Mock Version: 1.4.19
Mock Version: 1.4.19
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/f30-build-18107200-1293649/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': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0xb5c128b0>timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --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': 'C.UTF-8'} and shell False
Building target platforms: armv7hl
Building for target armv7hl
Wrote: /builddir/build/SRPMS/python-biopython-1.75-2.fc30.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/f30-build-18107200-1293649/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': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0xb5c128b0>timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target armv7hl --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': 'C.UTF-8'} and shell False
Building target platforms: armv7hl
Building for target armv7hl
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.fUiGoA
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf python-biopython-1.75
+ /usr/bin/mkdir -p python-biopython-1.75
+ cd python-biopython-1.75
+ /usr/bin/gzip -dc /builddir/build/SOURCES/biopython-1.75.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ pushd biopython-1.75
~/build/BUILD/python-biopython-1.75/biopython-1.75 ~/build/BUILD/python-biopython-1.75
+ 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-1.75
+ cp -a biopython-1.75 python3
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.p9qSHI
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.75
~/build/BUILD/python-biopython-1.75/python3 ~/build/BUILD/python-biopython-1.75
+ 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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard'
+ 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-armv7l-3.7
creating build/lib.linux-armv7l-3.7/Bio
copying Bio/bgzf.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/NaiveBayes.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/MaxEntropy.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/MarkovModel.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/File.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/pairwise2.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/SeqFeature.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/Index.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/LogisticRegression.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/Seq.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/_utils.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/SeqRecord.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/__init__.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/kNN.py -> build/lib.linux-armv7l-3.7/Bio
copying Bio/triefind.py -> build/lib.linux-armv7l-3.7/Bio
creating build/lib.linux-armv7l-3.7/Bio/Align
copying Bio/Align/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Align
copying Bio/Align/AlignInfo.py -> build/lib.linux-armv7l-3.7/Bio/Align
creating build/lib.linux-armv7l-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-armv7l-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-armv7l-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-armv7l-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-armv7l-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-armv7l-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-armv7l-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> build/lib.linux-armv7l-3.7/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-armv7l-3.7/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-armv7l-3.7/Bio/Align/Applications
creating build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/MsfIO.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/MauveIO.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/MafIO.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-armv7l-3.7/Bio/AlignIO
creating build/lib.linux-armv7l-3.7/Bio/Alphabet
copying Bio/Alphabet/IUPAC.py -> build/lib.linux-armv7l-3.7/Bio/Alphabet
copying Bio/Alphabet/Reduced.py -> build/lib.linux-armv7l-3.7/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Alphabet
creating build/lib.linux-armv7l-3.7/Bio/Application
copying Bio/Application/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Application
creating build/lib.linux-armv7l-3.7/Bio/Blast
copying Bio/Blast/Applications.py -> build/lib.linux-armv7l-3.7/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-armv7l-3.7/Bio/Blast
copying Bio/Blast/Record.py -> build/lib.linux-armv7l-3.7/Bio/Blast
copying Bio/Blast/NCBIXML.py -> build/lib.linux-armv7l-3.7/Bio/Blast
copying Bio/Blast/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> build/lib.linux-armv7l-3.7/Bio/Blast
creating build/lib.linux-armv7l-3.7/Bio/CAPS
copying Bio/CAPS/__init__.py -> build/lib.linux-armv7l-3.7/Bio/CAPS
creating build/lib.linux-armv7l-3.7/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> build/lib.linux-armv7l-3.7/Bio/codonalign
copying Bio/codonalign/codonseq.py -> build/lib.linux-armv7l-3.7/Bio/codonalign
copying Bio/codonalign/codonalphabet.py -> build/lib.linux-armv7l-3.7/Bio/codonalign
copying Bio/codonalign/__init__.py -> build/lib.linux-armv7l-3.7/Bio/codonalign
copying Bio/codonalign/chisq.py -> build/lib.linux-armv7l-3.7/Bio/codonalign
creating build/lib.linux-armv7l-3.7/Bio/Compass
copying Bio/Compass/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Compass
creating build/lib.linux-armv7l-3.7/Bio/Crystal
copying Bio/Crystal/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Crystal
creating build/lib.linux-armv7l-3.7/Bio/Data
copying Bio/Data/CodonTable.py -> build/lib.linux-armv7l-3.7/Bio/Data
copying Bio/Data/SCOPData.py -> build/lib.linux-armv7l-3.7/Bio/Data
copying Bio/Data/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Data
copying Bio/Data/IUPACData.py -> build/lib.linux-armv7l-3.7/Bio/Data
creating build/lib.linux-armv7l-3.7/Bio/Emboss
copying Bio/Emboss/Applications.py -> build/lib.linux-armv7l-3.7/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-armv7l-3.7/Bio/Emboss
copying Bio/Emboss/Primer3.py -> build/lib.linux-armv7l-3.7/Bio/Emboss
copying Bio/Emboss/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Emboss
creating build/lib.linux-armv7l-3.7/Bio/Entrez
copying Bio/Entrez/Parser.py -> build/lib.linux-armv7l-3.7/Bio/Entrez
copying Bio/Entrez/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Entrez
creating build/lib.linux-armv7l-3.7/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> build/lib.linux-armv7l-3.7/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> build/lib.linux-armv7l-3.7/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-armv7l-3.7/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> build/lib.linux-armv7l-3.7/Bio/ExPASy
copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-armv7l-3.7/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> build/lib.linux-armv7l-3.7/Bio/ExPASy
creating build/lib.linux-armv7l-3.7/Bio/FSSP
copying Bio/FSSP/FSSPTools.py -> build/lib.linux-armv7l-3.7/Bio/FSSP
copying Bio/FSSP/__init__.py -> build/lib.linux-armv7l-3.7/Bio/FSSP
copying Bio/FSSP/fssp_rec.py -> build/lib.linux-armv7l-3.7/Bio/FSSP
creating build/lib.linux-armv7l-3.7/Bio/GenBank
copying Bio/GenBank/utils.py -> build/lib.linux-armv7l-3.7/Bio/GenBank
copying Bio/GenBank/Record.py -> build/lib.linux-armv7l-3.7/Bio/GenBank
copying Bio/GenBank/Scanner.py -> build/lib.linux-armv7l-3.7/Bio/GenBank
copying Bio/GenBank/__init__.py -> build/lib.linux-armv7l-3.7/Bio/GenBank
creating build/lib.linux-armv7l-3.7/Bio/Geo
copying Bio/Geo/Record.py -> build/lib.linux-armv7l-3.7/Bio/Geo
copying Bio/Geo/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Geo
creating build/lib.linux-armv7l-3.7/Bio/Graphics
copying Bio/Graphics/Distribution.py -> build/lib.linux-armv7l-3.7/Bio/Graphics
copying Bio/Graphics/Comparative.py -> build/lib.linux-armv7l-3.7/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-armv7l-3.7/Bio/Graphics
copying Bio/Graphics/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-armv7l-3.7/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-armv7l-3.7/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> build/lib.linux-armv7l-3.7/Bio/Graphics
creating build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram
creating build/lib.linux-armv7l-3.7/Bio/HMM
copying Bio/HMM/MarkovModel.py -> build/lib.linux-armv7l-3.7/Bio/HMM
copying Bio/HMM/Trainer.py -> build/lib.linux-armv7l-3.7/Bio/HMM
copying Bio/HMM/__init__.py -> build/lib.linux-armv7l-3.7/Bio/HMM
copying Bio/HMM/Utilities.py -> build/lib.linux-armv7l-3.7/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-armv7l-3.7/Bio/HMM
creating build/lib.linux-armv7l-3.7/Bio/KEGG
copying Bio/KEGG/REST.py -> build/lib.linux-armv7l-3.7/Bio/KEGG
copying Bio/KEGG/__init__.py -> build/lib.linux-armv7l-3.7/Bio/KEGG
creating build/lib.linux-armv7l-3.7/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-armv7l-3.7/Bio/KEGG/Compound
creating build/lib.linux-armv7l-3.7/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-armv7l-3.7/Bio/KEGG/Enzyme
creating build/lib.linux-armv7l-3.7/Bio/KEGG/Gene
copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-armv7l-3.7/Bio/KEGG/Gene
creating build/lib.linux-armv7l-3.7/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> build/lib.linux-armv7l-3.7/Bio/KEGG/Map
creating build/lib.linux-armv7l-3.7/Bio/PDB
creating build/lib.linux-armv7l-3.7/Bio/PDB/mmtf
copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-armv7l-3.7/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-armv7l-3.7/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-armv7l-3.7/Bio/PDB/mmtf
creating build/lib.linux-armv7l-3.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-armv7l-3.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-armv7l-3.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-armv7l-3.7/Bio/KEGG/KGML
creating build/lib.linux-armv7l-3.7/Bio/Medline
copying Bio/Medline/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Medline
creating build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/pfm.py -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/mast.py -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/thresholds.py -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/minimal.py -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/meme.py -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/matrix.py -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/__init__.py -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/clusterbuster.py -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/alignace.py -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/transfac.py -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/motifs/xms.py -> build/lib.linux-armv7l-3.7/Bio/motifs
creating build/lib.linux-armv7l-3.7/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-armv7l-3.7/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> build/lib.linux-armv7l-3.7/Bio/motifs/applications
creating build/lib.linux-armv7l-3.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-armv7l-3.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> build/lib.linux-armv7l-3.7/Bio/motifs/jaspar
creating build/lib.linux-armv7l-3.7/Bio/Nexus
copying Bio/Nexus/StandardData.py -> build/lib.linux-armv7l-3.7/Bio/Nexus
copying Bio/Nexus/Nodes.py -> build/lib.linux-armv7l-3.7/Bio/Nexus
copying Bio/Nexus/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Nexus
copying Bio/Nexus/Trees.py -> build/lib.linux-armv7l-3.7/Bio/Nexus
copying Bio/Nexus/Nexus.py -> build/lib.linux-armv7l-3.7/Bio/Nexus
creating build/lib.linux-armv7l-3.7/Bio/NMR
copying Bio/NMR/__init__.py -> build/lib.linux-armv7l-3.7/Bio/NMR
copying Bio/NMR/NOEtools.py -> build/lib.linux-armv7l-3.7/Bio/NMR
copying Bio/NMR/xpktools.py -> build/lib.linux-armv7l-3.7/Bio/NMR
creating build/lib.linux-armv7l-3.7/Bio/Pathway
copying Bio/Pathway/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Pathway
creating build/lib.linux-armv7l-3.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-armv7l-3.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-armv7l-3.7/Bio/Pathway/Rep
copying Bio/PDB/PDBExceptions.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/Model.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/mmcifio.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/Structure.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/HSExposure.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/Dice.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/PDBParser.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/Selection.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/Atom.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/NACCESS.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/PDBIO.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/Residue.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/Chain.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/Superimposer.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/__init__.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/PSEA.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/Polypeptide.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/vectors.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/PDBList.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/Entity.py -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/DSSP.py -> build/lib.linux-armv7l-3.7/Bio/PDB
creating build/lib.linux-armv7l-3.7/Bio/PopGen
copying Bio/PopGen/__init__.py -> build/lib.linux-armv7l-3.7/Bio/PopGen
creating build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Utils.py -> build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop
creating build/lib.linux-armv7l-3.7/Bio/Restriction
copying Bio/Restriction/Restriction.py -> build/lib.linux-armv7l-3.7/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-armv7l-3.7/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> build/lib.linux-armv7l-3.7/Bio/Restriction
copying Bio/Restriction/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Restriction
creating build/lib.linux-armv7l-3.7/Bio/SCOP
copying Bio/SCOP/Dom.py -> build/lib.linux-armv7l-3.7/Bio/SCOP
copying Bio/SCOP/Raf.py -> build/lib.linux-armv7l-3.7/Bio/SCOP
copying Bio/SCOP/Des.py -> build/lib.linux-armv7l-3.7/Bio/SCOP
copying Bio/SCOP/Residues.py -> build/lib.linux-armv7l-3.7/Bio/SCOP
copying Bio/SCOP/Cla.py -> build/lib.linux-armv7l-3.7/Bio/SCOP
copying Bio/SCOP/Hie.py -> build/lib.linux-armv7l-3.7/Bio/SCOP
copying Bio/SCOP/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SCOP
creating build/lib.linux-armv7l-3.7/Bio/SearchIO
copying Bio/SearchIO/FastaIO.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO
copying Bio/SearchIO/_index.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO
copying Bio/SearchIO/BlatIO.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO
creating build/lib.linux-armv7l-3.7/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/ParserSupport.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/NCBIStandalone.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/_legacy
creating build/lib.linux-armv7l-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/_base.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/_model
creating build/lib.linux-armv7l-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/BlastIO
creating build/lib.linux-armv7l-3.7/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/HHsuiteIO
creating build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO
creating build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO
creating build/lib.linux-armv7l-3.7/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-armv7l-3.7/Bio/SearchIO/InterproscanIO
creating build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/GckIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/_index.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/_convert.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/NibIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/AceIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-armv7l-3.7/Bio/SeqIO
creating build/lib.linux-armv7l-3.7/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-armv7l-3.7/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-armv7l-3.7/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-armv7l-3.7/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-armv7l-3.7/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> build/lib.linux-armv7l-3.7/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-armv7l-3.7/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-armv7l-3.7/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-armv7l-3.7/Bio/SeqUtils
creating build/lib.linux-armv7l-3.7/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> build/lib.linux-armv7l-3.7/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> build/lib.linux-armv7l-3.7/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Sequencing
creating build/lib.linux-armv7l-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-armv7l-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-armv7l-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-armv7l-3.7/Bio/Sequencing/Applications
creating build/lib.linux-armv7l-3.7/Bio/Statistics
copying Bio/Statistics/lowess.py -> build/lib.linux-armv7l-3.7/Bio/Statistics
copying Bio/Statistics/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Statistics
creating build/lib.linux-armv7l-3.7/Bio/SubsMat
copying Bio/SubsMat/FreqTable.py -> build/lib.linux-armv7l-3.7/Bio/SubsMat
copying Bio/SubsMat/MatrixInfo.py -> build/lib.linux-armv7l-3.7/Bio/SubsMat
copying Bio/SubsMat/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SubsMat
creating build/lib.linux-armv7l-3.7/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SVDSuperimposer
creating build/lib.linux-armv7l-3.7/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.linux-armv7l-3.7/Bio/PDB/QCPSuperimposer
creating build/lib.linux-armv7l-3.7/Bio/SwissProt
copying Bio/SwissProt/KeyWList.py -> build/lib.linux-armv7l-3.7/Bio/SwissProt
copying Bio/SwissProt/__init__.py -> build/lib.linux-armv7l-3.7/Bio/SwissProt
creating build/lib.linux-armv7l-3.7/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> build/lib.linux-armv7l-3.7/Bio/TogoWS
creating build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/BaseTree.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/CDAO.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/Newick.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/_utils.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/_io.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/NeXML.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
copying Bio/Phylo/Consensus.py -> build/lib.linux-armv7l-3.7/Bio/Phylo
creating build/lib.linux-armv7l-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/Applications
creating build/lib.linux-armv7l-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-armv7l-3.7/Bio/Phylo/PAML
creating build/lib.linux-armv7l-3.7/Bio/UniGene
copying Bio/UniGene/__init__.py -> build/lib.linux-armv7l-3.7/Bio/UniGene
creating build/lib.linux-armv7l-3.7/Bio/UniProt
copying Bio/UniProt/GOA.py -> build/lib.linux-armv7l-3.7/Bio/UniProt
copying Bio/UniProt/__init__.py -> build/lib.linux-armv7l-3.7/Bio/UniProt
creating build/lib.linux-armv7l-3.7/Bio/Wise
copying Bio/Wise/dnal.py -> build/lib.linux-armv7l-3.7/Bio/Wise
copying Bio/Wise/psw.py -> build/lib.linux-armv7l-3.7/Bio/Wise
copying Bio/Wise/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Wise
creating build/lib.linux-armv7l-3.7/Bio/_py3k
copying Bio/_py3k/__init__.py -> build/lib.linux-armv7l-3.7/Bio/_py3k
creating build/lib.linux-armv7l-3.7/BioSQL
copying BioSQL/DBUtils.py -> build/lib.linux-armv7l-3.7/BioSQL
copying BioSQL/BioSeq.py -> build/lib.linux-armv7l-3.7/BioSQL
copying BioSQL/BioSeqDatabase.py -> build/lib.linux-armv7l-3.7/BioSQL
copying BioSQL/Loader.py -> build/lib.linux-armv7l-3.7/BioSQL
copying BioSQL/__init__.py -> build/lib.linux-armv7l-3.7/BioSQL
creating build/lib.linux-armv7l-3.7/Bio/Affy
copying Bio/Affy/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Affy
copying Bio/Affy/CelFile.py -> build/lib.linux-armv7l-3.7/Bio/Affy
creating build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices
copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices
creating build/lib.linux-armv7l-3.7/Bio/Cluster
copying Bio/Cluster/__init__.py -> build/lib.linux-armv7l-3.7/Bio/Cluster
creating build/lib.linux-armv7l-3.7/Bio/KDTree
copying Bio/KDTree/KDTree.py -> build/lib.linux-armv7l-3.7/Bio/KDTree
copying Bio/KDTree/__init__.py -> build/lib.linux-armv7l-3.7/Bio/KDTree
creating build/lib.linux-armv7l-3.7/Bio/phenotype
copying Bio/phenotype/phen_micro.py -> build/lib.linux-armv7l-3.7/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> build/lib.linux-armv7l-3.7/Bio/phenotype
copying Bio/phenotype/__init__.py -> build/lib.linux-armv7l-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'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
writing manifest file 'biopython.egg-info/SOURCES.txt'
copying Bio/cpairwise2module.c -> build/lib.linux-armv7l-3.7/Bio
copying Bio/trie.c -> build/lib.linux-armv7l-3.7/Bio
copying Bio/trie.h -> build/lib.linux-armv7l-3.7/Bio
copying Bio/triemodule.c -> build/lib.linux-armv7l-3.7/Bio
copying Bio/Align/_aligners.c -> build/lib.linux-armv7l-3.7/Bio/Align
creating build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs
creating build/lib.linux-armv7l-3.7/Bio/Entrez/XSDs
copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-armv7l-3.7/Bio/Entrez/XSDs
copying Bio/motifs/_pwm.c -> build/lib.linux-armv7l-3.7/Bio/motifs
copying Bio/Nexus/cnexus.c -> build/lib.linux-armv7l-3.7/Bio/Nexus
copying Bio/PDB/kdtrees.c -> build/lib.linux-armv7l-3.7/Bio/PDB
copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> build/lib.linux-armv7l-3.7/Bio/PDB/QCPSuperimposer
creating build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data
copying Bio/Cluster/cluster.c -> build/lib.linux-armv7l-3.7/Bio/Cluster
copying Bio/Cluster/cluster.h -> build/lib.linux-armv7l-3.7/Bio/Cluster
copying Bio/Cluster/clustermodule.c -> build/lib.linux-armv7l-3.7/Bio/Cluster
copying Bio/KDTree/KDTree.c -> build/lib.linux-armv7l-3.7/Bio/KDTree
copying Bio/KDTree/KDTree.h -> build/lib.linux-armv7l-3.7/Bio/KDTree
copying Bio/KDTree/KDTreemodule.c -> build/lib.linux-armv7l-3.7/Bio/KDTree
copying Bio/KDTree/Neighbor.h -> build/lib.linux-armv7l-3.7/Bio/KDTree
running build_ext
building 'Bio.Align._aligners' extension
creating build/temp.linux-armv7l-3.7
creating build/temp.linux-armv7l-3.7/Bio
creating build/temp.linux-armv7l-3.7/Bio/Align
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -I/usr/include/python3.7m -c Bio/Align/_aligners.c -o build/temp.linux-armv7l-3.7/Bio/Align/_aligners.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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard build/temp.linux-armv7l-3.7/Bio/Align/_aligners.o -L/usr/lib -lpython3.7m -o build/lib.linux-armv7l-3.7/Bio/Align/_aligners.cpython-37m-arm-linux-gnueabi.so
building 'Bio.cpairwise2' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -I/usr/include/python3.7m -c Bio/cpairwise2module.c -o build/temp.linux-armv7l-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard build/temp.linux-armv7l-3.7/Bio/cpairwise2module.o -L/usr/lib -lpython3.7m -o build/lib.linux-armv7l-3.7/Bio/cpairwise2.cpython-37m-arm-linux-gnueabi.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-armv7l-3.7/Bio/Nexus
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -I/usr/include/python3.7m -c Bio/Nexus/cnexus.c -o build/temp.linux-armv7l-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard build/temp.linux-armv7l-3.7/Bio/Nexus/cnexus.o -L/usr/lib -lpython3.7m -o build/lib.linux-armv7l-3.7/Bio/Nexus/cnexus.cpython-37m-arm-linux-gnueabi.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-armv7l-3.7/Bio/PDB
creating build/temp.linux-armv7l-3.7/Bio/PDB/QCPSuperimposer
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -I/usr/include/python3.7m -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armv7l-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard build/temp.linux-armv7l-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib -lpython3.7m -o build/lib.linux-armv7l-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-arm-linux-gnueabi.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-armv7l-3.7/Bio/motifs
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -I/usr/include/python3.7m -c Bio/motifs/_pwm.c -o build/temp.linux-armv7l-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard build/temp.linux-armv7l-3.7/Bio/motifs/_pwm.o -L/usr/lib -lpython3.7m -o build/lib.linux-armv7l-3.7/Bio/motifs/_pwm.cpython-37m-arm-linux-gnueabi.so
building 'Bio.Cluster._cluster' extension
creating build/temp.linux-armv7l-3.7/Bio/Cluster
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -I/usr/include/python3.7m -c Bio/Cluster/cluster.c -o build/temp.linux-armv7l-3.7/Bio/Cluster/cluster.o
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -I/usr/include/python3.7m -c Bio/Cluster/clustermodule.c -o build/temp.linux-armv7l-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard build/temp.linux-armv7l-3.7/Bio/Cluster/cluster.o build/temp.linux-armv7l-3.7/Bio/Cluster/clustermodule.o -L/usr/lib -lpython3.7m -o build/lib.linux-armv7l-3.7/Bio/Cluster/_cluster.cpython-37m-arm-linux-gnueabi.so
building 'Bio.PDB.kdtrees' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -I/usr/include/python3.7m -c Bio/PDB/kdtrees.c -o build/temp.linux-armv7l-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard build/temp.linux-armv7l-3.7/Bio/PDB/kdtrees.o -L/usr/lib -lpython3.7m -o build/lib.linux-armv7l-3.7/Bio/PDB/kdtrees.cpython-37m-arm-linux-gnueabi.so
building 'Bio.KDTree._CKDTree' extension
creating build/temp.linux-armv7l-3.7/Bio/KDTree
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -I/usr/include/python3.7m -c Bio/KDTree/KDTree.c -o build/temp.linux-armv7l-3.7/Bio/KDTree/KDTree.o
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -I/usr/include/python3.7m -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-armv7l-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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard build/temp.linux-armv7l-3.7/Bio/KDTree/KDTree.o build/temp.linux-armv7l-3.7/Bio/KDTree/KDTreemodule.o -L/usr/lib -lpython3.7m -o build/lib.linux-armv7l-3.7/Bio/KDTree/_CKDTree.cpython-37m-arm-linux-gnueabi.so
building 'Bio.trie' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -IBio -I/usr/include/python3.7m -c Bio/triemodule.c -o build/temp.linux-armv7l-3.7/Bio/triemodule.o
Bio/triemodule.c:585:5: warning: initialization of ‘Py_hash_t (*)(PyObject *)’ {aka ‘int (*)(struct _object *)’} from incompatible pointer type ‘long int (*)(PyObject *)’ {aka ‘long int (*)(struct _object *)’} [-Wincompatible-pointer-types]
  585 |     trie_nohash,        /*tp_hash */
      |     ^~~~~~~~~~~
Bio/triemodule.c:585:5: note: (near initialization for ‘Trie_Type.tp_hash’)
gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard -fPIC -IBio -I/usr/include/python3.7m -c Bio/trie.c -o build/temp.linux-armv7l-3.7/Bio/trie.o
In file included from /usr/include/string.h:494,
                 from Bio/trie.c:17:
In function ‘strncat’,
