok
BUILDSTDERR: test_sp008 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp008. ... ok
BUILDSTDERR: test_sp009 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp009. ... ok
BUILDSTDERR: test_sp010 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp010. ... ok
BUILDSTDERR: test_sp011 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp011. ... ok
BUILDSTDERR: test_sp012 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp012. ... ok
BUILDSTDERR: test_sp013 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp013. ... ok
BUILDSTDERR: test_sp014 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp014. ... ok
BUILDSTDERR: test_sp015 (test_SwissProt.TestSwissProt)
BUILDSTDERR: Parsing SwissProt file sp015. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 13.737 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TCoffee_tool.py
BUILDSTDERR: test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 9.503 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TogoWS.py
BUILDSTDERR: test_TogoWS ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.503 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TreeConstruction.py
BUILDSTDERR: test_TreeConstruction ... ok
BUILDSTDERR: test_known_matrices (test_TreeConstruction.DistanceCalculatorTest) ... ok
BUILDSTDERR: test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest) ... ok
BUILDSTDERR: test_bad_construction (test_TreeConstruction.DistanceMatrixTest) ... ok
BUILDSTDERR: test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest) ... ok
BUILDSTDERR: test_format_phylip (test_TreeConstruction.DistanceMatrixTest) ... ok
BUILDSTDERR: test_good_construction (test_TreeConstruction.DistanceMatrixTest) ... ok
BUILDSTDERR: test_good_manipulation (test_TreeConstruction.DistanceMatrixTest) ... ok
BUILDSTDERR: test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
BUILDSTDERR: test_nj (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
BUILDSTDERR: test_upgma (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
BUILDSTDERR: test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest) ... ok
BUILDSTDERR: test_get_score (test_TreeConstruction.ParsimonyScorerTest) ... ok
BUILDSTDERR: test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 59.482 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_UniGene.py
BUILDSTDERR: test_UniGene ... ok
BUILDSTDERR: test_parse (test_UniGene.TestUniGene) ... ok
BUILDSTDERR: test_read (test_UniGene.TestUniGene) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 2.023 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Uniprot.py
BUILDSTDERR: test_Uniprot ... ok
BUILDSTDERR: test_F2CXE6 (test_Uniprot.TestUniprot)
BUILDSTDERR: Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok
BUILDSTDERR: test_H2CNN8 (test_Uniprot.TestUniprot)
BUILDSTDERR: Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok
BUILDSTDERR: test_P84001 (test_Uniprot.TestUniprot)
BUILDSTDERR: Parse mass spec structured comment with unknown loc. ... ok
BUILDSTDERR: test_Q13639 (test_Uniprot.TestUniprot)
BUILDSTDERR: Compare SwissProt text and uniprot XML versions of Q13639. ... ok
BUILDSTDERR: test_multi_ex (test_Uniprot.TestUniprot)
BUILDSTDERR: Compare SwissProt text and uniprot XML versions of several examples. ... ok
BUILDSTDERR: test_multi_ex_index (test_Uniprot.TestUniprot)
BUILDSTDERR: Index SwissProt text and uniprot XML versions of several examples. ... ok
BUILDSTDERR: test_sp002 (test_Uniprot.TestUniprot)
BUILDSTDERR: Parsing SwissProt file sp002. ... ok
BUILDSTDERR: test_sp016 (test_Uniprot.TestUniprot)
BUILDSTDERR: Parsing SwissProt file sp016. ... ok
BUILDSTDERR: test_submittedName_allowed (test_Uniprot.TestUniprot)
BUILDSTDERR: Checks if parser supports new XML Element (submittedName). ... ok
BUILDSTDERR: test_uni001 (test_Uniprot.TestUniprot)
BUILDSTDERR: Parsing Uniprot file uni001. ... ok
BUILDSTDERR: test_uni003 (test_Uniprot.TestUniprot)
BUILDSTDERR: Parsing Uniprot file uni003. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 27.244 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Wise.py
BUILDSTDERR: test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.967 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_XXmotif_tool.py
BUILDSTDERR: test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 9.668 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_align.py
BUILDSTDERR: test_align ... ok
BUILDSTDERR: test_basic_alignment (test_align.TestBasics)
BUILDSTDERR: Basic tests on a simple alignment of three sequences. ... ok
BUILDSTDERR: test_empty_alignment (test_align.TestBasics)
BUILDSTDERR: Very simple tests on an empty alignment. ... ok
BUILDSTDERR: test_format_conversion (test_align.TestReading)
BUILDSTDERR: Parse the alignment file and get an aligment object. ... ok
BUILDSTDERR: test_read_clustal1 (test_align.TestReading)
BUILDSTDERR: Parse an alignment file and get an aligment object. ... ok
BUILDSTDERR: test_read_clustal2 (test_align.TestReading)
BUILDSTDERR: Parse an alignment file and get an aligment object. ... ok
BUILDSTDERR: test_read_fasta (test_align.TestReading) ... ok
BUILDSTDERR: test_read_write_clustal (test_align.TestReading)
BUILDSTDERR: Test the base alignment stuff. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 12.331 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_cellosaurus.py
BUILDSTDERR: test_cellosaurus ... ok
BUILDSTDERR: test__str__ (test_cellosaurus.TestCellosaurus)
BUILDSTDERR: Test string function. ... ok
BUILDSTDERR: test_parse (test_cellosaurus.TestCellosaurus)
BUILDSTDERR: Test parsing function. ... ok
BUILDSTDERR: test_read (test_cellosaurus.TestCellosaurus)
BUILDSTDERR: Test read function. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.608 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_codonalign.py
BUILDSTDERR: test_codonalign ... /builddir/build/BUILD/python-biopython-1.74/python3/build/lib.linux-riscv64-3.7/Bio/Seq.py:2695: 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.
BUILDSTDERR:   BiopythonWarning)
BUILDSTDERR: ok
BUILDSTDERR: test_TypeError (test_codonalign.TestAddition)
BUILDSTDERR: Check that TypeError is thrown for non CodonAlignment/MultipleSequenceAlignment objects. ... ok
BUILDSTDERR: test_ValueError (test_codonalign.TestAddition)
BUILDSTDERR: Check that ValueError is thrown for Alignments of different lengths. ... ok
BUILDSTDERR: test_addition_CodonAlignment (test_codonalign.TestAddition)
BUILDSTDERR: Check addition of CodonAlignment and CodonAlignment. ... ok
BUILDSTDERR: test_addition_MultipleSeqAlignment (test_codonalign.TestAddition)
BUILDSTDERR: Check addition of CodonAlignment and MultipleSeqAlignment. ... ok
BUILDSTDERR: test_IO (test_codonalign.TestBuildAndIO) ... ok
BUILDSTDERR: test_align (test_codonalign.TestCodonAlignment) ... ok
BUILDSTDERR: test_seq (test_codonalign.TestCodonSeq) ... ok
BUILDSTDERR: test_mk (test_codonalign.Test_MK) ... ok
BUILDSTDERR: test_build (test_codonalign.Test_build) ... ok
BUILDSTDERR: test_dn_ds (test_codonalign.Test_dn_ds) ... ok
BUILDSTDERR: test_dn_ds_matrix (test_codonalign.Test_dn_ds) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 673.096 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_geo.py
BUILDSTDERR: test_geo ... ok
BUILDSTDERR: test_GSE16 (test_geo.TestGeo) ... ok
BUILDSTDERR: test_GSM645 (test_geo.TestGeo) ... ok
BUILDSTDERR: test_GSM691 (test_geo.TestGeo) ... ok
BUILDSTDERR: test_GSM700 (test_geo.TestGeo) ... ok
BUILDSTDERR: test_GSM804 (test_geo.TestGeo) ... ok
BUILDSTDERR: test_soft_ex_affy (test_geo.TestGeo) ... ok
BUILDSTDERR: test_soft_ex_affy_chp (test_geo.TestGeo) ... ok
BUILDSTDERR: test_soft_ex_dual (test_geo.TestGeo) ... ok
BUILDSTDERR: test_soft_ex_family (test_geo.TestGeo) ... ok
BUILDSTDERR: test_soft_ex_platform (test_geo.TestGeo) ... ok
BUILDSTDERR: test_soft_ex_series (test_geo.TestGeo) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 5.386 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_kNN.py
BUILDSTDERR: test_kNN ... ok
BUILDSTDERR: test_calculate_model (test_kNN.TestKNN) ... ok
BUILDSTDERR: test_calculate_probability (test_kNN.TestKNN) ... ok
BUILDSTDERR: test_classify (test_kNN.TestKNN) ... ok
BUILDSTDERR: test_leave_one_out (test_kNN.TestKNN) ... ok
BUILDSTDERR: test_model_accuracy (test_kNN.TestKNN) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1.354 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_lowess.py
BUILDSTDERR: test_lowess ... ok
BUILDSTDERR: test_Precomputed (test_lowess.test_lowess) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.477 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_mmtf.py
BUILDSTDERR: test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 4.618 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_mmtf_online.py
BUILDSTDERR: test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 5.551 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_motifs.py
BUILDSTDERR: test_motifs ... ok
BUILDSTDERR: test_mixed_alphabets (test_motifs.MotifTestPWM)
BUILDSTDERR: Test creating motif with mixed alphabets. ... ok
BUILDSTDERR: test_simple (test_motifs.MotifTestPWM)
BUILDSTDERR: Test if Bio.motifs PWM scoring works. ... ok
BUILDSTDERR: test_with_alt_alphabet (test_motifs.MotifTestPWM)
BUILDSTDERR: Test motif search using alternative instance of alphabet. ... ok
BUILDSTDERR: test_with_bad_char (test_motifs.MotifTestPWM)
BUILDSTDERR: Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok
BUILDSTDERR: test_with_mixed_case (test_motifs.MotifTestPWM)
BUILDSTDERR: Test if Bio.motifs PWM scoring works with mixed case. ... ok
BUILDSTDERR: test_TFoutput (test_motifs.MotifTestsBasic)
BUILDSTDERR: Ensure that we can write proper TransFac output files. ... ok
BUILDSTDERR: test_alignace_parsing (test_motifs.MotifTestsBasic)
BUILDSTDERR: Test if Bio.motifs can parse AlignAce output files. ... ok
BUILDSTDERR: test_clusterbuster_parsing_and_output (test_motifs.MotifTestsBasic)
BUILDSTDERR: Test if Bio.motifs can parse and output Cluster Buster PFM files. ... ok
BUILDSTDERR: test_format (test_motifs.MotifTestsBasic) ... ok
BUILDSTDERR: test_pfm_parsing (test_motifs.MotifTestsBasic)
BUILDSTDERR: Test if Bio.motifs can parse JASPAR-style pfm files. ... ok
BUILDSTDERR: test_sites_parsing (test_motifs.MotifTestsBasic)
BUILDSTDERR: Test if Bio.motifs can parse JASPAR-style sites files. ... ok
BUILDSTDERR: test_xms_parsing (test_motifs.MotifTestsBasic)
BUILDSTDERR: Test if Bio.motifs can parse and output xms PFM files. ... ok
BUILDSTDERR: test_mast_parser_1 (test_motifs.TestMAST)
BUILDSTDERR: Parse motifs/mast.crp0.de.oops.txt.xml file. ... ok
BUILDSTDERR: test_mast_parser_2 (test_motifs.TestMAST)
BUILDSTDERR: Parse motifs/mast.adh.de.oops.html.xml file. ... ok
BUILDSTDERR: test_mast_parser_3 (test_motifs.TestMAST)
BUILDSTDERR: Parse motifs/mast.Klf1-200.cd.oops.xml.xml file. ... ok
BUILDSTDERR: test_meme_parser_1 (test_motifs.TestMEME)
BUILDSTDERR: Parsing motifs/meme.out file. ... ok
BUILDSTDERR: test_meme_parser_2 (test_motifs.TestMEME)
BUILDSTDERR: Parse motifs/meme.dna.oops.txt file. ... ok
BUILDSTDERR: test_meme_parser_3 (test_motifs.TestMEME)
BUILDSTDERR: Parse motifs/meme.protein.oops.txt file. ... ok
BUILDSTDERR: test_meme_parser_4 (test_motifs.TestMEME)
BUILDSTDERR: Parse motifs/meme.protein.tcm.txt file. ... ok
BUILDSTDERR: test_meme_parser_4_11_4 (test_motifs.TestMEME)
BUILDSTDERR: Parse motifs/meme_v_4_11_4.txt file. ... ok
BUILDSTDERR: test_meme_parser_rna (test_motifs.TestMEME)
BUILDSTDERR: Test if Bio.motifs can parse MEME output files using RNA. ... ok
BUILDSTDERR: test_minimal_meme_parser (test_motifs.TestMEME)
BUILDSTDERR: Parse motifs/minimal_test.meme file. ... ok
BUILDSTDERR: test_permissive_transfac_parser (test_motifs.TestTransfac)
BUILDSTDERR: Parse the TRANSFAC-like file motifs/MA0056.1.transfac. ... ok
BUILDSTDERR: test_transfac_parser (test_motifs.TestTransfac)
BUILDSTDERR: Parse motifs/transfac.dat file. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 12.286 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_motifs_online.py