    inlined from ‘_with_prefix_helper.constprop’ at Bio/trie.c:595:6:
/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]
  136 |   return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Bio/trie.c: In function ‘_with_prefix_helper.constprop’:
Bio/trie.c:561:14: note: length computed here
  561 |  suffixlen = strlen(suffix);
      |              ^~~~~~~~~~~~~~
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 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard build/temp.linux-armv7l-3.7/Bio/triemodule.o build/temp.linux-armv7l-3.7/Bio/trie.o -L/usr/lib -lpython3.7m -o build/lib.linux-armv7l-3.7/Bio/trie.cpython-37m-arm-linux-gnueabi.so
+ popd
~/build/BUILD/python-biopython-1.75
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Sdfjhg
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm
++ dirname /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm
+ cd python-biopython-1.75
~/build/BUILD/python-biopython-1.75/python3 ~/build/BUILD/python-biopython-1.75
+ pushd python3
+ /usr/bin/python3 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm --install-data=/usr/share/python-biopython
running install
running install_lib
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/UniProt
copying build/lib.linux-armv7l-3.7/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/UniProt
copying build/lib.linux-armv7l-3.7/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/UniProt
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/XSDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/XSDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez
copying build/lib.linux-armv7l-3.7/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-3.7/Bio/trie.cpython-37m-arm-linux-gnueabi.so -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-armv7l-3.7/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-armv7l-3.7/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-armv7l-3.7/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Medline
copying build/lib.linux-armv7l-3.7/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Medline
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/_legacy/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/_legacy/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/_legacy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/InterproscanIO
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/HHsuiteIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-armv7l-3.7/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HHsuiteIO
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-armv7l-3.7/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-armv7l-3.7/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-armv7l-3.7/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Emboss
copying build/lib.linux-armv7l-3.7/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Emboss
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/FSSP
copying build/lib.linux-armv7l-3.7/Bio/FSSP/FSSPTools.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/FSSP
copying build/lib.linux-armv7l-3.7/Bio/FSSP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/FSSP
copying build/lib.linux-armv7l-3.7/Bio/FSSP/fssp_rec.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/FSSP
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/UniGene
copying build/lib.linux-armv7l-3.7/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/UniGene
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Compass
copying build/lib.linux-armv7l-3.7/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Compass
copying build/lib.linux-armv7l-3.7/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-armv7l-3.7/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-armv7l-3.7/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-armv7l-3.7/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SwissProt
copying build/lib.linux-armv7l-3.7/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SwissProt
copying build/lib.linux-armv7l-3.7/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SwissProt
copying build/lib.linux-armv7l-3.7/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-armv7l-3.7/Bio/Index.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-armv7l-3.7/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen
copying build/lib.linux-armv7l-3.7/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop/Utils.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-3.7/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/TogoWS
copying build/lib.linux-armv7l-3.7/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/TogoWS
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-3.7/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-3.7/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-3.7/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-3.7/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-3.7/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-3.7/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-3.7/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing
copying build/lib.linux-armv7l-3.7/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-armv7l-3.7/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-armv7l-3.7/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-armv7l-3.7/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-armv7l-3.7/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-armv7l-3.7/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing
copying build/lib.linux-armv7l-3.7/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Alphabet
copying build/lib.linux-armv7l-3.7/Bio/Alphabet/IUPAC.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Alphabet
copying build/lib.linux-armv7l-3.7/Bio/Alphabet/Reduced.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Alphabet
copying build/lib.linux-armv7l-3.7/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Alphabet
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/MsfIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-3.7/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-armv7l-3.7/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-armv7l-3.7/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-armv7l-3.7/Bio/motifs/pfm.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs/applications
copying build/lib.linux-armv7l-3.7/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs/applications
copying build/lib.linux-armv7l-3.7/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs/applications
copying build/lib.linux-armv7l-3.7/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/_pwm.cpython-37m-arm-linux-gnueabi.so -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/clusterbuster.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-3.7/Bio/motifs/xms.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/SCHNEIDER -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/JOHNSON -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/BENNER22 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/JONES -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/MDM78 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/BENNER74 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/BLOSUM80 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/DAYHOFF -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/PAM250 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/BLOSUM45 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/FENG -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/NUC.4.4 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/RISLER -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/PAM30 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/GONNET1992 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/BLOSUM50 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/BENNER6 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/BLOSUM62 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/BLOSUM90 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/LEVIN -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/PAM70 -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/RAO -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/GENETIC -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/STR -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/data/MCLACHLAN -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/substitution_matrices
copying build/lib.linux-armv7l-3.7/Bio/Align/_aligners.cpython-37m-arm-linux-gnueabi.so -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-3.7/Bio/Align/_aligners.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align
copying build/lib.linux-armv7l-3.7/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align
copying build/lib.linux-armv7l-3.7/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align
copying build/lib.linux-armv7l-3.7/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/_py3k
copying build/lib.linux-armv7l-3.7/Bio/_py3k/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/_py3k
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Wise
copying build/lib.linux-armv7l-3.7/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Wise
copying build/lib.linux-armv7l-3.7/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Wise
copying build/lib.linux-armv7l-3.7/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Wise
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Geo
copying build/lib.linux-armv7l-3.7/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Geo
copying build/lib.linux-armv7l-3.7/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Geo
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Affy
copying build/lib.linux-armv7l-3.7/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Affy
copying build/lib.linux-armv7l-3.7/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Affy
copying build/lib.linux-armv7l-3.7/Bio/triemodule.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-armv7l-3.7/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/GckIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/_convert.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/XdnaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/NibIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/SnapGeneIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-3.7/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqIO
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-armv7l-3.7/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-armv7l-3.7/Bio/Cluster/_cluster.cpython-37m-arm-linux-gnueabi.so -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-armv7l-3.7/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-armv7l-3.7/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Cluster
copying build/lib.linux-armv7l-3.7/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Cluster
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/CAPS
copying build/lib.linux-armv7l-3.7/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/CAPS
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-3.7/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-3.7/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-3.7/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-3.7/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-3.7/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/HMM
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-3.7/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-armv7l-3.7/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-armv7l-3.7/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-armv7l-3.7/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-armv7l-3.7/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-armv7l-3.7/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-3.7/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Crystal
copying build/lib.linux-armv7l-3.7/Bio/Crystal/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Crystal
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-armv7l-3.7/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-armv7l-3.7/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-armv7l-3.7/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-armv7l-3.7/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-3.7/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-3.7/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-3.7/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-3.7/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-3.7/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-3.7/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-3.7/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SCOP
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-3.7/Bio/KDTree/Neighbor.h -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-3.7/Bio/KDTree/KDTreemodule.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-3.7/Bio/KDTree/KDTree.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-3.7/Bio/KDTree/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-3.7/Bio/KDTree/KDTree.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-3.7/Bio/KDTree/KDTree.h -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-3.7/Bio/KDTree/_CKDTree.cpython-37m-arm-linux-gnueabi.so -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-3.7/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-3.7/Bio/Nexus/cnexus.cpython-37m-arm-linux-gnueabi.so -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-3.7/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-3.7/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-3.7/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-3.7/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-3.7/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-3.7/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Nexus
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG
copying build/lib.linux-armv7l-3.7/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-armv7l-3.7/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-armv7l-3.7/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-armv7l-3.7/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/KGML
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/Enzyme
copying build/lib.linux-armv7l-3.7/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/Enzyme
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/Compound
copying build/lib.linux-armv7l-3.7/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/Compound
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/Map
copying build/lib.linux-armv7l-3.7/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/Map
copying build/lib.linux-armv7l-3.7/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/Gene
copying build/lib.linux-armv7l-3.7/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KEGG/Gene
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-3.7/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-3.7/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-3.7/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-3.7/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-3.7/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-3.7/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-3.7/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-3.7/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-3.7/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqUtils
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Data
copying build/lib.linux-armv7l-3.7/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Data
copying build/lib.linux-armv7l-3.7/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Data
copying build/lib.linux-armv7l-3.7/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Data
copying build/lib.linux-armv7l-3.7/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Data
copying build/lib.linux-armv7l-3.7/Bio/cpairwise2.cpython-37m-arm-linux-gnueabi.so -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/NMR
copying build/lib.linux-armv7l-3.7/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/NMR
copying build/lib.linux-armv7l-3.7/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/NMR
copying build/lib.linux-armv7l-3.7/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/NMR
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Application
copying build/lib.linux-armv7l-3.7/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Application
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-3.7/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-3.7/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-3.7/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-3.7/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-3.7/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-3.7/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/ExPASy
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-armv7l-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-arm-linux-gnueabi.so -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-armv7l-3.7/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-armv7l-3.7/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-armv7l-3.7/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-armv7l-3.7/Bio/PDB/mmtf/mmtfio.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-armv7l-3.7/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-armv7l-3.7/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-armv7l-3.7/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/kdtrees.cpython-37m-arm-linux-gnueabi.so -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-3.7/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-armv7l-3.7/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-armv7l-3.7/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-armv7l-3.7/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/GenBank
copying build/lib.linux-armv7l-3.7/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/GenBank
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SVDSuperimposer
copying build/lib.linux-armv7l-3.7/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SVDSuperimposer
copying build/lib.linux-armv7l-3.7/Bio/trie.c -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
copying build/lib.linux-armv7l-3.7/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-3.7/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-3.7/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-3.7/Bio/codonalign/codonalphabet.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-3.7/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-3.7/Bio/codonalign/chisq.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/codonalign
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/phenotype
copying build/lib.linux-armv7l-3.7/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/phenotype
copying build/lib.linux-armv7l-3.7/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/phenotype
copying build/lib.linux-armv7l-3.7/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/phenotype
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SubsMat
copying build/lib.linux-armv7l-3.7/Bio/SubsMat/FreqTable.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SubsMat
copying build/lib.linux-armv7l-3.7/Bio/SubsMat/MatrixInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SubsMat
copying build/lib.linux-armv7l-3.7/Bio/SubsMat/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SubsMat
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-armv7l-3.7/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-armv7l-3.7/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-armv7l-3.7/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Restriction
copying build/lib.linux-armv7l-3.7/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Restriction
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Statistics
copying build/lib.linux-armv7l-3.7/Bio/Statistics/lowess.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Statistics
copying build/lib.linux-armv7l-3.7/Bio/Statistics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Statistics
copying build/lib.linux-armv7l-3.7/Bio/trie.h -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-3.7/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-3.7/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-3.7/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-3.7/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-3.7/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-3.7/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-3.7/Bio/triefind.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/BioSQL
copying build/lib.linux-armv7l-3.7/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/BioSQL
copying build/lib.linux-armv7l-3.7/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/BioSQL
copying build/lib.linux-armv7l-3.7/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/BioSQL
copying build/lib.linux-armv7l-3.7/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/BioSQL
copying build/lib.linux-armv7l-3.7/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/BioSQL
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/UniProt/GOA.py to GOA.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/UniProt/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/Parser.py to Parser.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Entrez/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/bgzf.py to bgzf.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Medline/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/FastaIO.py to FastaIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy/ParserSupport.py to ParserSupport.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy/NCBIStandalone.py to NCBIStandalone.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_legacy/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_index.py to _index.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_utils.py to _utils.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/BlatIO.py to BlatIO.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model/query.py to query.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model/_base.py to _base.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model/hit.py to hit.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/_model/hsp.py to hsp.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO/blast_xml.py to blast_xml.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO/blast_text.py to blast_text.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/BlastIO/blast_tab.py to blast_tab.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HHsuiteIO/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py to hhsuite2_text.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Emboss/Applications.py to Applications.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Emboss/Primer3.py to Primer3.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Emboss/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/FSSP/FSSPTools.py to FSSPTools.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/FSSP/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/FSSP/fssp_rec.py to fssp_rec.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/UniGene/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Compass/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/MarkovModel.py to MarkovModel.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/File.py to File.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/pairwise2.py to pairwise2.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SwissProt/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/SeqFeature.py to SeqFeature.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Index.py to Index.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop/Controller.py to Controller.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop/Utils.py to Utils.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop/FileParser.py to FileParser.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop/EasyController.py to EasyController.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PopGen/GenePop/LargeFileParser.py to LargeFileParser.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/TogoWS/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/Distribution.py to Distribution.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/Comparative.py to Comparative.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing/Ace.py to Ace.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-37.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/BioSQL/Loader.py to Loader.cpython-37.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/BioSQL/__init__.py to __init__.cpython-37.pyc
writing byte-compilation script '/tmp/tmp_xctctg6.py'
/usr/bin/python3 /tmp/tmp_xctctg6.py
removing /tmp/tmp_xctctg6.py
running install_egg_info
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'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
writing manifest file 'biopython.egg-info/SOURCES.txt'
Copying biopython.egg-info to /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/biopython-1.75-py3.7.egg-info
running install_scripts
+ find Scripts -name '*.py'
+ xargs sed -i '1s|^#!/usr/bin/env python|#!/usr/bin/python3|'
+ popd
~/build/BUILD/python-biopython-1.75
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.75-2.fc30 --unique-debug-suffix -1.75-2.fc30.arm --unique-debug-src-base python-biopython-1.75-2.fc30.arm --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.75
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/_aligners.cpython-37m-arm-linux-gnueabi.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/trie.cpython-37m-arm-linux-gnueabi.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs/_pwm.cpython-37m-arm-linux-gnueabi.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Cluster/_cluster.cpython-37m-arm-linux-gnueabi.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/trie.cpython-37m-arm-linux-gnueabi.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Cluster/_cluster.cpython-37m-arm-linux-gnueabi.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Align/_aligners.cpython-37m-arm-linux-gnueabi.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/motifs/_pwm.cpython-37m-arm-linux-gnueabi.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KDTree/_CKDTree.cpython-37m-arm-linux-gnueabi.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/KDTree/_CKDTree.cpython-37m-arm-linux-gnueabi.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Nexus/cnexus.cpython-37m-arm-linux-gnueabi.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/cpairwise2.cpython-37m-arm-linux-gnueabi.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/cpairwise2.cpython-37m-arm-linux-gnueabi.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/Nexus/cnexus.cpython-37m-arm-linux-gnueabi.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-arm-linux-gnueabi.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-37m-arm-linux-gnueabi.so
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/kdtrees.cpython-37m-arm-linux-gnueabi.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages/Bio/PDB/kdtrees.cpython-37m-arm-linux-gnueabi.so
/usr/lib/rpm/sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match.