BUILDSTDERR: test_motifs_online ... skipping. internet not available
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 4.907 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2.py
BUILDSTDERR: test_pairwise2 ... ok
BUILDSTDERR: test_clean_alignments (pairwise2_testCases.TestOtherFunctions)
BUILDSTDERR: ``_clean_alignments`` removes redundant and wrong alignments. ... ok
BUILDSTDERR: test_print_matrix (pairwise2_testCases.TestOtherFunctions)
BUILDSTDERR: ``print_matrix`` prints nested lists as nice matrices. ... ok
BUILDSTDERR: test_recover_alignments (pairwise2_testCases.TestOtherFunctions)
BUILDSTDERR: One possible start position in local alignment is not a match. ... ok
BUILDSTDERR: test_function_name (pairwise2_testCases.TestPairwiseErrorConditions)
BUILDSTDERR: Test for wrong function names. ... ok
BUILDSTDERR: test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions)
BUILDSTDERR: Test for number of parameters. ... ok
BUILDSTDERR: test_param_names (pairwise2_testCases.TestPairwiseErrorConditions)
BUILDSTDERR: Test for unknown parameter in parameter names. ... ok
BUILDSTDERR: test_warnings (pairwise2_testCases.TestPairwiseErrorConditions)
BUILDSTDERR: Test for warnings. ... ok
BUILDSTDERR: test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty)
BUILDSTDERR: Test 1. ... ok
BUILDSTDERR: test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty)
BUILDSTDERR: Test 2. ... ok
BUILDSTDERR: test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal)
BUILDSTDERR: Test globalxx. ... ok
BUILDSTDERR: test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal)
BUILDSTDERR: Do the same test with sequence order reversed. ... ok
BUILDSTDERR: test_list_input (pairwise2_testCases.TestPairwiseGlobal)
BUILDSTDERR: Do a global aligment with sequences supplied as lists. ... ok
BUILDSTDERR: test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal)
BUILDSTDERR: Test one_alignment_only parameter. ... ok
BUILDSTDERR: test_blosum62 (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Test localds with blosum62. ... ok
BUILDSTDERR: test_empty_result (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Return no alignment. ... ok
BUILDSTDERR: test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Test if alignment is independent on direction of sequence. ... ok
BUILDSTDERR: test_localms (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Two different local alignments. ... ok
BUILDSTDERR: test_localxs (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Test localxx. ... ok
BUILDSTDERR: test_localxs_generic (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Test the generic method with local alignments. ... ok
BUILDSTDERR: test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary)
BUILDSTDERR: Test 1. ... ok
BUILDSTDERR: test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary)
BUILDSTDERR: Test 2. ... ok
BUILDSTDERR: test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary)
BUILDSTDERR: Test 3. ... ok
BUILDSTDERR: test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter)
BUILDSTDERR: Test sequence with only one match. ... ok
BUILDSTDERR: test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter)
BUILDSTDERR: Test sequences with two possible match positions. ... ok
BUILDSTDERR: test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter)
BUILDSTDERR: Like test 1, but global alignment. ... ok
BUILDSTDERR: test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty)
BUILDSTDERR: Test 1. ... ok
BUILDSTDERR: test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty)
BUILDSTDERR: Test 2. ... ok
BUILDSTDERR: test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty)
BUILDSTDERR: Test 3. ... ok
BUILDSTDERR: test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty)
BUILDSTDERR: Test 4. ... ok
BUILDSTDERR: test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps)
BUILDSTDERR: Turn off end-gap penalties. ... ok
BUILDSTDERR: test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps)
BUILDSTDERR: Do the same, but use the generic method (with the same result). ... ok
BUILDSTDERR: test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps)
BUILDSTDERR: Test alignment where end-gaps are differently penalized. ... ok
BUILDSTDERR: test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening)
BUILDSTDERR: Add gap-extend penalty to gap-opening penalty. ... ok
BUILDSTDERR: test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties)
BUILDSTDERR: Test 1. ... ok
BUILDSTDERR: test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties)
BUILDSTDERR: Test 2. ... ok
BUILDSTDERR: test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension)
BUILDSTDERR: Test separate gap-extension penalties and list input. ... ok
BUILDSTDERR: test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties)
BUILDSTDERR: Open a gap in second sequence only. ... ok
BUILDSTDERR: test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties)
BUILDSTDERR: Force a bad alignment. ... ok
BUILDSTDERR: test_score_only_global (pairwise2_testCases.TestScoreOnly)
BUILDSTDERR: Test ``score_only`` in a global alignment. ... ok
BUILDSTDERR: test_score_only_local (pairwise2_testCases.TestScoreOnly)
BUILDSTDERR: Test ``score_only`` in a local alignment. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7.441 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2_no_C.py
BUILDSTDERR: test_pairwise2_no_C ... ok
BUILDSTDERR: test_clean_alignments (pairwise2_testCases.TestOtherFunctions)
BUILDSTDERR: ``_clean_alignments`` removes redundant and wrong alignments. ... ok
BUILDSTDERR: test_print_matrix (pairwise2_testCases.TestOtherFunctions)
BUILDSTDERR: ``print_matrix`` prints nested lists as nice matrices. ... ok
BUILDSTDERR: test_recover_alignments (pairwise2_testCases.TestOtherFunctions)
BUILDSTDERR: One possible start position in local alignment is not a match. ... ok
BUILDSTDERR: test_function_name (pairwise2_testCases.TestPairwiseErrorConditions)
BUILDSTDERR: Test for wrong function names. ... ok
BUILDSTDERR: test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions)
BUILDSTDERR: Test for number of parameters. ... ok
BUILDSTDERR: test_param_names (pairwise2_testCases.TestPairwiseErrorConditions)
BUILDSTDERR: Test for unknown parameter in parameter names. ... ok
BUILDSTDERR: test_warnings (pairwise2_testCases.TestPairwiseErrorConditions)
BUILDSTDERR: Test for warnings. ... ok
BUILDSTDERR: test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty)
BUILDSTDERR: Test 1. ... ok
BUILDSTDERR: test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty)
BUILDSTDERR: Test 2. ... ok
BUILDSTDERR: test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal)
BUILDSTDERR: Test globalxx. ... ok
BUILDSTDERR: test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal)
BUILDSTDERR: Do the same test with sequence order reversed. ... ok
BUILDSTDERR: test_list_input (pairwise2_testCases.TestPairwiseGlobal)
BUILDSTDERR: Do a global aligment with sequences supplied as lists. ... ok
BUILDSTDERR: test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal)
BUILDSTDERR: Test one_alignment_only parameter. ... ok
BUILDSTDERR: test_blosum62 (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Test localds with blosum62. ... ok
BUILDSTDERR: test_empty_result (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Return no alignment. ... ok
BUILDSTDERR: test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Test if alignment is independent on direction of sequence. ... ok
BUILDSTDERR: test_localms (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Two different local alignments. ... ok
BUILDSTDERR: test_localxs (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Test localxx. ... ok
BUILDSTDERR: test_localxs_generic (pairwise2_testCases.TestPairwiseLocal)
BUILDSTDERR: Test the generic method with local alignments. ... ok
BUILDSTDERR: test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary)
BUILDSTDERR: Test 1. ... ok
BUILDSTDERR: test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary)
BUILDSTDERR: Test 2. ... ok
BUILDSTDERR: test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary)
BUILDSTDERR: Test 3. ... ok
BUILDSTDERR: test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter)
BUILDSTDERR: Test sequence with only one match. ... ok
BUILDSTDERR: test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter)
BUILDSTDERR: Test sequences with two possible match positions. ... ok
BUILDSTDERR: test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter)
BUILDSTDERR: Like test 1, but global alignment. ... ok
BUILDSTDERR: test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty)
BUILDSTDERR: Test 1. ... ok
BUILDSTDERR: test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty)
BUILDSTDERR: Test 2. ... ok
BUILDSTDERR: test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty)
BUILDSTDERR: Test 3. ... ok
BUILDSTDERR: test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty)
BUILDSTDERR: Test 4. ... ok
BUILDSTDERR: test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps)
BUILDSTDERR: Turn off end-gap penalties. ... ok
BUILDSTDERR: test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps)
BUILDSTDERR: Do the same, but use the generic method (with the same result). ... ok
BUILDSTDERR: test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps)
BUILDSTDERR: Test alignment where end-gaps are differently penalized. ... ok
BUILDSTDERR: test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening)
BUILDSTDERR: Add gap-extend penalty to gap-opening penalty. ... ok
BUILDSTDERR: test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties)
BUILDSTDERR: Test 1. ... ok
BUILDSTDERR: test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties)
BUILDSTDERR: Test 2. ... ok
BUILDSTDERR: test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension)
BUILDSTDERR: Test separate gap-extension penalties and list input. ... ok
BUILDSTDERR: test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties)
BUILDSTDERR: Open a gap in second sequence only. ... ok
BUILDSTDERR: test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties)
BUILDSTDERR: Force a bad alignment. ... ok
BUILDSTDERR: test_score_only_global (pairwise2_testCases.TestScoreOnly)
BUILDSTDERR: Test ``score_only`` in a global alignment. ... ok
BUILDSTDERR: test_score_only_local (pairwise2_testCases.TestScoreOnly)
BUILDSTDERR: Test ``score_only`` in a local alignment. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 7.591 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise_aligner.py
BUILDSTDERR: test_pairwise_aligner ... ok
BUILDSTDERR: test_aligner_nonexisting_property (test_pairwise_aligner.TestAlignerProperties) ... ok
BUILDSTDERR: test_aligner_property_epsilon (test_pairwise_aligner.TestAlignerProperties) ... ok
BUILDSTDERR: test_aligner_property_gapscores (test_pairwise_aligner.TestAlignerProperties) ... ok
BUILDSTDERR: test_aligner_property_match_mismatch (test_pairwise_aligner.TestAlignerProperties) ... ok
BUILDSTDERR: test_aligner_property_mode (test_pairwise_aligner.TestAlignerProperties) ... ok
BUILDSTDERR: test_extend_penalty1 (test_pairwise_aligner.TestPairwiseExtendPenalty) ... ok
BUILDSTDERR: test_extend_penalty2 (test_pairwise_aligner.TestPairwiseExtendPenalty) ... ok
BUILDSTDERR: test_align_affine1_score (test_pairwise_aligner.TestPairwiseGlobal) ... ok
BUILDSTDERR: test_needlemanwunsch_simple1 (test_pairwise_aligner.TestPairwiseGlobal) ... ok
BUILDSTDERR: test_gotoh_local (test_pairwise_aligner.TestPairwiseLocal) ... ok
BUILDSTDERR: test_smithwaterman (test_pairwise_aligner.TestPairwiseLocal) ... ok
BUILDSTDERR: test_match_dictionary1 (test_pairwise_aligner.TestPairwiseMatchDictionary) ... ok
BUILDSTDERR: test_match_dictionary2 (test_pairwise_aligner.TestPairwiseMatchDictionary) ... ok
BUILDSTDERR: test_match_dictionary3 (test_pairwise_aligner.TestPairwiseMatchDictionary) ... ok