1270 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/brp-python-bytecompile /usr/bin/python 1 0
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/debug/usr/lib/python3.7 using /usr/bin/python3.7
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/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.OOnBkH
+ umask 022
+ cd /builddir/build/BUILD
~/build/BUILD/python-biopython-1.75/python3/Tests ~/build/BUILD/python-biopython-1.75
+ cd python-biopython-1.75
+ pushd python3/Tests
+ find . -name run_tests.py
+ xargs sed -i '1s|^#!/usr/bin/env python|#!/usr/bin/python3|'
++ grep -v Nexus
++ 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_Blast_Record.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_Gck.py test_SeqIO_Insdc.py test_SeqIO_NibIO.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_SnapGene.py test_SeqIO_Xdna.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_GOA.py test_Uniprot.py test_Wise.py test_XXmotif_tool.py test_align.py test_align_substitution_matrices.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
++ grep -v Tutorial
++ grep -v SubsMat
++ grep -v bgzf
++ grep -v SearchIO_blast
++ grep -v Phylo
++ grep -v pairwise_aligner
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Ace.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Ace ... ok
test_check_ACEParser (test_Ace.AceTestOne)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestOne)
Test to check that contig parser parses each contig into a contig. ... ok
test_check_ACEParser (test_Ace.AceTestThree)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestThree)
Test to check that record parser parses each contig into a record. ... ok
test_check_ACEParser (test_Ace.AceTestTwo)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestTwo)
Test to check that record parser parses each contig into a record. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.214 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_Affy.py
test_Affy ... ok
testAffy3 (test_Affy.AffyTest) ... ok
testAffy3Backwards (test_Affy.AffyTest) ... ok
testAffy4 (test_Affy.AffyTest) ... ok
testAffyBadHeader (test_Affy.AffyTest) ... ok
testAffyStrict (test_Affy.AffyTest) ... ok
testAffyWrongModeRead (test_Affy.AffyTest) ... ok
testAffyWrongModeReadV4 (test_Affy.AffyTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.061 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO.py
test_AlignIO ... ok
test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions)
Check that parsing an empty file returns an empty list. ... ok
test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions)
Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok
test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions)
Check that writers can cope with no alignments. ... ok
test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions)
Check that writers reject records that are not alignments. ... ok
test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_msf1 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_msf2 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading) ... ok
test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading) ... ok
----------------------------------------------------------------------
Ran 1 test in 12.850 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_ClustalIO.py
test_AlignIO_ClustalIO ... ok
test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_empy (test_AlignIO_ClustalIO.TestClustalIO)
Checking empty file. ... ok
test_kalign_header (test_AlignIO_ClustalIO.TestClustalIO)
Make sure we can parse the Kalign header. ... ok
test_one (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_three (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_two (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_write_read (test_AlignIO_ClustalIO.TestClustalIO)
Checking write/read. ... ok
test_write_read_single (test_AlignIO_ClustalIO.TestClustalIO)
Testing write/read when there is only one sequence. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.724 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_EmbossIO.py
test_AlignIO_EmbossIO ... ok
test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.682 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_FastaIO.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_AlignIO_FastaIO ... ok
test_output001 (test_AlignIO_FastaIO.FastaIOTests)
Check output001.m10 file. ... ok
test_output002 (test_AlignIO_FastaIO.FastaIOTests)
Check output002.m10 file. ... ok
test_output003 (test_AlignIO_FastaIO.FastaIOTests)
Check output003.m10 file. ... ok
test_output004 (test_AlignIO_FastaIO.FastaIOTests)
Check output004.m10 file. ... ok
test_output005 (test_AlignIO_FastaIO.FastaIOTests)
Check output005.m10 file. ... ok
test_output006 (test_AlignIO_FastaIO.FastaIOTests)
Check output006.m10 file. ... ok
test_output007 (test_AlignIO_FastaIO.FastaIOTests)
Check output007.m10 file. ... ok
test_output008 (test_AlignIO_FastaIO.FastaIOTests)
Check output008.m10 file. ... ok
test_output009 (test_AlignIO_FastaIO.FastaIOTests)
Check output009.m10 file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.335 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_MauveIO.py
test_AlignIO_MauveIO ... ok
test_one (test_AlignIO_MauveIO.TestMauveIO) ... ok
test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO) ... ok
test_write_read (test_AlignIO_MauveIO.TestMauveIO) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.426 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_PhylipIO.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_AlignIO_PhylipIO ... ok
test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_five (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_five_a (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_four (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_one (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_write_read (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.288 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_convert.py
test_AlignIO_convert ... ok
test_Clustalw_hedgehog_aln_clustal_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to clustal ... ok
test_Clustalw_hedgehog_aln_clustal_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to fasta ... ok
test_Clustalw_hedgehog_aln_clustal_to_maf (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to maf ... ok
test_Clustalw_hedgehog_aln_clustal_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to mauve ... ok
test_Clustalw_hedgehog_aln_clustal_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to nexus ... ok
test_Clustalw_hedgehog_aln_clustal_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to phylip ... ok
test_Clustalw_hedgehog_aln_clustal_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to phylip-relaxed ... ok
test_Clustalw_hedgehog_aln_clustal_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to phylip-sequential ... ok
test_Clustalw_hedgehog_aln_clustal_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to stockholm ... ok
test_Fasta_output001_m10_fasta-m10_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to clustal ... ok
test_Fasta_output001_m10_fasta-m10_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to fasta ... ok
test_Fasta_output001_m10_fasta-m10_to_maf (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to maf ... ok
test_Fasta_output001_m10_fasta-m10_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to mauve ... ok
test_Fasta_output001_m10_fasta-m10_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to nexus ... ok
test_Fasta_output001_m10_fasta-m10_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to phylip ... ok
test_Fasta_output001_m10_fasta-m10_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to phylip-relaxed ... ok
test_Fasta_output001_m10_fasta-m10_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to phylip-sequential ... ok
test_Fasta_output001_m10_fasta-m10_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to stockholm ... ok
test_GFF_multi_fna_fasta_to_clustal (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to clustal ... ok
test_GFF_multi_fna_fasta_to_fasta (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to fasta ... ok
test_GFF_multi_fna_fasta_to_maf (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to maf ... ok
test_GFF_multi_fna_fasta_to_mauve (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to mauve ... ok
test_GFF_multi_fna_fasta_to_nexus (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to nexus ... ok
test_GFF_multi_fna_fasta_to_phylip (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to phylip ... ok
test_GFF_multi_fna_fasta_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to phylip-relaxed ... ok
test_GFF_multi_fna_fasta_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to phylip-sequential ... ok
test_GFF_multi_fna_fasta_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to stockholm ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_clustal (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to clustal ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_fasta (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to fasta ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_maf (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to maf ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_mauve (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to mauve ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_nexus (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to nexus ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip-relaxed ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip-sequential ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to stockholm ... ok
test_NBRF_clustalw_pir_pir_to_clustal (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to clustal ... ok
test_NBRF_clustalw_pir_pir_to_fasta (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to fasta ... ok
test_NBRF_clustalw_pir_pir_to_maf (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to maf ... ok
test_NBRF_clustalw_pir_pir_to_mauve (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to mauve ... ok
test_NBRF_clustalw_pir_pir_to_nexus (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to nexus ... ok
test_NBRF_clustalw_pir_pir_to_phylip (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to phylip ... ok
test_NBRF_clustalw_pir_pir_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to phylip-relaxed ... ok
test_NBRF_clustalw_pir_pir_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to phylip-sequential ... ok
test_NBRF_clustalw_pir_pir_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to stockholm ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to clustal ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to fasta ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_maf (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to maf ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to mauve ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to nexus ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to phylip ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to phylip-relaxed ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to phylip-sequential ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to stockholm ... ok
test_Quality_example_fastq_fastq-sanger_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to clustal ... ok
test_Quality_example_fastq_fastq-sanger_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fasta ... ok
test_Quality_example_fastq_fastq-sanger_to_maf (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to maf ... ok
test_Quality_example_fastq_fastq-sanger_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to mauve ... ok
test_Quality_example_fastq_fastq-sanger_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to nexus ... ok
test_Quality_example_fastq_fastq-sanger_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to phylip ... ok
test_Quality_example_fastq_fastq-sanger_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to phylip-relaxed ... ok
test_Quality_example_fastq_fastq-sanger_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to phylip-sequential ... ok
test_Quality_example_fastq_fastq-sanger_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to stockholm ... ok
test_Quality_example_fastq_fastq_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to clustal ... ok
test_Quality_example_fastq_fastq_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fasta ... ok
test_Quality_example_fastq_fastq_to_maf (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to maf ... ok
test_Quality_example_fastq_fastq_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to mauve ... ok
test_Quality_example_fastq_fastq_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to nexus ... ok
test_Quality_example_fastq_fastq_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to phylip ... ok
test_Quality_example_fastq_fastq_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to phylip-relaxed ... ok
test_Quality_example_fastq_fastq_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to phylip-sequential ... ok
test_Quality_example_fastq_fastq_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to stockholm ... ok
test_Stockholm_simple_sth_stockholm_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to clustal ... ok
test_Stockholm_simple_sth_stockholm_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to fasta ... ok
test_Stockholm_simple_sth_stockholm_to_maf (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to maf ... ok
test_Stockholm_simple_sth_stockholm_to_mauve (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to mauve ... ok
test_Stockholm_simple_sth_stockholm_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to nexus ... ok
test_Stockholm_simple_sth_stockholm_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to phylip ... ok
test_Stockholm_simple_sth_stockholm_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to phylip-relaxed ... ok
test_Stockholm_simple_sth_stockholm_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to phylip-sequential ... ok
test_Stockholm_simple_sth_stockholm_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to stockholm ... ok
----------------------------------------------------------------------
Ran 1 test in 1.603 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignInfo.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_AlignInfo ... ok
test_nucleotides (test_AlignInfo.AlignInfoTests) ... ok
test_proteins (test_AlignInfo.AlignInfoTests) ... ok
test_pseudo_count (test_AlignInfo.AlignInfoTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.404 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Application.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Application ... ok
test_echo (test_Application.TestApp) ... ok
test_echo_capture_both (test_Application.TestApp) ... ok
test_echo_capture_neither (test_Application.TestApp) ... ok
test_echo_capture_stderr (test_Application.TestApp) ... ok
test_echo_capture_stdout (test_Application.TestApp) ... ok
test_echo_file_both (test_Application.TestApp) ... ok
test_echo_file_same (test_Application.TestApp) ... ok
test_echo_file_stderr (test_Application.TestApp) ... ok
test_echo_file_stdout (test_Application.TestApp) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.166 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BWA_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.106 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.499 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb_online.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_BioSQL_MySQLdb_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.391 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.387 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector_online.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_BioSQL_mysql_connector_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.383 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.428 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2_online.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_BioSQL_psycopg2_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.377 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3.py
test_BioSQL_sqlite3 ... ok
test_SeqIO_loading (common_BioSQL.AutoSeqIOTests) ... ok
test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest)
Check can re-use an old BioSQL SQLite3 database. ... ok
test_NC_000932 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok
test_NC_005816 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok
test_NT_019265 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok
test_arab1 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok
test_cor6_6 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok
test_no_ref (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, noref. ... ok
test_one_of (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok
test_protein_refseq2 (common_BioSQL.ClosedLoopTest)
From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok
test_del_db_items (common_BioSQL.DeleteTest)
Check all associated data is deleted from an item. ... ok
test_server (common_BioSQL.DeleteTest)
Check BioSeqDatabase methods. ... ok
test_duplicate_id_load (common_BioSQL.DupLoadTest)
Make sure can't import records with same ID (in one go). ... ok
test_duplicate_load (common_BioSQL.DupLoadTest)
Make sure can't import a single record twice (in one go). ... ok
test_duplicate_load2 (common_BioSQL.DupLoadTest)
Make sure can't import a single record twice (in steps). ... ok
test_record_loading (common_BioSQL.InDepthLoadTest)
Make sure all records are correctly loaded. ... ok
test_reload (common_BioSQL.InDepthLoadTest)
Make sure can't reimport existing records. ... ok
test_seq_feature (common_BioSQL.InDepthLoadTest)
In depth check that SeqFeatures are transmitted through the db. ... ok
test_transfer (common_BioSQL.InDepthLoadTest)
Make sure can load record into another namespace. ... ok
test_load_database (common_BioSQL.LoaderTest)
Load SeqRecord objects into a BioSQL database. ... ok
test_cross_retrieval_of_items (common_BioSQL.MultiReadTest)
Test that valid ids can't be retrieved between namespaces. ... ok
test_get_db_items (common_BioSQL.MultiReadTest)
Check list, keys, length etc. ... ok
test_server (common_BioSQL.MultiReadTest)
Check BioSeqDatabase methods. ... ok
test_get_db_items (common_BioSQL.ReadTest)
Check list, keys, length etc. ... ok
test_lookup_items (common_BioSQL.ReadTest)
Test retrieval of items using various ids. ... ok
test_server (common_BioSQL.ReadTest)
Check BioSeqDatabase methods. ... ok
test_addition (common_BioSQL.SeqInterfaceTest)
Check can add DBSeq objects together. ... ok
test_convert (common_BioSQL.SeqInterfaceTest)
Check can turn a DBSeq object into a Seq or MutableSeq. ... ok
test_multiplication (common_BioSQL.SeqInterfaceTest)
Check can multiply DBSeq objects by integers. ... ok
test_record_slicing (common_BioSQL.SeqInterfaceTest)
Check that slices of DBSeqRecord are retrieved properly. ... ok
test_seq (common_BioSQL.SeqInterfaceTest)
Make sure Seqs from BioSQL implement the right interface. ... ok
test_seq_features (common_BioSQL.SeqInterfaceTest)
Check SeqFeatures of a sequence. ... ok
test_seq_record (common_BioSQL.SeqInterfaceTest)
Make sure SeqRecords from BioSQL implement the right interface. ... ok
test_seq_slicing (common_BioSQL.SeqInterfaceTest)
Check that slices of sequences are retrieved properly. ... ok
test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest)
Loaded uniprot-xml with ambiguous location in BioSQL. ... ok
test_NC_000932 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok
test_NC_005816 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok
test_NT_019265 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok
test_arab1 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok
test_cor6_6 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok
test_no_ref (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, noref. ... ok
test_one_of (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok
test_protein_refseq2 (common_BioSQL.TransferTest)
From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok
----------------------------------------------------------------------
Ran 1 test in 58.347 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3_online.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_BioSQL_sqlite3_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.455 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Blast_Record.py
test_Blast_Record ... ok
test_str (test_Blast_Record.TestHsp) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.284 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CAPS.py
test_CAPS ... ok
test (test_CAPS.TestCAPS) ... ok
testNoCAPS (test_CAPS.TestCAPS) ... ok
test_trivial (test_CAPS.TestCAPS) ... ok
test_uneven (test_CAPS.TestCAPS) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.549 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CelFile.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_CelFile ... ok
test_read (test_CelFile.testCelFile) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.042 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Chi2.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Chi2 ... ok
test_cdf_chi2 (test_Chi2.ModTest) ... ok
test_incomplete_gamma (test_Chi2.ModTest) ... ok
test_ln_gamma (test_Chi2.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.690 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ClustalOmega_tool.py
test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.506 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Clustalw_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.441 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Cluster.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Cluster ... ok
test_clusterdistance (test_Cluster.TestCluster) ... ok
test_distancematrix_kmedoids (test_Cluster.TestCluster) ... ok
test_kcluster (test_Cluster.TestCluster) ... ok
test_mask_parse (test_Cluster.TestCluster) ... ok
test_matrix_parse (test_Cluster.TestCluster) ... ok
test_pca (test_Cluster.TestCluster) ... ok
test_somcluster (test_Cluster.TestCluster) ... ok
test_tree (test_Cluster.TestCluster) ... ok
test_treecluster (test_Cluster.TestCluster) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.155 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CodonTable.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_CodonTable ... ok
test_coding (test_CodonTable.AmbiguousCodonsTests)
Check a few ambiguous codons for correct coding. ... ok
test_list_ambiguous_codons (test_CodonTable.AmbiguousCodonsTests)
Check if stop codons are properly extended. ... ok
test_start_codons (test_CodonTable.AmbiguousCodonsTests)
Test various ambiguous codons as start codon. ... ok
test_stop_codons (test_CodonTable.AmbiguousCodonsTests)
Test various ambiguous codons as stop codon. ... ok
test_ambiguous_tables (test_CodonTable.BasicSanityTests)
Check if all IDs and all names are present in ambiguous tables. ... ok
test_complete_tables (test_CodonTable.BasicSanityTests)
Check if all unambiguous codon tables have all entries. ... ok
test_number_of_tables (test_CodonTable.BasicSanityTests)
Check if we have the same number of tables for each type. ... ok
test_ambiguous_forward_table (test_CodonTable.ErrorConditions)
Raise errors in AmbiguousForwardTable. ... ok
test_list_possible_proteins (test_CodonTable.ErrorConditions)
Raise errors in list_possible proteins. ... ok
test_print_table (test_CodonTable.PrintTable)
Test output of __str__ function. ... ok
test_table01 (test_CodonTable.SingleTableTests)
Check table 1: Standard. ... ok
test_table02 (test_CodonTable.SingleTableTests)
Check table 2: Vertebrate Mitochondrial. ... ok
test_table03 (test_CodonTable.SingleTableTests)
Check table 3: Yeast Mitochondrial. ... ok
test_table04 (test_CodonTable.SingleTableTests)
Check table 4: Mold Mitochondrial and others. ... ok
test_table05 (test_CodonTable.SingleTableTests)
Check table 5: Invertebrate Mitochondrial. ... ok
test_table06 (test_CodonTable.SingleTableTests)
Check table 6: Ciliate and Other Nuclear. ... ok
test_table09 (test_CodonTable.SingleTableTests)
Check table 9: Echinoderm and Flatworm Mitochondrial. ... ok
test_table10 (test_CodonTable.SingleTableTests)
Check table 10: Euplotid Nuclear. ... ok
test_table11 (test_CodonTable.SingleTableTests)
Check table 11: Bacterial, Archaeal and Plant Plastid. ... ok
test_table12 (test_CodonTable.SingleTableTests)
Check table 12: Alternative Yeast Nuclear. ... ok
test_table13 (test_CodonTable.SingleTableTests)
Check table 13: Ascidian Mitochondrial. ... ok
test_table14 (test_CodonTable.SingleTableTests)
Check table 14: Alternative Flatworm Mitochondrial. ... ok
test_table16 (test_CodonTable.SingleTableTests)
Check table 16: Chlorophycean Mitochondrial. ... ok
test_table21 (test_CodonTable.SingleTableTests)
Check table 21: Trematode Mitochondrial. ... ok
test_table22 (test_CodonTable.SingleTableTests)
Check table 22: Scenedesmus obliquus Mitochondrial. ... ok
test_table23 (test_CodonTable.SingleTableTests)
Check table 9: Thraustochytrium Mitochondrial. ... ok
test_table24 (test_CodonTable.SingleTableTests)
Check table 24: Pterobranchia Mitochondrial. ... ok
test_table25 (test_CodonTable.SingleTableTests)
Check table 25: Candidate Division SR1 and Gracilibacteria. ... ok
test_table26 (test_CodonTable.SingleTableTests)
Check table 26: Pachysolen tannophilus Nuclear. ... ok
test_table27 (test_CodonTable.SingleTableTests)
Check table 27: Karyorelict Nuclear. ... ok
test_table28 (test_CodonTable.SingleTableTests)
Check table 28: Condylostoma Nuclear. ... ok
test_table29 (test_CodonTable.SingleTableTests)
Check table 29: Mesodinium Nuclear. ... ok
test_table30 (test_CodonTable.SingleTableTests)
Check table 30: Peritrich Nuclear. ... ok
test_table31 (test_CodonTable.SingleTableTests)
Check table 31: Blastocrithidia Nuclear. ... ok
test_table32 (test_CodonTable.SingleTableTests)
Check table 32: Balanophoraceae Plastid. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.299 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ColorSpiral.py
test_ColorSpiral ... ok
test_dict (test_ColorSpiral.DictTest)
get_color_dict() for classes A-D, no jitter. ... ok
test_colorlist (test_ColorSpiral.SpiralTest)
Get set of eight colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SpiralTest)
Get set of 16 colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SquareTest)
Set of 625 colours, with jitter, using get_colors(). ... ok
----------------------------------------------------------------------
Ran 1 test in 1.367 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Compass.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Compass ... ok
testAlignmentParsingOne (test_Compass.CompassTest) ... ok
testAlignmentParsingTwo (test_Compass.CompassTest) ... ok
testCompassIteratorEasy (test_Compass.CompassTest) ... ok
testCompassIteratorHard (test_Compass.CompassTest) ... ok
testCompassParser (test_Compass.CompassTest) ... ok
testCompassScanAndConsume (test_Compass.CompassTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.236 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Consensus.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Consensus ... ok
test_bitstring (test_Consensus.BitStringTest) ... ok
test_bootstrap (test_Consensus.BootstrapTest) ... ok
test_bootstrap_consensus (test_Consensus.BootstrapTest) ... ok
test_bootstrap_trees (test_Consensus.BootstrapTest) ... ok
test_adam_consensus (test_Consensus.ConsensusTest) ... ok
test_count_clades (test_Consensus.ConsensusTest) ... ok
test_get_support (test_Consensus.ConsensusTest) ... ok
test_majority_consensus (test_Consensus.ConsensusTest) ... ok
test_strict_consensus (test_Consensus.ConsensusTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 13.544 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Crystal.py
test_Crystal ... ok
testAdd (test_Crystal.ChainTestCase) ... ok
testAppend (test_Crystal.ChainTestCase) ... ok
testContains (test_Crystal.ChainTestCase) ... ok
testCount (test_Crystal.ChainTestCase) ... ok
testDelItem (test_Crystal.ChainTestCase) ... ok
testDelSlice (test_Crystal.ChainTestCase) ... ok
testEquals (test_Crystal.ChainTestCase) ... ok
testGetItem (test_Crystal.ChainTestCase) ... ok
testGetSlice (test_Crystal.ChainTestCase) ... ok
testIndex (test_Crystal.ChainTestCase) ... ok
testInsert (test_Crystal.ChainTestCase) ... ok
testLen (test_Crystal.ChainTestCase) ... ok
testRemove (test_Crystal.ChainTestCase) ... ok
testSetItem (test_Crystal.ChainTestCase) ... ok
testSetSlice (test_Crystal.ChainTestCase) ... ok
testClear (test_Crystal.CrystalTestCase) ... ok
testDelItem (test_Crystal.CrystalTestCase) ... ok
testGetItem (test_Crystal.CrystalTestCase) ... ok
testHasKey (test_Crystal.CrystalTestCase) ... ok
testItems (test_Crystal.CrystalTestCase) ... ok
testKeys (test_Crystal.CrystalTestCase) ... ok
testLen (test_Crystal.CrystalTestCase) ... ok
testSetItem (test_Crystal.CrystalTestCase) ... ok
testValues (test_Crystal.CrystalTestCase) ... ok
testEquals (test_Crystal.HeteroTestCase) ... ok
testInit (test_Crystal.HeteroTestCase) ... ok
testLen (test_Crystal.HeteroTestCase) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.092 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_DSSP_tool.py
test_DSSP_tool ... skipping. Install dssp if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.422 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Dialign_tool.py
test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.275 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EMBL_unittest.py
test_EMBL_unittest ... ok
test_embl_0_line (test_EMBL_unittest.EMBLTests)
Test SQ line with 0 length sequence. ... ok
test_embl_content_after_co (test_EMBL_unittest.EMBLTests)
Test a ValueError is thrown by content after a CO line. ... ok
test_embl_no_coords (test_EMBL_unittest.EMBLTests)
Test sequence lines without coordinates. ... ok
test_embl_wrong_dr_line (test_EMBL_unittest.EMBLTests)
Test files with wrong DR lines. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.402 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Emboss.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss.
----------------------------------------------------------------------
Ran 1 test in 0.521 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPhylipNew.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools.
----------------------------------------------------------------------
Ran 1 test in 0.393 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPrimer.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_EmbossPrimer ... ok
test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure we get info right from a single primer find. ... ok
test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure we get the data from normal primer3 files okay. ... ok
test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure we can parse an internal oligo file correctly. ... ok
test_mutli_record_full (test_EmbossPrimer.Primer3ParseTest)
Test parsing multiple primer sets (NirK full). ... ok
test_mutli_record_fwd (test_EmbossPrimer.Primer3ParseTest)
Test parsing multiple primer sets (NirK forward). ... ok
test_simple_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure that we can use all single target primer3 files. ... ok
test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest)
Make sure we can output primer information correctly. ... ok
test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest)
Make sure the output from a simple primersearch file is correct. ... ok
test_simple_parse (test_EmbossPrimer.PrimersearchParseTest)
Make sure that we can parse all primersearch files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Entrez ... ok
test_custom_directory (test_Entrez.CustomDirectoryTest) ... ok
test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction) ... ok
test_construct_cgi_efetch (test_Entrez.TestURLConstruction) ... ok
test_construct_cgi_einfo (test_Entrez.TestURLConstruction)
Test constructed url for request to Entrez. ... ok
test_construct_cgi_elink1 (test_Entrez.TestURLConstruction) ... ok
test_construct_cgi_elink2 (test_Entrez.TestURLConstruction)
Commas: Link from protein to gene. ... ok
test_construct_cgi_elink3 (test_Entrez.TestURLConstruction)
Multiple ID entries: Find one-to-one links from protein to gene. ... ok
test_construct_cgi_epost1 (test_Entrez.TestURLConstruction) ... ok
test_construct_cgi_epost2 (test_Entrez.TestURLConstruction) ... ok
test_email_warning (test_Entrez.TestURLConstruction)
Test issuing warning when user does not specify email address. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.088 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez_online.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Entrez_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.429 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez_parser.py
test_Entrez_parser ... ok
test_efetch_schemas (test_Entrez_parser.EFetchTest)
Test parsing XML using Schemas. ... ok
test_fasta (test_Entrez_parser.EFetchTest)
Test error handling when presented with Fasta non-XML data. ... ok
test_genbank (test_Entrez_parser.EFetchTest)
Test error handling when presented with GenBank non-XML data. ... ok
test_nucleotide1 (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok
test_nucleotide2 (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok
test_omim (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, OMIM database. ... ok
test_protein (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, Protein database. ... ok
test_pubmed1 (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database (first test). ... ok
test_pubmed2 (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database (second test). ... ok
test_pubmed_html (test_Entrez_parser.EFetchTest)
Test error handling when presented with HTML (so XML-like) data. ... ok
test_pubmed_html_escaping (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok
test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok
test_pubmed_html_tags (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok
test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok
test_taxonomy (test_Entrez_parser.EFetchTest)
Test parsing XML returned by EFetch, Taxonomy database. ... ok
test_truncated_xml (test_Entrez_parser.EFetchTest)
Test error handling for a truncated XML declaration. ... ok
test_xml_without_declaration (test_Entrez_parser.EFetchTest)
Test error handling for a missing XML declaration. ... ok
test_egquery1 (test_Entrez_parser.EGQueryTest)
Test parsing XML output returned by EGQuery (first test). ... ok
test_egquery2 (test_Entrez_parser.EGQueryTest)
Test parsing XML output returned by EGQuery (second test). ... ok
test_corrupted (test_Entrez_parser.EInfoTest)
Test if corrupted XML is handled correctly. ... ok
test_list (test_Entrez_parser.EInfoTest)
Test parsing database list returned by EInfo. ... ok
test_pubmed1 (test_Entrez_parser.EInfoTest)
Test parsing database info returned by EInfo. ... ok
test_pubmed2 (test_Entrez_parser.EInfoTest)
Test validating the XML against the DTD. ... ok
test_pubmed3 (test_Entrez_parser.EInfoTest)
Test non-validating parser on XML with an inconsistent DTD. ... ok
test_medline (test_Entrez_parser.ELinkTest)
Test parsing medline indexed articles returned by ELink. ... ok
test_nucleotide (test_Entrez_parser.ELinkTest)
Test parsing Nucleotide to Protein links returned by ELink. ... ok
test_pubmed1 (test_Entrez_parser.ELinkTest)
Test parsing pubmed links returned by ELink (first test). ... ok
test_pubmed2 (test_Entrez_parser.ELinkTest)
Test parsing pubmed links returned by ELink (second test). ... ok
test_pubmed3 (test_Entrez_parser.ELinkTest)
Test parsing pubmed link returned by ELink (third test). ... ok
test_pubmed4 (test_Entrez_parser.ELinkTest)
Test parsing pubmed links returned by ELink (fourth test). ... ok
test_pubmed5 (test_Entrez_parser.ELinkTest)
Test parsing pubmed links returned by ELink (fifth test). ... ok
test_pubmed6 (test_Entrez_parser.ELinkTest)
Test parsing pubmed links returned by ELink (sixth test). ... ok
test_epost (test_Entrez_parser.EPostTest)
Test parsing XML returned by EPost. ... ok
test_invalid (test_Entrez_parser.EPostTest)
Test parsing XML returned by EPost with invalid id (overflow tag). ... ok
test_wrong (test_Entrez_parser.EPostTest)
Test parsing XML returned by EPost with incorrect arguments. ... ok
test_journals (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from the Journals database. ... ok
test_notfound (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch when no items were found. ... ok
test_nucleotide (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from the Nucleotide database. ... ok
test_pmc (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from PubMed Central. ... ok
test_protein (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from the Protein database. ... ok
test_pubmed1 (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from PubMed (first test). ... ok
test_pubmed2 (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from PubMed (second test). ... ok
test_pubmed3 (test_Entrez_parser.ESearchTest)
Test parsing XML returned by ESearch from PubMed (third test). ... ok
test_espell (test_Entrez_parser.ESpellTest)
Test parsing XML output returned by ESpell. ... ok
test_integer_none (test_Entrez_parser.ESummaryTest)
Test parsing ESummary XML where an Integer is not defined. ... ok
test_journals (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the Journals database. ... ok
test_nucleotide (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the Nucleotide database. ... ok
test_protein (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the Protein database. ... ok
test_pubmed (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from PubMed. ... ok
test_structure (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the Structure database. ... ok
test_taxonomy (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the Taxonomy database. ... ok
test_unists (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary from the UniSTS database. ... ok
test_wrong (test_Entrez_parser.ESummaryTest)
Test parsing XML returned by ESummary with incorrect arguments. ... ok
test_BytesIO (test_Entrez_parser.GeneralTests)
Test parsing a BytesIO handle (bytes not unicode). ... ok
test_StringIO (test_Entrez_parser.GeneralTests)
Test parsing a StringIO handle (unicode not bytes). ... ok
test_bytes_handle (test_Entrez_parser.GeneralTests)
Test parsing a handle opened in binary mode. ... ok
test_closed_handle (test_Entrez_parser.GeneralTests)
Test parsing closed handle fails gracefully. ... ok
test_text_handle (test_Entrez_parser.GeneralTests)
Test parsing a handle opened in text mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.320 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Enzyme.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Enzyme ... ok
test_lactate (test_Enzyme.TestEnzyme)
Parsing ENZYME record for lactate racemase (5.1.2.1). ... ok
test_lipoprotein (test_Enzyme.TestEnzyme)
Parsing ENZYME record for lipoprotein lipase (3.1.1.34). ... ok
test_parse_many (test_Enzyme.TestEnzyme)
Check parse function with multiple records. ... ok
test_parse_one (test_Enzyme.TestEnzyme)
Check parse function with one record. ... ok
test_parse_zero (test_Enzyme.TestEnzyme) ... ok
test_proline (test_Enzyme.TestEnzyme)
Parsing ENZYME record for proline racemase (5.1.1.4). ... ok
test_valine (test_Enzyme.TestEnzyme)
Parsing ENZYME record for valine decarboxylase (4.1.1.14). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.054 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ExPASy.py
test_ExPASy ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.176 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_FSSP.py
test_FSSP ... ok
test_alignment (test_FSSP.TestGeo) ... ok
test_attributes (test_FSSP.TestGeo) ... ok
----------------------------------------------------------------------
Ran 1 test in 15.410 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Fasttree_tool.py
test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.560 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_File.py
test_File ... ok
test_custom_path_like_object (test_File.AsHandleTestCase)
Test as_handle with a custom path-like object. ... ok
test_handle (test_File.AsHandleTestCase)
Test as_handle with a file-like object argument. ... ok
test_path_object (test_File.AsHandleTestCase)
Test as_handle with a pathlib.Path object. ... ok
test_string_path (test_File.AsHandleTestCase)
Test as_handle with a string path argument. ... ok
test_stringio (test_File.AsHandleTestCase)
Testing passing StringIO handles. ... ok
test_bgzf (test_File.RandomAccess)
Test BGZF compressed file. ... ok
test_gzip (test_File.RandomAccess)
Test gzip compressed file. ... ok
test_plain (test_File.RandomAccess)
Test plain text file. ... ok
test_one (test_File.UndoHandleTests)
First test. ... ok
test_read (test_File.UndoHandleTests)
Test read method. ... ok
test_undohandle_read_block (test_File.UndoHandleTests)
Test reading in blocks. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.062 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenBank.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_GenBank ... ok
test_embl_cds_interaction (test_GenBank.GenBankScannerTests)
Test EMBL CDS interaction, parse CDS features on embl files. ... ok
test_embl_record_interaction (test_GenBank.GenBankScannerTests)
Test EMBL Record interaction on embl files. ... ok
test_genbank_cds_interaction (test_GenBank.GenBankScannerTests)
Test CDS interaction, parse CDS features on gb(k) files. ... ok
test_genbank_interaction (test_GenBank.GenBankScannerTests)
Test GenBank records interaction on gbk files. ... ok
test_000_genbank_bad_loc_wrap_warning (test_GenBank.GenBankTests)
Feature line wrapping warning. ... ok
test_001_genbank_bad_origin_wrapping_location (test_GenBank.GenBankTests)
Bad origin wrapping. ... ok
test_001_implicit_orign_wrap_fix (test_GenBank.GenBankTests)
Attempt to fix implied origin wrapping. ... ok
test_001_negative_location_warning (test_GenBank.GenBankTests)
Un-parsable feature location warning. ... ok
test_compound_complex_origin_wrap (test_GenBank.GenBankTests)
Test the attempts to fix compound complex origin wrapping. ... ok
test_dbline_embl_gb (test_GenBank.GenBankTests)
Parse GenBank/EMBL paired records with PR project entry: EMBL. ... ok
test_dbline_gb_embl (test_GenBank.GenBankTests)
Parse GenBank/EMBL paired records with PR project entry: GenBank. ... ok
test_dblink (test_GenBank.GenBankTests)
Parse GenBank record with old DBLINK project entry. ... ok
test_dblink_two (test_GenBank.GenBankTests)
Parse GenBank record with old and new DBLINK project entries. ... ok
test_dot_lineage (test_GenBank.GenBankTests)
Missing taxonomy lineage. ... ok
test_fuzzy_origin_wrap (test_GenBank.GenBankTests)
Test features that wrap an origin, and have fuzzy location. ... ok
test_genbank_bad_loc_wrap_parsing (test_GenBank.GenBankTests)
Bad location wrapping. ... ok
test_genbank_date_correct (test_GenBank.GenBankTests)
Check if user provided date is inserted correctly. ... ok
test_genbank_date_datetime (test_GenBank.GenBankTests)
Check if datetime objects are handled correctly. ... ok
test_genbank_date_default (test_GenBank.GenBankTests)
Check if default date is handled correctly. ... ok
test_genbank_date_invalid (test_GenBank.GenBankTests)
Check if invalid dates are treated as default. ... ok
test_genbank_date_list (test_GenBank.GenBankTests)
Check if date lists are handled correctly. ... ok
test_genbank_read (test_GenBank.GenBankTests)
GenBank.read(...) simple test. ... ok
test_genbank_read_invalid (test_GenBank.GenBankTests)
GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok
test_genbank_read_multirecord (test_GenBank.GenBankTests)
GenBank.read(...) error on multiple record input. ... ok
test_genbank_read_no_origin_no_end (test_GenBank.GenBankTests)
GenBank.read(...) error on malformed file. ... ok
test_implicit_orign_wrap_extract_and_translate (test_GenBank.GenBankTests)
Test that features wrapped around origin give expected data. ... ok
test_invalid_product_line_raises_value_error (test_GenBank.GenBankTests)