BUILDSTDERR: test_align_one_char1 (test_pairwise_aligner.TestPairwiseOneCharacter) ... ok
BUILDSTDERR: test_align_one_char2 (test_pairwise_aligner.TestPairwiseOneCharacter) ... ok
BUILDSTDERR: test_align_one_char3 (test_pairwise_aligner.TestPairwiseOneCharacter) ... ok
BUILDSTDERR: test_align_one_char_score3 (test_pairwise_aligner.TestPairwiseOneCharacter) ... ok
BUILDSTDERR: test_match_score_open_penalty1 (test_pairwise_aligner.TestPairwiseOpenPenalty) ... ok
BUILDSTDERR: test_match_score_open_penalty2 (test_pairwise_aligner.TestPairwiseOpenPenalty) ... ok
BUILDSTDERR: test_match_score_open_penalty3 (test_pairwise_aligner.TestPairwiseOpenPenalty) ... ok
BUILDSTDERR: test_match_score_open_penalty4 (test_pairwise_aligner.TestPairwiseOpenPenalty) ... ok
BUILDSTDERR: test_penalize_end_gaps (test_pairwise_aligner.TestPairwisePenalizeEndgaps) ... ok
BUILDSTDERR: test_penalize_extend_when_opening (test_pairwise_aligner.TestPairwisePenalizeExtendWhenOpening) ... ok
BUILDSTDERR: test_separate_gap_penalties1 (test_pairwise_aligner.TestPairwiseSeparateGapPenalties) ... ok
BUILDSTDERR: test_separate_gap_penalties2 (test_pairwise_aligner.TestPairwiseSeparateGapPenalties) ... ok
BUILDSTDERR: test_separate_gap_penalties_with_extension (test_pairwise_aligner.TestPairwiseSeparateGapPenaltiesWithExtension) ... ok
BUILDSTDERR: test_broken_gap_function (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
BUILDSTDERR: test_gap_here_only_1 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
BUILDSTDERR: test_gap_here_only_2 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
BUILDSTDERR: test_gap_here_only_3 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
BUILDSTDERR: test_gap_here_only_local_1 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
BUILDSTDERR: test_gap_here_only_local_2 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
BUILDSTDERR: test_gap_here_only_local_3 (test_pairwise_aligner.TestPerSiteGapPenalties) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 19.202 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype.py
BUILDSTDERR: test_phenotype ... ok
BUILDSTDERR: test_PlateRecord (test_phenotype.TestPhenoMicro)
BUILDSTDERR: Test basic functionalities of PlateRecord objects. ... ok
BUILDSTDERR: test_PlateRecord_errors (test_phenotype.TestPhenoMicro)
BUILDSTDERR: Test bad arguments with PlateRecord objects. ... ok
BUILDSTDERR: test_WellRecord (test_phenotype.TestPhenoMicro)
BUILDSTDERR: Test basic functionalities of WellRecord objects. ... ok
BUILDSTDERR: test_bad_fit_args (test_phenotype.TestPhenoMicro)
BUILDSTDERR: Test error handling of the fit method. ... ok
BUILDSTDERR: test_phenotype_IO (test_phenotype.TestPhenoMicro)
BUILDSTDERR: Test basic functionalities of phenotype IO methods. ... ok
BUILDSTDERR: test_phenotype_IO_errors (test_phenotype.TestPhenoMicro)
BUILDSTDERR: Test bad arguments to phenotype IO methods. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 660.179 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype_fit.py
BUILDSTDERR: test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.176 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phyml_tool.py
BUILDSTDERR: test_phyml_tool ... skipping. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 6.475 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prodoc.py
BUILDSTDERR: test_prodoc ... ok
BUILDSTDERR: test_parse_pdoc (test_prodoc.TestProdocParse)
BUILDSTDERR: Parsing an excerpt of prosite.doc. ... ok
BUILDSTDERR: test_read_pdoc00100 (test_prodoc.TestProdocRead)
BUILDSTDERR: Reading Prodoc record PDOC00100. ... ok
BUILDSTDERR: test_read_pdoc00113 (test_prodoc.TestProdocRead)
BUILDSTDERR: Reading Prodoc record PDOC00113. ... ok
BUILDSTDERR: test_read_pdoc00144 (test_prodoc.TestProdocRead)
BUILDSTDERR: Reading Prodoc record PDOC00144. ... ok
BUILDSTDERR: test_read_pdoc00149 (test_prodoc.TestProdocRead)
BUILDSTDERR: Reading Prodoc record PDOC00149. ... ok
BUILDSTDERR: test_read_pdoc00340 (test_prodoc.TestProdocRead)
BUILDSTDERR: Reading Prodoc record PDOC00340. ... ok
BUILDSTDERR: test_read_pdoc00424 (test_prodoc.TestProdocRead)
BUILDSTDERR: Reading Prodoc record PDOC00424. ... ok
BUILDSTDERR: test_read_pdoc00472 (test_prodoc.TestProdocRead)
BUILDSTDERR: Reading Prodoc record PDOC00472. ... ok
BUILDSTDERR: test_read_pdoc00640 (test_prodoc.TestProdocRead)
BUILDSTDERR: Reading Prodoc record PDOC00640. ... ok
BUILDSTDERR: test_read_pdoc00787 (test_prodoc.TestProdocRead)
BUILDSTDERR: Reading Prodoc record PDOC00787. ... ok
BUILDSTDERR: test_read_pdoc0933 (test_prodoc.TestProdocRead)
BUILDSTDERR: Reading Prodoc record PDOC00933. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.640 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prosite1.py
BUILDSTDERR: test_prosite1 ... ok
BUILDSTDERR: test_read1 (test_prosite1.TestPrositeRead)
BUILDSTDERR: Parsing Prosite record ps00107.txt. ... ok
BUILDSTDERR: test_read2 (test_prosite1.TestPrositeRead)
BUILDSTDERR: Parsing Prosite record ps00159.txt. ... ok
BUILDSTDERR: test_read3 (test_prosite1.TestPrositeRead)
BUILDSTDERR: Parsing Prosite record ps00165.txt. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 3.111 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prosite2.py
BUILDSTDERR: test_prosite2 ... ok
BUILDSTDERR: test_read4 (test_prosite2.TestPrositeRead)
BUILDSTDERR: Parsing Prosite record ps00432.txt. ... ok
BUILDSTDERR: test_read5 (test_prosite2.TestPrositeRead)
BUILDSTDERR: Parsing Prosite record ps00488.txt. ... ok
BUILDSTDERR: test_read6 (test_prosite2.TestPrositeRead)
BUILDSTDERR: Parsing Prosite record ps00546.txt. ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 1.359 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_psw.py
BUILDSTDERR: test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.223 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_raxml_tool.py
BUILDSTDERR: test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper.