Parsing invalid product line. ... ok
test_locus_line_topogoly (test_GenBank.GenBankTests)
Test if chromosome topology is conserved. ... ok
test_long_names (test_GenBank.GenBankTests)
Various GenBank names which push the column based LOCUS line. ... ok
test_longer_locus_line (test_GenBank.GenBankTests)
Check that we can read and write files with longer locus lines. ... ok
test_negative_location (test_GenBank.GenBankTests)
Negative feature locations. ... ok
test_qualifier_escaping_read (test_GenBank.GenBankTests)
Check qualifier escaping is preserved when parsing. ... ok
test_qualifier_escaping_write (test_GenBank.GenBankTests)
Check qualifier escaping is preserved when writing. ... ok
test_qualifier_order (test_GenBank.GenBankTests)
Check the qualifier order is preserved. ... ok
test_structured_comment_parsing (test_GenBank.GenBankTests)
Structued comment parsing. ... ok
test_first_line_imgt (test_GenBank.LineOneTests)
Check IMGT ID line parsing. ... ok
test_topology_embl (test_GenBank.LineOneTests)
Check EMBL ID line parsing. ... ok
test_topology_genbank (test_GenBank.LineOneTests)
Check GenBank LOCUS line parsing. ... ok
test_000_write_invalid_but_parsed_locus_line (test_GenBank.OutputTests)
Make sure we survive writing slightly invalid LOCUS lines we could parse. ... ok
test_mad_dots (test_GenBank.OutputTests)
Writing and reading back accesssion.version variants. ... ok
test_seqrecord_default_description (test_GenBank.OutputTests)
Read in file using SeqRecord default description. ... ok
test_cleaning_features (test_GenBank.TestBasics)
Test the ability to clean up feature values. ... ok
test_ensembl_locus (test_GenBank.TestBasics)
Test the ENSEMBL locus line. ... ok
test_write_format (test_GenBank.TestBasics)
Test writing to the difference formats. ... ok
test_feature_parser_01 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_02 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_03 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_04 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_05 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_06 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_07 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_08 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_09 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_10 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_11 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_12 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_13 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_14 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_15 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_16 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_17 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_18 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_19 (test_GenBank.TestFeatureParser) ... ok
test_feature_parser_20 (test_GenBank.TestFeatureParser) ... ok
test_record_parser_01 (test_GenBank.TestRecordParser) ... ok
test_record_parser_02 (test_GenBank.TestRecordParser) ... ok
test_record_parser_03 (test_GenBank.TestRecordParser) ... ok
test_record_parser_04 (test_GenBank.TestRecordParser) ... ok
test_record_parser_05 (test_GenBank.TestRecordParser) ... ok
test_record_parser_06 (test_GenBank.TestRecordParser) ... ok
test_record_parser_07 (test_GenBank.TestRecordParser) ... ok
test_record_parser_08 (test_GenBank.TestRecordParser) ... ok
test_record_parser_09 (test_GenBank.TestRecordParser) ... ok
test_record_parser_10 (test_GenBank.TestRecordParser) ... ok
test_record_parser_11 (test_GenBank.TestRecordParser) ... ok
test_record_parser_12 (test_GenBank.TestRecordParser) ... ok
test_record_parser_13 (test_GenBank.TestRecordParser) ... ok
test_record_parser_14 (test_GenBank.TestRecordParser) ... ok
test_record_parser_15 (test_GenBank.TestRecordParser) ... ok
test_record_parser_16 (test_GenBank.TestRecordParser) ... ok
test_record_parser_17 (test_GenBank.TestRecordParser) ... ok
test_record_parser_18 (test_GenBank.TestRecordParser) ... ok
test_record_parser_19 (test_GenBank.TestRecordParser) ... ok
test_record_parser_20 (test_GenBank.TestRecordParser) ... ok
test_record_parser_tsa (test_GenBank.TestRecordParser) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.483 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenomeDiagram.py
test_GenomeDiagram ... Warn: Can't find .pfb for face 'Times-Roman'
ok
test_color_conversions (test_GenomeDiagram.ColorsTest)
Test color translations. ... ok
test_add_track (test_GenomeDiagram.DiagramTest)
Add track. ... ok
test_add_track_error (test_GenomeDiagram.DiagramTest)
Test adding unspecified track. ... ok
test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest)
Add track to occupied level. ... ok
test_del_tracks (test_GenomeDiagram.DiagramTest)
Delete track. ... ok
test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest)
Construct and draw PDF using method approach. ... ok
test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest)
Construct and draw PDF using object approach. ... ok
test_get_tracks (test_GenomeDiagram.DiagramTest)
Get track. ... ok
test_move_track (test_GenomeDiagram.DiagramTest)
Move a track. ... ok
test_partial_diagram (test_GenomeDiagram.DiagramTest)
Construct and draw SVG and PDF for just part of a SeqRecord. ... ok
test_renumber (test_GenomeDiagram.DiagramTest)
Test renumbering tracks. ... ok
test_str (test_GenomeDiagram.DiagramTest)
Test diagram's info as string. ... ok
test_write_arguments (test_GenomeDiagram.DiagramTest)
Check how the write methods respond to output format arguments. ... ok
test_limits (test_GenomeDiagram.GraphTest)
Check line graphs. ... ok
test_slicing (test_GenomeDiagram.GraphTest)
Check GraphData slicing. ... ok
test_label_default (test_GenomeDiagram.LabelTest)
Feature labels - default. ... ok
test_all_sigils (test_GenomeDiagram.SigilsTest)
All sigils. ... ok
test_arrow_heads (test_GenomeDiagram.SigilsTest)
Feature arrow sigils, varying heads. ... ok
test_arrow_shafts (test_GenomeDiagram.SigilsTest)
Feature arrow sigils, varying shafts. ... ok
test_big_arrow_shafts (test_GenomeDiagram.SigilsTest)
Feature big-arrow sigils, varying shafts. ... ok
test_labels (test_GenomeDiagram.SigilsTest)
Feature labels. ... ok
test_long_arrow_heads (test_GenomeDiagram.SigilsTest)
Feature ARROW sigil heads within bounding box. ... ok
test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest)
Feature BIGARROW sigil heads within bounding box. ... ok
test_long_jaggy (test_GenomeDiagram.SigilsTest)
Feature JAGGY sigil heads within bounding box. ... ok
test_long_octo_heads (test_GenomeDiagram.SigilsTest)
Feature OCTO sigil heads within bounding box. ... ok
test_short_arrow (test_GenomeDiagram.SigilsTest)
Feature arrow sigil heads within bounding box. ... ok
test_short_bigarrow (test_GenomeDiagram.SigilsTest)
Feature big-arrow sigil heads within bounding box. ... ok
test_short_jaggy (test_GenomeDiagram.SigilsTest)
Feature arrow sigil heads within bounding box. ... ok
test_short_octo (test_GenomeDiagram.SigilsTest)
Feature big-arrow sigil heads within bounding box. ... ok
----------------------------------------------------------------------
Ran 1 test in 17.263 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsBitmaps.py
test_GraphicsBitmaps ... Warn: Can't find .pfb for face 'Times-Roman'
skipping. Check the fonts needed by ReportLab if you want bitmaps from Bio.Graphics
Can't setFont(Times-Roman) missing the T1 files?
Originally <class 'TypeError'>: makeT1Font() argument 2 must be str, not None
----------------------------------------------------------------------
Ran 1 test in 1.692 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsChromosome.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_GraphicsChromosome ... ok
test_add_count (test_GraphicsChromosome.ChromosomeCountTest)
Add counts to specific chromosome segments. ... ok
test_add_label (test_GraphicsChromosome.ChromosomeCountTest)
Add labels to chromosome segments. ... ok
test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest)
Retrieve a color from a count number with the default color scheme. ... ok
test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest)
Test filling out the information on a chromosome. ... ok
test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest)
Test retrieval of segment information. ... ok
test_set_scale (test_GraphicsChromosome.ChromosomeCountTest)
Set the scale for a chromosome segment. ... ok
test_random_organism (test_GraphicsChromosome.OrganismGraphicTest)
Generate an organism with random chromosome info. ... ok
test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest)
Test the basic functionality of drawing an organism. ... ok
test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest)
Output a simple organism to a PDF file. ... ok
test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest)
Output a simple organism to a postscript file. ... ok
test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest)
Output a simple organism to an SVG file. ... ok
test_widget (test_GraphicsChromosome.OrganismGraphicTest)
Try widget derived functionality. ... ok
test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest)
Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis. ... ok
test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest)
Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis. ... ok
----------------------------------------------------------------------
Ran 1 test in 6.588 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsDistribution.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_GraphicsDistribution ... ok
test_multi_page (test_GraphicsDistribution.BarChartTest)
Create a page with multiple distributions on it. ... ok
test_simple_page (test_GraphicsDistribution.BarChartTest)
Test displaying a page with single distribution. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.693 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsGeneral.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_GraphicsGeneral ... ok
test_simple_scatter_plot_1 (test_GraphicsGeneral.ComparativeTest)
Test creation of a simple ScatterPlot with one list. ... ok
test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest)
Test creation of a simple ScatterPlot with more lists. ... ok
----------------------------------------------------------------------
Ran 1 test in 3.923 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMCasino.py
test_HMMCasino ... ok
test_baum_welch_training_standard (test_HMMCasino.TestHMMCasino)
Standard Training with known states. ... ok
test_baum_welch_training_without (test_HMMCasino.TestHMMCasino)
Baum-Welch training without known state sequences. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.413 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_HMMGeneral.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_HMMGeneral ... ok
test_log_likelihood (test_HMMGeneral.AbstractTrainerTest)
Calculate log likelihood. ... ok
test_ml_estimator (test_HMMGeneral.AbstractTrainerTest)
Test the maximum likelihood estimator for simple cases. ... ok
test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest)
Testing allow_transition. ... ok
test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest)
Non-ergodic model (meaning that some transitions are not allowed). ... ok
test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest)
Test a simple model with 2 states and 2 symbols. ... ok
test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest)
Testing the calculation of transitions_from. ... ok
test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest)
Testing the calculation of transitions_to. ... ok
test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest)
Testing allow_all_transitions. ... ok
test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest)
Making sure MarkovModelBuilder is initialized correctly. ... ok
test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest)
Testing the calculation of s values. ... ok
test_empty_state_training_sequence (test_HMMGeneral.TrainingSequenceTest) ... ok
test_invalid_training_sequence (test_HMMGeneral.TrainingSequenceTest) ... ok
test_valid_training_sequence (test_HMMGeneral.TrainingSequenceTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.282 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_KDTree.py
test_KDTree ... ok
test_KDTree (test_KDTree.KDTreeTest) ... ok
test_KDTree_exceptions (test_KDTree.KDTreeTest) ... ok
test_KDTree_neighbour (test_KDTree.KDTreeTest) ... ok
test_all_search (test_KDTree.KDTreeTest) ... ok
test_search (test_KDTree.KDTreeTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 7.167 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG.py
test_KEGG ... ok
test_irregular (test_KEGG.CompoundTests) ... ok
test_sample (test_KEGG.CompoundTests) ... ok
test_4letter (test_KEGG.EnzymeTests) ... ok
test_exceptions (test_KEGG.EnzymeTests) ... ok
test_irregular (test_KEGG.EnzymeTests) ... ok
test_new (test_KEGG.EnzymeTests) ... ok
test_sample (test_KEGG.EnzymeTests) ... ok
test_map00950 (test_KEGG.MapTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 4.336 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG_online.py
test_KEGG_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 2.457 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_KGML_graphics ... ok
test_render_KGML_basic (test_KGML_graphics.KGMLPathwayTest)
Basic rendering of KGML: write to PDF without modification. ... ok
test_render_KGML_modify (test_KGML_graphics.KGMLPathwayTest)
Rendering of KGML to PDF, with modification. ... ok
test_render_KGML_transparency (test_KGML_graphics.KGMLPathwayTest)
Rendering of KGML to PDF, with color alpha channel. ... ok
----------------------------------------------------------------------
Ran 1 test in 65.066 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics_online.py
test_KGML_graphics_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.165 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_nographics.py
test_KGML_nographics ... ok
test_read_and_write_KGML_files (test_KGML_nographics.KGMLPathwayTest)
Read KGML from, and write KGML to, local files. ... ok
----------------------------------------------------------------------
Ran 1 test in 15.575 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KeyWList.py
test_KeyWList ... ok
test_parse (test_KeyWList.KeyWListTest)
Test parsing keywlist.txt works. ... ok
test_parse2 (test_KeyWList.KeyWListTest)
Parsing keywlist2.txt (without header and footer). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.148 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_LogisticRegression.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_LogisticRegression ... ok
test_calculate_model (test_LogisticRegression.TestLogisticRegression) ... ok
test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression) ... ok
test_calculate_probability (test_LogisticRegression.TestLogisticRegression) ... ok
test_classify (test_LogisticRegression.TestLogisticRegression) ... ok
test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression) ... ok
test_leave_one_out (test_LogisticRegression.TestLogisticRegression) ... ok
test_model_accuracy (test_LogisticRegression.TestLogisticRegression) ... ok
test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression) ... ok
test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.337 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MSAProbs_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.427 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MafIO_index.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_MafIO_index ... ok
test_bundle_without_target (test_MafIO_index.NewIndexTest) ... ok
test_good_big (test_MafIO_index.NewIndexTest) ... ok
test_good_small (test_MafIO_index.NewIndexTest) ... ok
test_length_coords_mismatch (test_MafIO_index.NewIndexTest) ... ok
test_old (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest) ... ok
test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest) ... ok
test_region2bin (test_MafIO_index.StaticMethodTest) ... ok
test_ucscbin (test_MafIO_index.StaticMethodTest) ... ok
test_records_begin (test_MafIO_index.TestGetRecord) ... ok
test_records_end (test_MafIO_index.TestGetRecord) ... ok
test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF) ... ok
test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF)
Following issues 504 and 1086. ... ok
test_correct_block_length (test_MafIO_index.TestSearchGoodMAF)
Following issues 504 and 1086. ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF)
Correct retrieval of Cnksr3 in mouse. ... ok
test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF) ... ok
test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF)
Following issue 1083. ... ok
test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF)
Checking that spliced sequences are correct. ... ok
test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF)
Checking that spliced sequences are correct. ... ok
test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF) ... ok
test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF) ... ok
test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF) ... ok
test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF) ... ok
test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF) ... ok
test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF) ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF)
Correct retrieval of Cnksr3 in mouse. ... ok
test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF) ... ok
test_no_alignment (test_MafIO_index.TestSpliceGoodMAF) ... ok
----------------------------------------------------------------------
Ran 1 test in 5.129 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Mafft_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.276 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MarkovModel.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_MarkovModel ... ok
test_argmaxes (test_MarkovModel.TestMarkovModel) ... ok
test_backward (test_MarkovModel.TestMarkovModel) ... ok
test_baum_welch (test_MarkovModel.TestMarkovModel) ... ok
test_forward (test_MarkovModel.TestMarkovModel) ... ok
test_logsum_and_exp_logsum (test_MarkovModel.TestMarkovModel) ... ok
test_logvecadd (test_MarkovModel.TestMarkovModel) ... ok
test_mle (test_MarkovModel.TestMarkovModel) ... ok
test_normalize_and_copy_and_check (test_MarkovModel.TestMarkovModel) ... ok
test_random_norm (test_MarkovModel.TestMarkovModel) ... ok
test_readline_and_check_start (test_MarkovModel.TestMarkovModel) ... ok
test_save_and_load (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder1 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder2 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder3 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder4 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder5 (test_MarkovModel.TestMarkovModel) ... ok
test_train_bw (test_MarkovModel.TestMarkovModel) ... ok
test_train_visible (test_MarkovModel.TestMarkovModel) ... ok
test_uniform_norm (test_MarkovModel.TestMarkovModel) ... ok
test_viterbi (test_MarkovModel.TestMarkovModel) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.387 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_Medline.py
test_Medline ... ok
test_multiline_mesh (test_Medline.TestMedline) ... ok
test_parse (test_Medline.TestMedline) ... ok
test_read (test_Medline.TestMedline) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.053 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Muscle_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.519 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NACCESS_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_NACCESS_tool ... skipping. Install naccess if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.327 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBITextParser.py
test_NCBITextParser ... ok
test_conversion (test_NCBITextParser.TestBlastRecord)
Converting a Blast record multiple alignment. ... ok
test_text_2010L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.0.10 output (text_2010L_blastn_001). ... ok
test_text_2010L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.0.10 output without alignments (text_2010L_blastn_002). ... ok
test_text_2010L_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.0.10 output without descriptions (text_2010L_blastn_003). ... ok
test_text_2010L_blastn_004 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.0.10 output (text_2010L_blastn_004). ... ok
test_text_2010L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_001). ... ok
test_text_2010L_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.10 output without hits (text_2010L_blastp_002). ... ok
test_text_2010L_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_003). ... ok
test_text_2010L_blastp_004 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.10 output without descriptions (text_2010L_blastp_004). ... ok
test_text_2010L_blastp_005 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.10 output without alignments (text_2010L_blastp_005). ... ok
test_text_2010L_blastp_006 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_006). ... ok
test_text_2010L_blastp_007 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_007). ... ok
test_text_2010L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.0.10 output (text_2010L_blastx_001). ... ok
test_text_2010L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.0.10 output without hits (text_2010L_blastx_002). ... ok
test_text_2010L_phiblast_001 (test_NCBITextParser.TestNCBITextParser)
Parsing PHI-BLAST, BLASTP 2.0.10 output, one round (text_2010L_phiblast_001). ... ok
test_text_2010L_phiblast_002 (test_NCBITextParser.TestNCBITextParser)
Parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (text_2010L_phiblast_002). ... ok
test_text_2010L_phiblast_003 (test_NCBITextParser.TestNCBITextParser)
Parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (text_2010L_phiblast_003). ... ok
test_text_2010L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTN 2.0.10 output (text_2010L_tblastn_001). ... ok