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 8.116 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_samtools_tool.py
BUILDSTDERR: test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program
BUILDSTDERR:         if you want to use it from Biopython
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 0.881 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_seq.py
BUILDSTDERR: test_seq ... ok
BUILDSTDERR: test_ambiguous_values (test_seq.TestAmbiguousComplements)
BUILDSTDERR: Test that other tests do not introduce characters to our values. ... ok
BUILDSTDERR: test_complement_ambiguous_dna_values (test_seq.TestComplement) ... ok
BUILDSTDERR: test_complement_ambiguous_rna_values (test_seq.TestComplement) ... ok
BUILDSTDERR: test_complement_incompatible_alphabets (test_seq.TestComplement) ... ok
BUILDSTDERR: test_complement_of_dna (test_seq.TestComplement) ... ok
BUILDSTDERR: test_complement_of_mixed_dna_rna (test_seq.TestComplement) ... ok
BUILDSTDERR: test_complement_of_rna (test_seq.TestComplement) ... ok
BUILDSTDERR: test_complement_on_proteins (test_seq.TestComplement)
BUILDSTDERR: Check complement fails on a protein. ... ok
BUILDSTDERR: test_reverse_complements (test_seq.TestDoubleReverseComplement)
BUILDSTDERR: Test double reverse complement preserves the sequence. ... ok
BUILDSTDERR: test_add_method (test_seq.TestMutableSeq)
BUILDSTDERR: Test adding wrong type to MutableSeq. ... ok
BUILDSTDERR: test_appending (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_as_string (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_complement (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_complement_dna_string (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_complement_mixed_aphabets (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_complement_rna (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_complement_rna_string (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_converting_to_immutable (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_count (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_delete_stride_slice (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_deleting_item (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_deleting_slice (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_equal_comparison (test_seq.TestMutableSeq)
BUILDSTDERR: Test __eq__ comparison method. ... ok
BUILDSTDERR: test_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_extend_method (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_extend_with_mutable_seq (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_extract_third_nucleotide (test_seq.TestMutableSeq)
BUILDSTDERR: Test extracting every third nucleotide (slicing with stride 3). ... ok
BUILDSTDERR: test_first_nucleotide (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_greater_than_comparison (test_seq.TestMutableSeq)
BUILDSTDERR: Test __gt__ comparison method. ... ok
BUILDSTDERR: test_greater_than_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_greater_than_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_greater_than_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_greater_than_or_equal_comparison (test_seq.TestMutableSeq)
BUILDSTDERR: Test __ge__ comparison method. ... ok
BUILDSTDERR: test_greater_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_greater_than_or_equal_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_index (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_inserting (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_length (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_less_than_comparison (test_seq.TestMutableSeq)
BUILDSTDERR: Test __lt__ comparison method. ... ok
BUILDSTDERR: test_less_than_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_less_than_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_less_than_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_less_than_or_equal_comparison (test_seq.TestMutableSeq)
BUILDSTDERR: Test __le__ comparison method. ... ok
BUILDSTDERR: test_less_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_less_than_or_equal_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_mutableseq_creation (test_seq.TestMutableSeq)
BUILDSTDERR: Test creating MutableSeqs in multiple ways. ... ok
BUILDSTDERR: test_not_equal_comparison (test_seq.TestMutableSeq)
BUILDSTDERR: Test __ne__ comparison method. ... ok
BUILDSTDERR: test_popping_last_item (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_radd_method (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_radd_method_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_radd_method_using_seq_object (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_radd_method_wrong_type (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_remove_items (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_repr (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_reverse (test_seq.TestMutableSeq)
BUILDSTDERR: Test using reverse method. ... ok
BUILDSTDERR: test_reverse_complement (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_reverse_complement_of_protein (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_reverse_with_stride (test_seq.TestMutableSeq)
BUILDSTDERR: Test reverse using -1 stride. ... ok
BUILDSTDERR: test_set_wobble_codon_to_n (test_seq.TestMutableSeq)
BUILDSTDERR: Test setting wobble codon to N (set slice with stride 3). ... ok
BUILDSTDERR: test_setting_item (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_setting_slices (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_truncated_repr (test_seq.TestMutableSeq) ... ok
BUILDSTDERR: test_reverse_complement (test_seq.TestReverseComplement) ... ok
BUILDSTDERR: test_reverse_complement_of_dna (test_seq.TestReverseComplement) ... ok
BUILDSTDERR: test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement) ... ok
BUILDSTDERR: test_reverse_complement_of_rna (test_seq.TestReverseComplement) ... ok
BUILDSTDERR: test_reverse_complement_on_proteins (test_seq.TestReverseComplement)
BUILDSTDERR: Check reverse complement fails on a protein. ... ok
BUILDSTDERR: test_alphabet (test_seq.TestSeq)
BUILDSTDERR: Test alphabet of derived Seq object. ... ok
BUILDSTDERR: test_alphabet_letters (test_seq.TestSeq)
BUILDSTDERR: Test nucleotides in DNA Seq. ... ok
BUILDSTDERR: test_as_string (test_seq.TestSeq)
BUILDSTDERR: Test converting Seq to string. ... ok
BUILDSTDERR: test_concatenation_error (test_seq.TestSeq)
BUILDSTDERR: DNA Seq objects cannot be concatenated with Protein Seq objects. ... ok
BUILDSTDERR: test_concatenation_of_ambiguous_and_unambiguous_dna (test_seq.TestSeq)
BUILDSTDERR: Concatenate Seq object with ambiguous and unambiguous DNA returns ambiguous Seq. ... ok
BUILDSTDERR: test_concatenation_of_seq (test_seq.TestSeq) ... ok
BUILDSTDERR: test_construction_using_a_seq_object (test_seq.TestSeq)
BUILDSTDERR: Test using a Seq object to initialize another Seq object. ... ok
BUILDSTDERR: test_extract_third_nucleotide (test_seq.TestSeq)
BUILDSTDERR: Test extracting every third nucleotide (slicing with stride 3). ... ok
BUILDSTDERR: test_first_nucleotide (test_seq.TestSeq)
BUILDSTDERR: Test getting first nucleotide of Seq. ... ok
BUILDSTDERR: test_last_nucleotide (test_seq.TestSeq)
BUILDSTDERR: Test getting last nucleotide of Seq. ... ok
BUILDSTDERR: test_length (test_seq.TestSeq)
BUILDSTDERR: Test len method on Seq object. ... ok
BUILDSTDERR: test_length_concatenated_unambiguous_seq (test_seq.TestSeq)
BUILDSTDERR: Test length of concatenated Seq object with unambiguous DNA. ... ok
BUILDSTDERR: test_repr (test_seq.TestSeq)
BUILDSTDERR: Test representation of Seq object. ... ok
BUILDSTDERR: test_reverse (test_seq.TestSeq)
BUILDSTDERR: Test reverse using -1 stride. ... ok
BUILDSTDERR: test_slicing (test_seq.TestSeq)
BUILDSTDERR: Test slicing of Seq. ... ok
BUILDSTDERR: test_truncated_repr (test_seq.TestSeq) ... ok
BUILDSTDERR: test_ungap (test_seq.TestSeq) ... ok
BUILDSTDERR: test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_adding_generic_nucleotide_with_other_nucleotides_inplace (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_addition_dna_rna_with_generic_nucleotides_inplace (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_addition_dna_with_dna (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_addition_dna_with_dna_inplace (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_addition_dna_with_rna (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_addition_proteins (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_addition_proteins_inplace (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_addition_rna_with_rna (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_addition_rna_with_rna_inplace (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_exception_when_added_protein_has_more_than_one_gap_type (test_seq.TestSeqAddition)
BUILDSTDERR: Test resulting protein has gap types '-' and '.'. ... ok
BUILDSTDERR: test_exception_when_added_protein_has_several_stop_codon_types (test_seq.TestSeqAddition)
BUILDSTDERR: Test resulting protein has stop codon types '*' and '@'. ... ok
BUILDSTDERR: test_exception_when_added_rna_has_more_than_one_gap_type (test_seq.TestSeqAddition)
BUILDSTDERR: Test resulting sequence has gap types '-' and '.'. ... ok
BUILDSTDERR: test_exception_when_adding_protein_with_nucleotides (test_seq.TestSeqAddition) ... ok
BUILDSTDERR: test_imul_method (test_seq.TestSeqMultiplication)
BUILDSTDERR: Test imul method; relies on addition and mull methods. ... ok
BUILDSTDERR: test_imul_method_exceptions (test_seq.TestSeqMultiplication)
BUILDSTDERR: Test imul method exceptions. ... ok
BUILDSTDERR: test_mul_method (test_seq.TestSeqMultiplication)
BUILDSTDERR: Test mul method; relies on addition method. ... ok
BUILDSTDERR: test_mul_method_exceptions (test_seq.TestSeqMultiplication)
BUILDSTDERR: Test mul method exceptions. ... ok
BUILDSTDERR: test_rmul_method (test_seq.TestSeqMultiplication)
BUILDSTDERR: Test rmul method; relies on addition method. ... ok
BUILDSTDERR: test_rmul_method_exceptions (test_seq.TestSeqMultiplication)
BUILDSTDERR: Test rmul method exceptions. ... ok
BUILDSTDERR: test_add_method_using_wrong_object (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_append_nucleotides (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_append_proteins (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_contains_method (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_counting_characters (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_endswith (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test __eq__ comparison method. ... ok
BUILDSTDERR: test_exception_when_clashing_alphabets (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test by setting up clashing alphabet sequences. ... ok
BUILDSTDERR: test_finding_characters (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_greater_than_comparison (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test __gt__ comparison method. ... ok
BUILDSTDERR: test_greater_than_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test incompatible alphabet __gt__ comparison method. ... ok
BUILDSTDERR: test_greater_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test incompatible types __gt__ comparison method. ... ok
BUILDSTDERR: test_greater_than_or_equal_comparison (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test __ge__ comparison method. ... ok
BUILDSTDERR: test_greater_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test incompatible alphabet __ge__ comparison method. ... ok
BUILDSTDERR: test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test incompatible types __ge__ comparison method. ... ok
BUILDSTDERR: test_hash (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_less_than_comparison (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test __lt__ comparison method. ... ok
BUILDSTDERR: test_less_than_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test incompatible alphabet __lt__ comparison method. ... ok
BUILDSTDERR: test_less_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test incompatible types __lt__ comparison method. ... ok
BUILDSTDERR: test_less_than_or_equal_comparison (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test __le__ comparison method. ... ok
BUILDSTDERR: test_less_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test incompatible alphabet __le__ comparison method. ... ok
BUILDSTDERR: test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test incompatible types __le__ comparison method. ... ok
BUILDSTDERR: test_not_equal_comparsion (test_seq.TestSeqStringMethods)
BUILDSTDERR: Test __ne__ comparison method. ... ok
BUILDSTDERR: test_radd_method (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_radd_method_using_incompatible_alphabets (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_splits (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_startswith (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_string_methods (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_stripping_characters (test_seq.TestSeqStringMethods) ... ok
BUILDSTDERR: test_sequence_alphabets (test_seq.TestSequenceAlphabets)
BUILDSTDERR: Sanity test on the test sequence alphabets. ... ok
BUILDSTDERR: test_stops (test_seq.TestStopCodons) ... ok
BUILDSTDERR: test_translation_of_stops (test_seq.TestStopCodons) ... ok
BUILDSTDERR: test_back_transcribe_rna_into_dna (test_seq.TestTranscription) ... ok
BUILDSTDERR: test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription) ... ok
BUILDSTDERR: test_back_transcription_of_dna (test_seq.TestTranscription)
BUILDSTDERR: Check back-transcription fails on DNA. ... ok
BUILDSTDERR: test_back_transcription_of_proteins (test_seq.TestTranscription)
BUILDSTDERR: Check back-transcription fails on a protein. ... ok
BUILDSTDERR: test_seq_object_back_transcription_method (test_seq.TestTranscription) ... ok
BUILDSTDERR: test_seq_object_transcription_method (test_seq.TestTranscription) ... ok
BUILDSTDERR: test_transcription_dna_into_rna (test_seq.TestTranscription) ... ok
BUILDSTDERR: test_transcription_dna_string_into_rna (test_seq.TestTranscription) ... ok
BUILDSTDERR: test_transcription_of_proteins (test_seq.TestTranscription)
BUILDSTDERR: Check transcription fails on a protein. ... ok
BUILDSTDERR: test_transcription_of_rna (test_seq.TestTranscription)
BUILDSTDERR: Check transcription fails on RNA. ... ok
BUILDSTDERR: test_alphabet_of_translated_gapped_seq (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_alphabets_of_translated_seqs (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_gapped_seq_no_gap_char_given (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_gapped_seq_no_gap_char_given_and_inferred_from_alphabet (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_gapped_seq_with_gap_char_given (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_gapped_seq_with_gap_char_given_and_inferred_from_alphabet (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_gapped_seq_with_gap_char_given_and_inferred_from_alphabet2 (test_seq.TestTranslating)
BUILDSTDERR: Test using stop codon in sequence. ... ok
BUILDSTDERR: test_gapped_seq_with_stop_codon_and_gap_char_given (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_extra_stop_codon (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_incomplete_codon (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_of_asparagine (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_of_gapped_string_no_gap_char_given (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_of_gapped_string_with_gap_char_given (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_of_glutamine (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_of_invalid_codon (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_of_leucine (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_of_string (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_on_proteins (test_seq.TestTranslating)