test_text_2010L_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTN 2.0.10 output without hits (text_2010L_tblastn_002). ... ok
test_text_2010L_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTX 2.0.10 output (text_2010L_tblastx_001). ... ok
test_text_2011L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.0.11 output (text_2011L_blastn_001). ... ok
test_text_2011L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.0.11 output without alignments (text_2011L_blastn_002). ... ok
test_text_2011L_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.0.11 output without descriptions (text_2011L_blastn_003). ... ok
test_text_2011L_blastn_004 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.0.11 output (text_2011L_blastn_004). ... ok
test_text_2011L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_001). ... ok
test_text_2011L_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.11 output without hits (text_2011L_blastp_002). ... ok
test_text_2011L_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_003). ... ok
test_text_2011L_blastp_004 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.11 output without descriptions (text_2011L_blastp_004). ... ok
test_text_2011L_blastp_005 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.11 output without alignments (text_2011L_blastp_005). ... ok
test_text_2011L_blastp_006 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_006). ... ok
test_text_2011L_blastp_007 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_007). ... ok
test_text_2011L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.0.11 output (text_2011L_blastx_001). ... ok
test_text_2011L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.0.11 output without hits (text_2011L_blastx_002). ... ok
test_text_2011L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_001). ... ok
test_text_2011L_psiblast_002 (test_NCBITextParser.TestNCBITextParser)
Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_002). ... ok
test_text_2011L_psiblast_003 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.11 output (text_2011L_psiblast_003). ... ok
test_text_2011L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTN 2.0.11 output (text_2011L_tblastn_001). ... ok
test_text_2011L_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTN 2.0.11 output without hits (text_2011L_tblastn_002). ... ok
test_text_2011L_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTX 2.0.11 output (text_2011L_tblastx_001). ... ok
test_text_2012L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.12 output (text_2012L_psiblast_001). ... ok
test_text_2014L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.0.14 output (text_2014L_blastn_001). ... ok
test_text_2014L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.0.14 output (text_2014L_psiblast_001). ... ok
test_text_2201L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.2.1 output (text_2201L_blastx_001). ... ok
test_text_2202L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.2.2 output with error messages (text_2202L_blastn_001). ... ok
test_text_2202L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.2.2 output with missing error messages (text_2202L_blastn_002). ... ok
test_text_2202L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.2.2 output with multiple records (text_2202L_blastp_001). ... ok
test_text_2208L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.2.8 output (text_2208L_psiblast_001). ... ok
test_text_2215L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.2.15 output with no hits (text_2215L_blastx_001). ... ok
test_text_2216L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTN 2.2.16 output (text_2216L_tblastn_001). ... ok
test_text_2220L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.2.20 output (text_2220L_blastx_001). ... ok
test_text_2220L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.2.20 output with multiple queries (text_2220L_blastx_002). ... ok
test_text_2221L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.2.21 output with multiple queries (text_2221L_blastp_001). ... ok
test_text_2222L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.2.22 output with multiple queries (text_2222L_blastx_001). ... ok
test_text_2222_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.2.22+ output with multiple queries (text_2222_blastx_001). ... ok
test_text_2226_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.2.26+ output with no results. ... ok
test_text_2226_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.2.26+ with no results. ... ok
test_text_2226_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.2.26+ with single hsp results. ... ok
test_text_2226_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.2.26+ with no results. ... ok
test_text_2226_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTX 2.2.26+ with single hsp results. ... ok
test_text_2226_blastx_003 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTN 2.2.26+ output with no results. ... ok
test_text_2226_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastn_003 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTX 2.2.26+ output with no results. ... ok
test_text_2226_tblastx_002 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTX 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastx_003 (test_NCBITextParser.TestNCBITextParser)
Parsing TBLASTX 2.2.26+ output with multiple hsp results present. ... ok
test_text_2230_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Parsing BLASTP 2.2.30+ output with line of dashes. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.463 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBIXML.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_NCBIXML ... ok
test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001). ... ok
test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001). ... ok
test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001). ... ok
test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML)
Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001). ... ok
test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML)
Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001). ... ok
test_xml_2218L_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001). ... ok
test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML)
Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001). ... ok
test_xml_2218_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001). ... ok
test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002). ... ok
test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001). ... ok
test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001). ... ok
test_xml_2900_blastn_001_v1 (test_NCBIXML.TestNCBIXML) ... ok
test_xml_2900_blastn_001_v2 (test_NCBIXML.TestNCBIXML) ... ok
test_xml_2900_blastp_001_v1 (test_NCBIXML.TestNCBIXML) ... ok
test_xml_2900_blastp_001_v2 (test_NCBIXML.TestNCBIXML) ... ok
test_xml_2900_blastx_001_v1 (test_NCBIXML.TestNCBIXML) ... ok
test_xml_2900_blastx_001_v2 (test_NCBIXML.TestNCBIXML) ... ok
test_xml_2900_tblastn_001_v1 (test_NCBIXML.TestNCBIXML) ... ok
test_xml_2900_tblastn_001_v2 (test_NCBIXML.TestNCBIXML) ... ok
test_xml_2900_tblastx_001_v1 (test_NCBIXML.TestNCBIXML) ... ok
test_xml_2900_tblastx_001_v2 (test_NCBIXML.TestNCBIXML) ... ok
----------------------------------------------------------------------
Ran 1 test in 35.009 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBI_BLAST_tools.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.068 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBI_qblast.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_NCBI_qblast ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.264 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NMR.py
test_NMR ... ok
test_noetools (test_NMR.NmrTests)
Self test for NMR.NOEtools. ... ok
test_xpktools (test_NMR.NmrTests)
Self test for NMR.xpktools. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NaiveBayes.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_NaiveBayes ... ok
test_car_data (test_NaiveBayes.CarTest)
Simple example using car data. ... ok
test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest) ... ok
test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest) ... ok
test_classify_function (test_NaiveBayes.NaiveBayesTest) ... ok
test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest) ... ok
test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest) ... ok
test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest) ... ok
test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.047 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_baseml.py
test_PAML_baseml ... ok
testAlignmentExists (test_PAML_baseml.ModTest) ... ok
testAlignmentFileIsValid (test_PAML_baseml.ModTest) ... ok
testAlignmentSpecified (test_PAML_baseml.ModTest) ... ok
testCtlFileExistsOnRead (test_PAML_baseml.ModTest) ... ok
testCtlFileExistsOnRun (test_PAML_baseml.ModTest) ... ok
testCtlFileValidOnRead (test_PAML_baseml.ModTest) ... ok
testCtlFileValidOnRun (test_PAML_baseml.ModTest) ... ok
testOptionExists (test_PAML_baseml.ModTest) ... ok
testOutputFileSpecified (test_PAML_baseml.ModTest) ... ok
testPamlErrorsCaught (test_PAML_baseml.ModTest) ... ok
testParseAllVersions (test_PAML_baseml.ModTest) ... ok
testParseAlpha1Rho1 (test_PAML_baseml.ModTest) ... ok
testParseModel (test_PAML_baseml.ModTest) ... ok
testParseNhomo (test_PAML_baseml.ModTest) ... ok
testParseSEs (test_PAML_baseml.ModTest) ... ok
testResultsExist (test_PAML_baseml.ModTest) ... ok
testResultsParsable (test_PAML_baseml.ModTest) ... ok
testResultsValid (test_PAML_baseml.ModTest) ... ok
testTreeExists (test_PAML_baseml.ModTest) ... ok
testTreeFileValid (test_PAML_baseml.ModTest) ... ok
testTreeSpecified (test_PAML_baseml.ModTest) ... ok
testWorkingDirValid (test_PAML_baseml.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.019 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_codeml.py
test_PAML_codeml ... ok
testAlignmentExists (test_PAML_codeml.ModTest) ... ok
testAlignmentFileIsValid (test_PAML_codeml.ModTest) ... ok
testAlignmentSpecified (test_PAML_codeml.ModTest) ... ok
testCtlFileExistsOnRead (test_PAML_codeml.ModTest) ... ok
testCtlFileExistsOnRun (test_PAML_codeml.ModTest) ... ok
testCtlFileValidOnRead (test_PAML_codeml.ModTest) ... ok
testCtlFileValidOnRun (test_PAML_codeml.ModTest) ... ok
testOptionExists (test_PAML_codeml.ModTest) ... ok
testOutputFileSpecified (test_PAML_codeml.ModTest) ... ok
testPamlErrorsCaught (test_PAML_codeml.ModTest) ... ok
testParseAA (test_PAML_codeml.ModTest) ... ok
testParseAAPairwise (test_PAML_codeml.ModTest) ... ok
testParseAllNSsites (test_PAML_codeml.ModTest) ... ok
testParseBranchSiteA (test_PAML_codeml.ModTest) ... ok
testParseCladeModelC (test_PAML_codeml.ModTest) ... ok
testParseFreeRatio (test_PAML_codeml.ModTest) ... ok
testParseM2arel (test_PAML_codeml.ModTest) ... ok
testParseNSsite3 (test_PAML_codeml.ModTest) ... ok
testParseNgene2Mgene02 (test_PAML_codeml.ModTest) ... ok
testParseNgene2Mgene1 (test_PAML_codeml.ModTest) ... ok
testParseNgene2Mgene34 (test_PAML_codeml.ModTest) ... ok
testParsePairwise (test_PAML_codeml.ModTest) ... ok
testParseSEs (test_PAML_codeml.ModTest) ... ok
testParseSitesParamsForPairwise (test_PAML_codeml.ModTest)
Verify that pairwise site estimates are indeed parsed. Fixes #483. ... ok
testResultsExist (test_PAML_codeml.ModTest) ... ok
testResultsParsable (test_PAML_codeml.ModTest) ... ok
testResultsValid (test_PAML_codeml.ModTest) ... ok
testTreeExists (test_PAML_codeml.ModTest) ... ok
testTreeFileValid (test_PAML_codeml.ModTest) ... ok
testTreeParseVersatility (test_PAML_codeml.ModTest)
Test finding trees in the results. ... ok
testTreeSpecified (test_PAML_codeml.ModTest) ... ok
testWorkingDirValid (test_PAML_codeml.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 4.209 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_tools.py
test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.607 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_yn00.py
test_PAML_yn00 ... ok
testAlignmentExists (test_PAML_yn00.ModTest) ... ok
testAlignmentFileIsValid (test_PAML_yn00.ModTest) ... ok
testAlignmentSpecified (test_PAML_yn00.ModTest) ... ok
testCtlFileExistsOnRead (test_PAML_yn00.ModTest) ... ok
testCtlFileExistsOnRun (test_PAML_yn00.ModTest) ... ok
testCtlFileValidOnRead (test_PAML_yn00.ModTest) ... ok
testCtlFileValidOnRun (test_PAML_yn00.ModTest) ... ok
testOptionExists (test_PAML_yn00.ModTest) ... ok
testOutputFileSpecified (test_PAML_yn00.ModTest) ... ok
testParseAllVersions (test_PAML_yn00.ModTest) ... ok
testParseDottedNames (test_PAML_yn00.ModTest) ... ok
testParseDottedNumNames (test_PAML_yn00.ModTest) ... ok
testParseLongNames (test_PAML_yn00.ModTest) ... ok
testResultsExist (test_PAML_yn00.ModTest) ... ok
testResultsParsable (test_PAML_yn00.ModTest) ... ok
testResultsValid (test_PAML_yn00.ModTest) ... ok
testWorkingDirValid (test_PAML_yn00.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.953 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB.py
test_PDB ... ok
test_1_warnings (test_PDB.A_ExceptionTest)
Check warnings: Parse a flawed PDB file in permissive mode. ... ok
test_2_strict (test_PDB.A_ExceptionTest)
Check error: Parse a flawed PDB file in strict mode. ... ok
test_3_bad_xyz (test_PDB.A_ExceptionTest)
Check error: Parse an entry with bad x,y,z value. ... ok
test_4_occupancy (test_PDB.A_ExceptionTest)
Parse file with missing occupancy. ... ok
test_AtomElement (test_PDB.Atom_Element)
Atom Element. ... ok
test_hydrogens (test_PDB.Atom_Element) ... ok
test_ions (test_PDB.Atom_Element)
Element for magnesium is assigned correctly. ... ok
test_change_chain_id (test_PDB.ChangingIdTests)
Change the id of a model. ... ok
test_change_id_to_self (test_PDB.ChangingIdTests)
Changing the id to itself does nothing (does not raise). ... ok
test_change_model_id (test_PDB.ChangingIdTests)
Change the id of a model. ... ok
test_change_model_id_raises (test_PDB.ChangingIdTests)
Cannot change id to a value already in use by another child. ... ok
test_change_residue_id (test_PDB.ChangingIdTests)
Change the id of a residue. ... ok
test_full_id_is_updated_chain (test_PDB.ChangingIdTests)
Invalidate cached full_ids if an id is changed. ... ok
test_full_id_is_updated_residue (test_PDB.ChangingIdTests)
Invalidate cached full_ids if an id is changed. ... ok
test_atom_copy (test_PDB.CopyTests) ... ok
test_entity_copy (test_PDB.CopyTests)
Make a copy of a residue. ... ok
test_DSSP_RSA (test_PDB.DsspTests)
Tests the usage of different ASA tables. ... ok
test_DSSP_file (test_PDB.DsspTests)
Test parsing of pregenerated DSSP. ... ok
test_DSSP_hbonds (test_PDB.DsspTests)
Test parsing of DSSP hydrogen bond information. ... ok
test_DSSP_in_model_obj (test_PDB.DsspTests)
All elements correctly added to xtra attribute of input model object. ... ok
test_DSSP_noheader_file (test_PDB.DsspTests)
Test parsing of pregenerated DSSP missing header information. ... ok
test_ExposureCN (test_PDB.Exposure)
HSExposureCN. ... ok
test_HSExposureCA (test_PDB.Exposure)
HSExposureCA. ... ok
test_HSExposureCB (test_PDB.Exposure)
HSExposureCB. ... ok
test_capsid (test_PDB.HeaderTests)
Parse the header of a known PDB file (1A8O). ... ok
test_fibril (test_PDB.HeaderTests)
Parse the header of another PDB file (2BEG). ... ok
test_get_atoms (test_PDB.IterationTests)
Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok
test_get_chains (test_PDB.IterationTests)
Yields chains from different models separately. ... ok
test_get_residues (test_PDB.IterationTests)
Yields all residues from all models. ... ok
test_NACCESS_asa_file (test_PDB.NACCESSTests)
Test parsing of pregenerated asa NACCESS file. ... ok
test_NACCESS_rsa_file (test_PDB.NACCESSTests)
Test parsing of pregenerated rsa NACCESS file. ... ok
test_PDBParser (test_PDB.PDBParserTests)
Walk down the structure hierarchy and test parser reliability. ... ok
test_c_n (test_PDB.ParseReal)
Extract polypeptides from 1A80. ... ok
test_empty (test_PDB.ParseReal)
Parse an empty file. ... ok
test_model_numbering (test_PDB.ParseReal)
Preserve model serial numbers during I/O. ... ok
test_residue_sort (test_PDB.ParseReal)
Sorting atoms in residues. ... ok
test_strict (test_PDB.ParseReal)
Parse 1A8O.pdb file in strict mode. ... ok
test_c_n (test_PDB.ParseTest)
Extract polypeptides using C-N. ... ok
test_ca_ca (test_PDB.ParseTest)
Extract polypeptides using CA-CA. ... ok
test_comparison_entities (test_PDB.ParseTest)
Test comparing and sorting the several SMCRA objects. ... ok
test_details (test_PDB.ParseTest)
Verify details of the parsed example PDB file. ... ok
test_pdbio_write_truncated (test_PDB.ParseTest)
Test parsing of truncated lines. ... ok
test_structure (test_PDB.ParseTest)
Verify the structure of the parsed example PDB file. ... ok
test_pdb_to_xyzr (test_PDB.ResidueDepthTests)
Test generation of xyzr (atomic radii) file. ... ok
test_transform (test_PDB.TransformTests)
Transform entities (rotation and translation). ... ok
test_mmcifio_multimodel (test_PDB.WriteTest)
Write a multi-model, multi-chain mmCIF file. ... ok
test_mmcifio_select (test_PDB.WriteTest)
Write a selection of the structure using a Select subclass. ... ok
test_mmcifio_write_dict (test_PDB.WriteTest)
Write an mmCIF dictionary out, read it in and compare them. ... ok
test_mmcifio_write_residue (test_PDB.WriteTest)
Write a single residue using MMCIFIO. ... ok
test_mmcifio_write_structure (test_PDB.WriteTest)
Write a full structure using MMCIFIO. ... ok
test_pdbio_missing_occupancy (test_PDB.WriteTest)
Write PDB file with missing occupancy. ... ok
test_pdbio_select (test_PDB.WriteTest)
Write a selection of the structure using a Select subclass. ... ok
test_pdbio_write_custom_residue (test_PDB.WriteTest)
Write a chainless residue using PDBIO. ... ok
test_pdbio_write_residue (test_PDB.WriteTest)
Write a single residue using PDBIO. ... ok
test_pdbio_write_structure (test_PDB.WriteTest)
Write a full structure using PDBIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 19.199 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_PDBList.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_PDBList ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.279 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Dice.py
test_PDB_Dice ... ok
test_dice (test_PDB_Dice.DiceTests)
Self test for PDB.Dice module. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.518 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_FragmentMapper.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_PDB_FragmentMapper ... ok
test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests)
Self test for FragmentMapper module. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.670 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_KDTree.py
test_PDB_KDTree ... ok
test_KDTree_exceptions (test_PDB_KDTree.KDTreeTest) ... ok
test_KDTree_neighbor_search_manual (test_PDB_KDTree.KDTreeTest)
Test all fixed radius neighbor search. ... ok
test_KDTree_neighbor_search_simple (test_PDB_KDTree.KDTreeTest)
Test all fixed radius neighbor search. ... ok
test_KDTree_point_search (test_PDB_KDTree.KDTreeTest)
Test searching all points within a certain radius of center. ... ok
test_neighbor_search (test_PDB_KDTree.NeighborTest)
NeighborSearch: Find nearby randomly generated coordinates. ... ok
----------------------------------------------------------------------
Ran 1 test in 29.133 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIF2Dict.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_PDB_MMCIF2Dict ... ok
test_MMCIF2dict (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
test_inline_comments (test_PDB_MMCIF2Dict.MMCIF2dictTests)
Comments may begin outside of column 1 if preceded by whitespace. ... ok
test_loop_keyword_case_insensitive (test_PDB_MMCIF2Dict.MMCIF2dictTests)
Comments may begin outside of column 1. ... ok
test_quotefix (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
test_splitline (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
test_underscores (test_PDB_MMCIF2Dict.MMCIF2dictTests) ... ok
test_verbatim_block (test_PDB_MMCIF2Dict.MMCIF2dictTests)
Verbatim bocks parsed correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.546 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFParser.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_PDB_MMCIFParser ... ok
test_conversion (test_PDB_MMCIFParser.CIFtoPDB)
Parse 1A8O.cif, write 1A8O.pdb, parse again and compare. ... ok
testModels (test_PDB_MMCIFParser.ParseReal)
Test file with multiple models. ... ok
test_filehandle (test_PDB_MMCIFParser.ParseReal)
Test if the parser can handle file handle as well as filename. ... ok
test_insertions (test_PDB_MMCIFParser.ParseReal)
Test file with residue insertion codes. ... ok
test_parsers (test_PDB_MMCIFParser.ParseReal)
Extract polypeptides from 1A80. ... ok
test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal)
Test if FastMMCIFParser can parse point mutations correctly. ... ok
test_point_mutations_main (test_PDB_MMCIFParser.ParseReal)
Test if MMCIFParser parse point mutations correctly. ... ok
test_with_anisotrop (test_PDB_MMCIFParser.ParseReal) ... ok
----------------------------------------------------------------------
Ran 1 test in 9.722 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Polypetide.py
test_PDB_Polypetide ... ok
test_polypeptide (test_PDB_Polypetide.PolypeptideTests)
Tests on polypetide class and methods. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.689 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_ResidueDepth.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_PDB_ResidueDepth ... skipping. Install MSMS if you want to use it in Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.492 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_StructureAlignment.py
test_PDB_StructureAlignment ... /builddir/build/BUILD/python-biopython-1.75/python3/build/lib.linux-armv7l-3.7/Bio/PDB/StructureBuilder.py:92: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298.
  PDBConstructionWarning,
/builddir/build/BUILD/python-biopython-1.75/python3/build/lib.linux-armv7l-3.7/Bio/PDB/StructureBuilder.py:92: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344.
  PDBConstructionWarning,
ok
test_StructAlign (test_PDB_StructureAlignment.StructureAlignTests)
Tests on module to align two proteins according to a FASTA alignment file. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.597 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Superimposer.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_PDB_Superimposer ... ok
test_Superimposer (test_PDB_Superimposer.SuperimposerTests)
Test on module that superimpose two protein structures. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.774 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_parse_pdb_header.py
test_PDB_parse_pdb_header ... ok
test_parse_header_line (test_PDB_parse_pdb_header.ParseReal)
Unit test for parsing and converting fields in HEADER record. ... ok
test_parse_pdb_with_remark_465 (test_PDB_parse_pdb_header.ParseReal)
Tests that parse_pdb_header now can identify some REMARK 465 entries. ... ok
test_parse_pdb_with_remark_99 (test_PDB_parse_pdb_header.ParseReal)
Tests that parse_pdb_header can identify REMARK 99 ASTRAL entries. ... ok
test_parse_remark_465 (test_PDB_parse_pdb_header.ParseReal)
A UNIT-test for the private function _parse_remark_465. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.499 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_vectors.py
test_PDB_vectors ... ok
test_Vector (test_PDB_vectors.VectorTests)
Test Vector object. ... ok
test_Vector_angles (test_PDB_vectors.VectorTests)
Test Vector angles. ... ok
test_division (test_PDB_vectors.VectorTests)
Confirm division works. ... ok
test_m2rotaxis_0 (test_PDB_vectors.VectorTests)
Test 0 deg rotation. Axis must be [1, 0, 0] as per Vector documentation. ... ok
test_m2rotaxis_180 (test_PDB_vectors.VectorTests)
Test 180 deg rotation. ... ok
test_m2rotaxis_90 (test_PDB_vectors.VectorTests)
Test 90 deg rotation. ... ok
test_normalization (test_PDB_vectors.VectorTests)
Test Vector normalization. ... ok
test_refmat (test_PDB_vectors.VectorTests) ... ok
test_rotmat_0 (test_PDB_vectors.VectorTests)
Test rotmat when the rotation is 0 deg (singularity). ... ok
test_rotmat_180 (test_PDB_vectors.VectorTests)
Test rotmat when the rotation is 180 deg (singularity). ... ok
test_rotmat_90 (test_PDB_vectors.VectorTests)
Test regular 90 deg rotation. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.072 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Pathway.py
test_Pathway ... ok
testAdditionalFunctions (test_Pathway.GraphTestCase) ... ok
test_Edges (test_Pathway.GraphTestCase) ... ok
test_Equals (test_Pathway.GraphTestCase) ... ok
test_Nodes (test_Pathway.GraphTestCase) ... ok
test_RemoveNode (test_Pathway.GraphTestCase) ... ok
testAdditionalFunctions (test_Pathway.MultiGraphTestCase) ... ok
test_Edges (test_Pathway.MultiGraphTestCase) ... ok
test_Equals (test_Pathway.MultiGraphTestCase) ... ok
test_Nodes (test_Pathway.MultiGraphTestCase) ... ok
test_RemoveNode (test_Pathway.MultiGraphTestCase) ... ok
test_eq (test_Pathway.ReactionTestCase) ... ok
test_rev (test_Pathway.ReactionTestCase) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.247 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Phd.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Phd ... ok
test_check_SeqIO (test_Phd.PhdTest454)
Test phd_454 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestOne)
Test phd1 using parser via SeqIO. ... ok
test_check_record_parser (test_Phd.PhdTestOne)
Test phd1 file in detail. ... ok
test_check_SeqIO (test_Phd.PhdTestSolexa)
Test phd2 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestTwo)
Test phd2 using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.550 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.089 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.057 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_nodepend.py
test_PopGen_GenePop_nodepend ... ok
test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest)
Basic operation of the File Record Parser. ... ok
test_remove_features (test_PopGen_GenePop_nodepend.FileParserTest)
Testing the ability to remove population/loci via class methods. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest)
Testing the ability to deal with wrongly formatted files. ... ok
test_record_parser (test_PopGen_GenePop_nodepend.ParserTest)
Basic operation of the Record Parser. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest)
Testing the ability to deal with wrongly formatted files. ... ok
test_record_basic (test_PopGen_GenePop_nodepend.RecordTest)
Basic test on Record. ... ok
test_utils (test_PopGen_GenePop_nodepend.UtilsTest)
Basic operation of GenePop Utils. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.216 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Prank_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.519 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Probcons_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.593 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ProtParam.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_ProtParam ... ok
test_aromaticity (test_ProtParam.ProtParamTest)
Calculate protein aromaticity. ... ok
test_charge_at_pH (test_ProtParam.ProtParamTest)
Test charge_at_pH function. ... ok
test_count_amino_acids (test_ProtParam.ProtParamTest)
Calculate amino acid counts. ... ok
test_flexibility (test_ProtParam.ProtParamTest)
Calculate protein flexibility. ... ok
test_get_amino_acids_percent (test_ProtParam.ProtParamTest)
Calculate amino acid percentages. ... ok
test_get_molecular_weight (test_ProtParam.ProtParamTest)
Calculate protein molecular weight. ... ok
test_get_molecular_weight_identical (test_ProtParam.ProtParamTest)
Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest)
Calculate monoisotopic molecular weight. ... ok
test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest)
Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
test_gravy (test_ProtParam.ProtParamTest)
Calculate gravy. ... ok
test_instability_index (test_ProtParam.ProtParamTest)
Calculate protein instability index. ... ok
test_isoelectric_point (test_ProtParam.ProtParamTest)
Calculate the isoelectric point. ... ok
test_molar_extinction_coefficient (test_ProtParam.ProtParamTest)
Molar extinction coefficient. ... ok
test_protein_scale (test_ProtParam.ProtParamTest)
Calculate the Kite Doolittle scale. ... ok
test_secondary_structure_fraction (test_ProtParam.ProtParamTest)
Calculate secondary structure fractions. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.332 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_QCPSuperimposer.py
test_QCPSuperimposer ... ok
test_get_init_rms (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_get_rms (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_get_rotran (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_get_transformed (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_oldTest (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_run (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
test_set (test_QCPSuperimposer.QCPSuperimposerTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.352 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_RCSBFormats.py
test_RCSBFormats ... ok
test_compare_chains (test_RCSBFormats.CompareStructures)
Compare parsed chains. ... ok
test_compare_models (test_RCSBFormats.CompareStructures)
Compared parsed models. ... ok
----------------------------------------------------------------------
Ran 1 test in 5.964 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Restriction.py
test_Restriction ... ok
test_basic_isochizomers (test_Restriction.EnzymeComparison)
Test to be sure isochizomer and neoschizomers are as expected. ... ok
test_comparisons (test_Restriction.EnzymeComparison)
Test comparison operators between different enzymes. ... ok
test_change (test_Restriction.RestrictionBatchPrintTest)
Test that change() changes something. ... ok
test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_analysis_restrictions (test_Restriction.RestrictionBatches)
Test Fancier restriction analysis. ... ok
test_batch_analysis (test_Restriction.RestrictionBatches)
Sequence analysis with a restriction batch. ... ok
test_creating_batch (test_Restriction.RestrictionBatches)
Creating and modifying a restriction batch. ... ok
test_premade_batches (test_Restriction.RestrictionBatches)
Test content of premade batches CommOnly, NoComm, AllEnzymes. ... ok
test_search_premade_batches (test_Restriction.RestrictionBatches)
Test search with pre-made batches CommOnly, NoComm, AllEnzymes. ... ok
test_formatted_seq (test_Restriction.SequenceTesting)
Test several methods of FormattedSeq. ... ok
test_non_iupac_letters (test_Restriction.SequenceTesting)
Test if non-IUPAC letters raise a TypeError. ... ok
test_sequence_object (test_Restriction.SequenceTesting)
Test if sequence must be a Seq or MutableSeq object. ... ok
test_circular_sequences (test_Restriction.SimpleEnzyme)
Deal with cutting circular sequences. ... ok
test_cutting_border_positions (test_Restriction.SimpleEnzyme)
Check if cutting after first and penultimate position works. ... ok
test_ear_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with EarI (ambiguous overhang). ... ok
test_eco_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with EcoRI (5'overhang). ... ok
test_init (test_Restriction.SimpleEnzyme)
Check for error during __init__. ... ok
test_kpn_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with KpnI (3'overhang). ... ok
test_overlapping_cut_sites (test_Restriction.SimpleEnzyme)
Check if overlapping recognition sites are properly handled. ... ok
test_recognition_site_on_both_strands (test_Restriction.SimpleEnzyme)
Check if recognition sites on both strands are properly handled. ... ok
test_shortcuts (test_Restriction.SimpleEnzyme)
Check if '/' and '//' work as '.search' and '.catalyse'. ... ok
test_sma_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with SmaI (blunt cutter). ... ok
test_sna_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with SnaI (unknown). ... ok
test_print_that (test_Restriction.TestPrintOutputs)
Test print_that function. ... ok
test_str_method (test_Restriction.TestPrintOutputs)
Test __str__ and __repr__ outputs. ... ok
test_supplier (test_Restriction.TestPrintOutputs)
Test output of supplier list for different enzyme types. ... ok
----------------------------------------------------------------------
Ran 1 test in 3.148 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Astral.py
test_SCOP_Astral ... ok
testConstructWithCustomFile (test_SCOP_Astral.AstralTests) ... ok
testGetDomainsClustered (test_SCOP_Astral.AstralTests) ... ok
testGetDomainsFromFile (test_SCOP_Astral.AstralTests) ... ok
testGetSeq (test_SCOP_Astral.AstralTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.848 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Cla.py
test_SCOP_Cla ... ok
testError (test_SCOP_Cla.ClaTests)
Test if a corrupt record raises the appropriate exception. ... ok
testIndex (test_SCOP_Cla.ClaTests)
Test CLA file indexing. ... ok
testParse (test_SCOP_Cla.ClaTests)
Test if all records in a CLA file are being read. ... ok
testRecord (test_SCOP_Cla.ClaTests)
Test one record in detail. ... ok
testStr (test_SCOP_Cla.ClaTests)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.688 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Des.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SCOP_Des ... ok
testError (test_SCOP_Des.DesTests)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Des.DesTests)
Test if all records in a DES file are being read. ... ok
testRecord (test_SCOP_Des.DesTests)
Test one record in detail. ... ok
testStr (test_SCOP_Des.DesTests)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.453 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Dom.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SCOP_Dom ... ok
testError (test_SCOP_Dom.DomTests)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Dom.DomTests)
Test if all records in a DOM file are being read. ... ok
testRecord (test_SCOP_Dom.DomTests)
Test one record in detail. ... ok
testStr (test_SCOP_Dom.DomTests)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.509 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Hie.py
test_SCOP_Hie ... ok
testError (test_SCOP_Hie.HieTests)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Hie.HieTests)
Test if all records in a HIE file are being read. ... ok
testStr (test_SCOP_Hie.HieTests)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.450 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Raf.py
test_SCOP_Raf ... ok
testParse (test_SCOP_Raf.RafTests)
Parse a RAF record. ... ok
testSeqMapAdd (test_SCOP_Raf.RafTests) ... ok
testSeqMapIndex (test_SCOP_Raf.RafTests) ... ok
testSeqMapSlice (test_SCOP_Raf.RafTests) ... ok
test_SeqMap_getAtoms_err (test_SCOP_Raf.RafTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.519 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Residues.py
test_SCOP_Residues ... ok
testAstralParse (test_SCOP_Residues.ResiduesTests)
Test if we can parse residue subsets enclosed in brackets. ... ok
testJustPdbId (test_SCOP_Residues.ResiduesTests) ... ok
testParse (test_SCOP_Residues.ResiduesTests) ... ok
testParseError (test_SCOP_Residues.ResiduesTests) ... ok
testPdbId (test_SCOP_Residues.ResiduesTests) ... ok
testStr (test_SCOP_Residues.ResiduesTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.479 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Scop.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SCOP_Scop ... ok
testConstructFromDirectory (test_SCOP_Scop.ScopTests) ... ok
testGetAscendent (test_SCOP_Scop.ScopTests) ... ok
testParse (test_SCOP_Scop.ScopTests) ... ok
testParseDomain (test_SCOP_Scop.ScopTests) ... ok
testSccsOrder (test_SCOP_Scop.ScopTests) ... ok
test_get_descendents (test_SCOP_Scop.ScopTests)
Test getDescendents method. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.497 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_online.py
test_SCOP_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.488 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SVDSuperimposer.py
test_SVDSuperimposer ... ok
test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest) ... ok
test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.045 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl.py
test_SearchIO_blat_psl ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_003.psl). ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_004.psl). ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_005.psl). ... ok
test_psl_35_001 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_35_001.psl). ... ok
test_psl_35_002 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_35_002.psl). ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_003.psl). ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_004.psl). ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_005.psl). ... ok
test_psl_35_001 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_35_001.psl). ... ok
test_psl_35_002 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_35_002.psl). ... ok
test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_001.pslx). ... ok
test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_002.pslx). ... ok
test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_003.pslx). ... ok
test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_004.pslx). ... ok
test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_005.pslx). ... ok
test_pslx_35_002 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_35_002.pslx). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.757 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl_index.py
test_SearchIO_blat_psl_index ... ok
test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, multiple queries. ... ok
test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, single query, no hits. ... ok
test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, single query, single hit. ... ok
test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok
test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, multiple queries, no header. ... ok
test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, multiple queries. ... ok
test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, single query, no hits. ... ok
test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, single query, single hit. ... ok
test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok
test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, multiple queries, no header. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.082 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate.py
test_SearchIO_exonerate ... ok
test_exn_22_o_vulgar_cigar (test_SearchIO_exonerate.ExonerateCigarCases)
Test parsing exonerate output (exn_22_o_vulgar_cigar.exn). ... ok
test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases)
Compares vulgar-text coordinate parsing for the coding2coding model. ... ok
test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases)
Compares vulgar-text coordinate parsing for the genome2genome model. ... ok
test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases)
Compares vulgar-text coordinate parsing for the protein2dna model. ... ok
test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_affine_local.exn). ... ok
test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_cdna2genome.exn). ... ok
test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_coding2coding.exn). ... ok
test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn). ... ok
test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_coding2genome.exn). ... ok
test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_dna2protein.exn). ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_est2genome.exn). ... ok
test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_genome2genome.exn). ... ok
test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_ner.exn). ... ok
test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn). ... ok
test_exn_22_m_protein2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_protein2genome.exn). ... ok
test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_ungapped.exn). ... ok
test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_ungapped_trans.exn). ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_q_multiple.exn). ... ok
test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_q_none.exn). ... ok
test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases)
Test parsing exonerate output (exn_22_o_vulgar.exn). ... ok
test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases)
Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn). ... ok
----------------------------------------------------------------------
Ran 1 test in 1.031 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_text_index.py
test_SearchIO_exonerate_text_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases)
Test exonerate-text indexing, single. ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases)
Test exonerate-text indexing, single. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.895 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_vulgar_index.py
test_SearchIO_exonerate_vulgar_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases)
Test exonerate-vulgar indexing, single. ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases)
Test exonerate-vulgar indexing, single. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.345 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10.py
test_SearchIO_fasta_m10 ... ok
test_output002 (test_SearchIO_fasta_m10.Fasta34Cases)
Test parsing fasta34 output (output002.m10). ... ok
test_output003 (test_SearchIO_fasta_m10.Fasta34Cases)
Test parsing fasta34 output (output003.m10). ... ok
test_output001 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing fasta35 output (output001.m10). ... ok
test_output004 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing fasta35 output (output004.m10). ... ok
test_output005 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing ssearch35 output (output005.m10). ... ok
test_output006 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing fasta35 output (output006.m10). ... ok
test_output007 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output007.m10). ... ok
test_output008 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing tfastx36 output (output008.m10). ... ok
test_output009 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output009.m10). ... ok
test_output010 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output010.m10). ... ok
test_output011 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output011.m10). ... ok
test_output012 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output012.m10). ... ok
test_output013 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output013.m10). ... ok
test_output014 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output014.m10). ... ok
test_output015 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output015.m10). ... ok
test_output016 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output016.m10). ... ok
----------------------------------------------------------------------
Ran 1 test in 3.738 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10_index.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SearchIO_fasta_m10_index ... ok
test_output_001 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta35, multiple queries. ... ok
test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta34, multiple queries. ... ok
test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, ssearch35, multiple queries. ... ok
test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, tfastx36, multiple queries. ... ok
test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, multiple queries. ... ok
test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, single query, no hits. ... ok
test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, single query, hits with single hsp. ... ok
test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, single query with multiple hsps. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.876 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hhsuite2_text.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SearchIO_hhsuite2_text ... ok
test_2uvo (test_SearchIO_hhsuite2_text.HhsuiteCases)
Parsing 2uvo. ... ok
test_2uvo_emptytable (test_SearchIO_hhsuite2_text.HhsuiteCases)
Parsing 4uvo with empty results table. ... ok
test_2uvo_onlyheader (test_SearchIO_hhsuite2_text.HhsuiteCases)
Parsing 4uvo with only header present. ... ok
test_4p79 (test_SearchIO_hhsuite2_text.HhsuiteCases)
Parsing 4p79_hhsearch_server_NOssm.hhr file. ... ok
test_4y9h_nossm (test_SearchIO_hhsuite2_text.HhsuiteCases)
Parsing 4y9h_hhsearch_server_NOssm.hhr file. ... ok
test_9590198 (test_SearchIO_hhsuite2_text.HhsuiteCases)
Parsing hhpred_9590198.hhr file. ... ok
test_allx (test_SearchIO_hhsuite2_text.HhsuiteCases)
Parsing allx.hhr file. ... ok
test_q9bsu1 (test_SearchIO_hhsuite2_text.HhsuiteCases)
Parsing hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.850 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text.py
test_SearchIO_hmmer2_text ... ok
test_hmmpfam_21 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out). ... ok
test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out). ... ok
test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out). ... ok
test_hmmpfam_23_break_in_end_of_seq (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file with a line break in the end of seq marker. ... ok
test_hmmpfam_23_missing_consensus (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out). ... ok
test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out). ... ok
test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out). ... ok
test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests)
Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out). ... ok
test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests)
Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 1.563 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text_index.py
test_SearchIO_hmmer2_text_index ... ok
test_hmmertext_text_21_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.1. ... ok
test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.2. ... ok
test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.2. ... ok
test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.3. ... ok
test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.4. ... ok
test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, single query, hmmpfam. ... ok
test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, single query, hmmsearch. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.900 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SearchIO_hmmer3_domtab ... ok
test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases)
Parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001). ... ok
test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases)
Parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001). ... ok
test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001). ... ok
test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Parsing hmmscan-domtab, hmmscan 3.0, single query, no hits (domtab_30_hmmscan_002). ... ok
test_domtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003). ... ok
test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004). ... ok