BUILDSTDERR: Check translation fails on a protein. ... ok
BUILDSTDERR: test_translation_to_stop (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_using_cds (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_using_tables_with_ambiguous_stop_codons (test_seq.TestTranslating)
BUILDSTDERR: Check for error and warning messages. ... ok
BUILDSTDERR: test_translation_with_bad_table_argument (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating) ... ok
BUILDSTDERR: test_translation_wrong_type (test_seq.TestTranslating)
BUILDSTDERR: Test translation table cannot be CodonTable. ... ok
BUILDSTDERR: test_add_method (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_back_transcribe (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_complement (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_complement_of_protein (test_seq.TestUnknownSeq)
BUILDSTDERR: Check reverse complement fails on a protein. ... ok
BUILDSTDERR: test_construction (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_count (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_getitem_method (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_length (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_lower (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_repr (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_reverse_complement (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_reverse_complement_of_protein (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_transcribe (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_translation (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_translation_of_proteins (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_ungap (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: test_upper (test_seq.TestUnknownSeq) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 10.945 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_translate.py
BUILDSTDERR: test_translate ... ok
BUILDSTDERR: test_ambiguous (test_translate.TestTranscriptionTranslation) ... ok
BUILDSTDERR: test_dna_rna_translation (test_translate.TestTranscriptionTranslation) ... ok
BUILDSTDERR: test_transcription (test_translate.TestTranscriptionTranslation) ... ok
BUILDSTDERR: test_translation (test_translate.TestTranscriptionTranslation) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 4.988 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/lib64/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_trie.py
C
BUILDSTDERR: test_trie ... ok
BUILDSTDERR: test_get_approximate (test_trie.TestTrie) ... ok
BUILDSTDERR: test_get_set (test_trie.TestTrie) ... ok
BUILDSTDERR: test_large_save_load (test_trie.TestTrie)
BUILDSTDERR: Generate random key/val pairs in three length categories. ... ok
BUILDSTDERR: test_prefix (test_trie.TestTrie) ... ok
BUILDSTDERR: test_save (test_trie.TestTrie) ... ok
BUILDSTDERR: test_with_prefix (test_trie.TestTrie) ... ok
BUILDSTDERR: test_find (test_trie.TestTrieFind) ... ok
BUILDSTDERR: ----------------------------------------------------------------------
BUILDSTDERR: Ran 1 test in 4054.085 seconds
Skipping any tests requiring internet access
Python version: 3.7.4 (default, Aug  8 2019, 06:37:05) 
[GCC 9.1.1 20190605 (Red Hat 9.1.1-2)]
Operating system: posix linux
+ popd
~/build/BUILD/python-biopython-1.74
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Processing files: python3-biopython-1.74-1.fc31.riscv64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.o3ASKr
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.74
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/doc/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/doc/python3-biopython
+ cp -pr python3/Scripts /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/doc/python3-biopython
+ cp -pr python3/CONTRIB.rst /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/doc/python3-biopython
+ cp -pr python3/DEPRECATED.rst /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/doc/python3-biopython
+ cp -pr python3/NEWS.rst /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/doc/python3-biopython
+ cp -pr python3/README.rst /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/doc/python3-biopython
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.4ichzr
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.74
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/licenses/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/licenses/python3-biopython
+ cp -pr python3/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/licenses/python3-biopython
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Provides: python-biopython = 1.74-1.fc31 python3-biopython = 1.74-1.fc31 python3-biopython(riscv-64) = 1.74-1.fc31 python3.7dist(biopython) = 1.74 python3dist(biopython) = 1.74
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libpython3.7m.so.1.0()(64bit) python(abi) = 3.7 python3.7dist(numpy) rtld(GNU_HASH)
Obsoletes: python-biopython < 1.74-1.fc31
Processing files: python-biopython-doc-1.74-1.fc31.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.lxImhq
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.74
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/doc/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/doc/python-biopython-doc
+ cp -pr biopython-1.74/Doc /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/doc/python-biopython-doc
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.hBvbZt
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.74
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/licenses/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/licenses/python-biopython-doc
+ cp -pr biopython-1.74/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64/usr/share/licenses/python-biopython-doc
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Provides: python-biopython-doc = 1.74-1.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-biopython-debugsource-1.74-1.fc31.riscv64
Provides: python-biopython-debugsource = 1.74-1.fc31 python-biopython-debugsource(riscv-64) = 1.74-1.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python3-biopython-debuginfo-1.74-1.fc31.riscv64
Provides: debuginfo(build-id) = 1c448ba5e456ef279dbb7640d9fabaa4a8e6f3b6 debuginfo(build-id) = 20856cdd2d29e1c3989e56bb939402962cf0b452 debuginfo(build-id) = 3c690716bcafb9ba6c2a5ae3d7c75f6e14edccdb debuginfo(build-id) = 70e796f5a09b0f923864d09fb77d62db727cf240 debuginfo(build-id) = 7f457f71376f3e3e97a38f679d49e601c20d7f08 debuginfo(build-id) = 9d3883c182de63f13332c4045ae9250b800e0a28 debuginfo(build-id) = ae7a86d6de0638cd2f1c66c49e0d1282c7a3206f debuginfo(build-id) = cec6bd92f9c5603bb82137b54ce3cd2361bea756 debuginfo(build-id) = e605545311abc3e4b58b91ab6f8d5d8d5a1008af python3-biopython-debuginfo = 1.74-1.fc31 python3-biopython-debuginfo(riscv-64) = 1.74-1.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: python-biopython-debugsource(riscv-64) = 1.74-1.fc31
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64
Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.74-1.fc31.riscv64.rpm
Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.74-1.fc31.riscv64.rpm
Wrote: /builddir/build/RPMS/python-biopython-doc-1.74-1.fc31.noarch.rpm
Wrote: /builddir/build/RPMS/python3-biopython-1.74-1.fc31.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.RDwWUt
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.74
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.74-1.fc31.riscv64
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Child return code was: 0