test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.390 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab_index.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SearchIO_hmmer3_domtab_index ... ok
test_hmmerdomtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, multiple queries. ... ok
test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, first (domtab_30_hmmscan_001.out). ... ok
test_hmmerdomtab_30_multiple_last (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, last (domtab_30_hmmscan_001.out). ... ok
test_hmmerdomtab_30_multiple_middle (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, middle (domtab_30_hmmscan_001.out). ... ok
test_hmmerdomtab_30_single (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.485 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SearchIO_hmmer3_tab ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001). ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, single query, no hits (tab_30_hmmscan_002). ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, single query, single hit, single hsp (tab_30_hmmscan_003). ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, single query, multiple hits (tab_30_hmmscan_004). ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases)
Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.395 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab_index.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SearchIO_hmmer3_tab_index ... ok
test_hmmer3tab_30_hmmscan_001 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, multiple queries. ... ok
test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, first (tab_30_hmmscan_001.out). ... ok
test_hmmer3tab_30_multiple_last (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, last (tab_30_hmmscan_001.out). ... ok
test_hmmer3tab_30_multiple_middle (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, middle (tab_30_hmmscan_001.out). ... ok
test_hmmer3tab_30_single (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.486 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SearchIO_hmmer3_text ... ok
test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Parsing hmmersearch 3.0 (text_30_hmmsearch_001). ... ok
test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases)
Parsing hmmersearch 3.0 (text_30_hmmsearch_002). ... ok
test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases)
Parsing hmmersearch 3.0 (text_30_hmmsearch_003). ... ok
test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases)
Parsing hmmersearch 3.0 (text_30_hmmsearch_004). ... ok
test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases)
Parsing hmmersearch 3.0 (text_30_hmmsearch_005). ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001). ... ok
test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001). ... ok
test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001). ... ok
test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002). ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.0 (text_30_hmmscan_001). ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.0 (text_30_hmmscan_002). ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.0 (text_30_hmmscan_003). ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.0 (text_30_hmmscan_004). ... ok
test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.0 (text_30_hmmscan_005). ... ok
test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.0 (text_30_hmmscan_006). ... ok
test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.0 (text_30_hmmscan_007). ... ok
test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.0 (text_30_hmmscan_008). ... ok
test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.0 (text_30_hmmscan_009). ... ok
test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.0 (text_30_hmmscan_010). ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases)
Parsing hmmscan 3.1b1 (text_31b1_hmmscan_001). ... ok
test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases)
Parsing phmmer 3.1b2 (text_31b2_phmmer_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 1.069 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text_index.py
test_SearchIO_hmmer3_text_index ... ok
test_hmmertext_text_30_hmmscan_001 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok
test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmertext_text_30_hmmscan_006 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmertext_text_30_hmmscan_007 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmertext_text_30_hmmscan_008 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width. ... ok
test_hmmertext_text_30_hmmsearch_005 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok
test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out). ... ok
test_hmmer3text_30_multiple_last (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out). ... ok
test_hmmer3text_30_multiple_middle (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out). ... ok
test_hmmer3text_30_single (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.584 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_interproscan_xml.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SearchIO_interproscan_xml ... ok
test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.475 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_legacy.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SearchIO_legacy ... ok
test_TaggingConsumer (test_SearchIO_legacy.TestParserSupport) ... ok
test_attempt_read_and_call (test_SearchIO_legacy.TestParserSupport) ... ok
test_is_blank_line (test_SearchIO_legacy.TestParserSupport) ... ok
test_read_and_call (test_SearchIO_legacy.TestParserSupport) ... ok
test_safe_peekline (test_SearchIO_legacy.TestParserSupport) ... ok
test_safe_readline (test_SearchIO_legacy.TestParserSupport) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.284 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_model.py
test_SearchIO_model ... ok
test_alphabet_no_seq (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment alphabet property, query and hit sequences not present. ... ok
test_alphabet_with_seq (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment alphabet property, query or hit sequences present. ... ok
test_coords_setters_getters (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit coordinate-related setters and getters. ... ok
test_coords_setters_readonly (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit coordinate-related read-only getters. ... ok
test_default_attrs (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment attributes' default values. ... ok
test_frame_set_error (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit frame setters, invalid values. ... ok
test_frame_set_ok (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit frame setters. ... ok
test_getitem (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__getitem__. ... ok
test_getitem_alignment_annot (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__getitem__, with alignment annotation. ... ok
test_getitem_attrs (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__getitem__, with attributes. ... ok
test_id_desc_set (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit id and description setters. ... ok
test_init_with_seqrecord (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__init__, with SeqRecord. ... ok
test_init_wrong_seqtypes (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__init__, wrong sequence argument types. ... ok
test_len (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__len__. ... ok
test_pickle (test_SearchIO_model.HSPFragmentCases)
Test pickling and unpickling of HSPFragment. ... ok
test_repr (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__repr__. ... ok
test_seq_unequal_hit_query_len (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment sequence setter with unequal hit and query lengths. ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment sequence attribute types and default values. ... ok
test_strand_set_error (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand setters, invalid values. ... ok
test_strand_set_from_minus_frame (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand getters, from minus frame. ... ok
test_strand_set_from_plus_frame (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand getters, from plus frame. ... ok
test_strand_set_from_zero_frame (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand getters, from zero frame. ... ok
test_strand_set_ok (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand setters. ... ok
test_getitem (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__getitem__, no alignments. ... ok
test_getitem_only_hit (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__getitem__, only hit. ... ok
test_getitem_only_query (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__getitem__, only query. ... ok
test_init (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__init__ attributes. ... ok
test_iter (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSP.__iter__, no alignments. ... ok
test_len (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__len__, no alignments. ... ok
test_repr (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__repr__, no alignments. ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment sequence attributes, no alignments. ... ok
test_alphabet (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.alphabet getter. ... ok
test_alphabet_set (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.alphabet setter. ... ok
test_contains (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__contains__. ... ok
test_delitem (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__delitem__. ... ok
test_fragments (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.fragments property. ... ok
test_getitem (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__getitem__. ... ok
test_id_desc_set (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP query and hit id and description setters. ... ok
test_is_fragmented (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.is_fragmented property. ... ok
test_len (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__len__. ... ok
test_pickle (test_SearchIO_model.HSPMultipleFragmentCases)
Test pickling and unpickling of HSP. ... ok
test_range (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP range properties. ... ok
test_ranges (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP ranges properties. ... ok
test_seqs (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP sequence properties. ... ok
test_setitem_multiple (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__setitem__, multiple items. ... ok
test_setitem_single (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__setitem___, single item. ... ok
test_setters_readonly (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP read-only properties. ... ok
test_span (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP span properties. ... ok
test_alignment (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.alignment property. ... ok
test_aln_span (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.aln_span property. ... ok
test_fragment (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.fragment property. ... ok
test_init_no_fragment (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.__init__ without fragments. ... ok
test_is_fragmented (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.is_fragmented property. ... ok
test_len (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.__len__. ... ok
test_range (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP range properties. ... ok
test_seq (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP sequence properties. ... ok
test_setters_readonly (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP read-only properties. ... ok
test_span (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP span properties. ... ok
test_append (test_SearchIO_model.HitCases)
Test Hit.append. ... ok
test_delitem (test_SearchIO_model.HitCases)
Test Hit.__delitem__. ... ok
test_desc_set (test_SearchIO_model.HitCases)
Test Hit.description setter. ... ok
test_desc_set_no_seqrecord (test_SearchIO_model.HitCases)
Test Hit.description setter, without HSP SeqRecords. ... ok
test_filter (test_SearchIO_model.HitCases)
Test Hit.filter. ... ok
test_filter_no_filtered (test_SearchIO_model.HitCases)
Test Hit.hit_filter, all hits filtered out. ... ok
test_filter_no_func (test_SearchIO_model.HitCases)
Test Hit.filter, without arguments. ... ok
test_fragments (test_SearchIO_model.HitCases)
Test Hit.fragments. ... ok
test_getitem_multiple (test_SearchIO_model.HitCases)
Test Hit.__getitem__, multiple items. ... ok
test_getitem_single (test_SearchIO_model.HitCases)
Test Hit.__getitem__, single item. ... ok
test_hsp_map_no_func (test_SearchIO_model.HitCases)
Test Hit.map, without arguments. ... ok
test_hsps (test_SearchIO_model.HitCases)
Test Hit.hsps. ... ok
test_id_set (test_SearchIO_model.HitCases)
Test Hit.id setter. ... ok
test_index (test_SearchIO_model.HitCases)
Test Hit.index. ... ok
test_index_not_present (test_SearchIO_model.HitCases)
Test Hit.index, when index is not present. ... ok
test_init_hsps_only (test_SearchIO_model.HitCases)
Test Hit.__init__, with hsps only. ... ok
test_init_id_only (test_SearchIO_model.HitCases)
Test Hit.__init__, with ID only. ... ok
test_init_none (test_SearchIO_model.HitCases)
Test Hit.__init__, no arguments. ... ok
test_item_multiple (test_SearchIO_model.HitCases)
Test Hit.__setitem__, multiple items. ... ok
test_iter (test_SearchIO_model.HitCases)
Test Hit.__iter__. ... ok
test_len (test_SearchIO_model.HitCases)
Test Hit.__len__. ... ok
test_map (test_SearchIO_model.HitCases)
Test Hit.hsp_map. ... ok
test_nonzero (test_SearchIO_model.HitCases)
Test Hit.__nonzero__. ... ok
test_pickle (test_SearchIO_model.HitCases)
Test pickling and unpickling of Hit. ... ok
test_pop (test_SearchIO_model.HitCases)
Test Hit.pop. ... ok
test_repr (test_SearchIO_model.HitCases)
Test Hit.__repr__. ... ok
test_setitem_single (test_SearchIO_model.HitCases)
Test Hit.__setitem__, single item. ... ok
test_sort (test_SearchIO_model.HitCases)
Test Hit.sort. ... ok
test_sort_not_in_place (test_SearchIO_model.HitCases)
Test Hit.sort, not in place. ... ok
test_validate_hsp_ok (test_SearchIO_model.HitCases)
Test Hit._validate_hsp. ... ok
test_validate_hsp_wrong_hit_id (test_SearchIO_model.HitCases)
Test Hit._validate_hsp, wrong hit ID. ... ok
test_validate_hsp_wrong_query_id (test_SearchIO_model.HitCases)
Test Hit._validate_hsp, wrong query ID. ... ok
test_validate_hsp_wrong_type (test_SearchIO_model.HitCases)
Test Hit._validate_hsp, wrong type. ... ok
test_absorb_hit_does_not_exist (test_SearchIO_model.QueryResultCases)
Test QueryResult.absorb, hit does not exist. ... ok
test_absorb_hit_exists (test_SearchIO_model.QueryResultCases)
Test QueryResult.absorb, hit with the same ID exists. ... ok
test_append_alt_id_exists (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, when alt ID exists. ... ok
test_append_alt_id_exists_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, when alt ID exists as primary. ... ok
test_append_custom_hit_key_function_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, with custom hit key function. ... ok
test_append_id_exists (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, when ID exists. ... ok
test_append_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.append. ... ok
test_contains (test_SearchIO_model.QueryResultCases)
Test QueryResult.__contains__. ... ok
test_contains_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.__contains__, with alternative IDs. ... ok
test_delitem_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__delitem__, with alt ID. ... ok
test_delitem_int_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__delitem__. ... ok
test_delitem_slice_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__delitem__, with slice. ... ok
test_delitem_string_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with string. ... ok
test_description_set (test_SearchIO_model.QueryResultCases)
Test QueryResult.description setter. ... ok
test_description_set_no_seqrecord (test_SearchIO_model.QueryResultCases)
Test QueryResult.description setter, without HSP SeqRecords. ... ok
test_fragments (test_SearchIO_model.QueryResultCases)
Test QueryResult.fragments. ... ok
test_getitem_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, single item with alternative ID. ... ok
test_getitem_default_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__. ... ok
test_getitem_int_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with integer. ... ok
test_getitem_slice_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with slice. ... ok
test_getitm_slice_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with slice and alt IDs. ... ok
test_hit_filter (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_filter. ... ok
test_hit_filter_no_filtered (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_filter, all hits filtered out. ... ok
test_hit_filter_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_filter, without arguments. ... ok
test_hit_keys (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_keys. ... ok
test_hit_map (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_map. ... ok
test_hit_map_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_map, without arguments. ... ok
test_hits (test_SearchIO_model.QueryResultCases)
Test QueryResult.hits. ... ok
test_hsp_filter (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_filter. ... ok
test_hsp_filter_no_filtered (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_filter, all hits filtered out. ... ok
test_hsp_filter_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_filter, no arguments. ... ok
test_hsp_map (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_map. ... ok
test_hsp_map_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_map, without arguments. ... ok
test_hsps (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsps. ... ok
test_id_set (test_SearchIO_model.QueryResultCases)
Test QueryResult.id setter. ... ok
test_index (test_SearchIO_model.QueryResultCases)
Test QueryResult.index. ... ok
test_index_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.index, with alt ID. ... ok
test_index_not_present (test_SearchIO_model.QueryResultCases)
Test QueryResult.index, when index is not present. ... ok
test_init_hits_only (test_SearchIO_model.QueryResultCases)
Test QueryResult.__init__, with hits only. ... ok
test_init_id_only (test_SearchIO_model.QueryResultCases)
Test QueryResult.__init__, with ID only. ... ok
test_init_none (test_SearchIO_model.QueryResultCases)
Test QueryResult.__init__, no arguments. ... ok
test_items (test_SearchIO_model.QueryResultCases)
Test QueryResult.items. ... ok
test_iter (test_SearchIO_model.QueryResultCases)
Test QueryResult.__iter__. ... ok
test_len (test_SearchIO_model.QueryResultCases)
Test QueryResult.__len__. ... ok
test_nonzero (test_SearchIO_model.QueryResultCases)
Test QueryResult.__nonzero__. ... ok
test_order (test_SearchIO_model.QueryResultCases) ... ok
test_pickle (test_SearchIO_model.QueryResultCases)
Test pickling and unpickling of QueryResult. ... ok
test_pop_int_index_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop, with integer index. ... ok
test_pop_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop. ... ok
test_pop_string_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop, with alternative ID. ... ok
test_pop_string_index_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop, with string index. ... ok
test_repr (test_SearchIO_model.QueryResultCases)
Test QueryResult.__repr__. ... ok
test_setitem_from_empty (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, from empty container. ... ok
test_setitem_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__. ... ok
test_setitem_ok_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, checking alt hit IDs. ... ok
test_setitem_ok_alt_existing (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, existing key. ... ok
test_setitem_ok_alt_ok_promote (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, previously alt ID. ... ok
test_setitem_wrong_key_type (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, wrong key type. ... ok
test_setitem_wrong_query_id (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, wrong query ID. ... ok
test_setitem_wrong_type (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, wrong type. ... ok
test_sort_key_not_in_place_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, with custom key, not in place. ... ok
test_sort_key_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, with custom key. ... ok
test_sort_not_in_place_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, not in place. ... ok
test_sort_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort. ... ok
test_sort_reverse_not_in_place_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, reverse, not in place. ... ok
test_sort_reverse_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, reverse. ... ok
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
C
----------------------------------------------------------------------
Ran 1 test in 3.339 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_write.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SearchIO_write ... ok
test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt). ... ok
test_write_multiple_from_blasttabc (test_SearchIO_write.BlastTabWriteCases)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt). ... ok
test_write_multiple_from_blasttabc_allfields (test_SearchIO_write.BlastTabWriteCases)
Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt). ... ok
test_write_single_from_blasttab (test_SearchIO_write.BlastTabWriteCases)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt). ... ok
test_write_single_from_blasttabc (test_SearchIO_write.BlastTabWriteCases)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt). ... ok
test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml). ... ok
test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml). ... ok
test_write_multiple_from_blatpsl (test_SearchIO_write.BlatPslWriteCases)
Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl). ... ok
test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases)
Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx). ... ok
test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases)
Test blat-psl writing from blat-psl, single query (psl_34_004.psl). ... ok
test_write_single_from_blatpsl_protein_query (test_SearchIO_write.BlatPslWriteCases)
Test blat-psl writing from blat-psl, single query (psl_35_002.psl). ... ok
test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases)
Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx). ... ok
test_write_single_from_blatpslx_protein_query (test_SearchIO_write.BlatPslWriteCases)
Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx). ... ok
test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok
test_write_single_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
test_write_single_from_hmmsearchdomtab (test_SearchIO_write.HmmerDomtabWriteCases)
Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
test_write_multiple_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok
test_write_single_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 9.368 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqFeature.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SeqFeature ... ok
test_eq_identical (test_SeqFeature.TestCompoundLocation)
Test two identical locations are equal. ... ok
test_eq_not_identical (test_SeqFeature.TestCompoundLocation)
Test two different locations are not equal. ... ok
test_eq_identical (test_SeqFeature.TestFeatureLocation)
Test two identical locations are equal. ... ok
test_eq_not_identical (test_SeqFeature.TestFeatureLocation)
Test two different locations are not equal. ... ok
test_start_before_end (test_SeqFeature.TestFeatureLocation) ... ok
test_fuzzy (test_SeqFeature.TestLocations)
Test fuzzy representations. ... ok
test_pickle (test_SeqFeature.TestPositions)
Test pickle behaviour of position instances. ... ok
test_eq_identical (test_SeqFeature.TestReference)
Test two identical references eq() to True. ... ok
test_translation_checks_cds (test_SeqFeature.TestSeqFeature)
Test that a CDS feature is subject to respective checks. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.407 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SeqIO ... ok
test_abi1 (test_SeqIO.TestSeqIO) ... ok
test_abi2 (test_SeqIO.TestSeqIO) ... ok
test_abi3 (test_SeqIO.TestSeqIO) ... ok
test_ace1 (test_SeqIO.TestSeqIO) ... ok
test_ace2 (test_SeqIO.TestSeqIO) ... ok
test_ace3 (test_SeqIO.TestSeqIO) ... ok
test_cif_atom1 (test_SeqIO.TestSeqIO) ... ok
test_cif_atom2 (test_SeqIO.TestSeqIO) ... ok
test_cif_seqres1 (test_SeqIO.TestSeqIO) ... ok
test_cif_seqres2 (test_SeqIO.TestSeqIO) ... ok
test_clustal1 (test_SeqIO.TestSeqIO) ... ok
test_clustal2 (test_SeqIO.TestSeqIO) ... ok
test_clustal3 (test_SeqIO.TestSeqIO) ... ok
test_clustal4 (test_SeqIO.TestSeqIO) ... ok
test_embl1 (test_SeqIO.TestSeqIO) ... ok
test_embl10 (test_SeqIO.TestSeqIO) ... ok
test_embl11 (test_SeqIO.TestSeqIO) ... ok
test_embl12 (test_SeqIO.TestSeqIO) ... ok
test_embl13 (test_SeqIO.TestSeqIO)
Test parsing embl file with wrapped locations and unspecified type. ... ok
test_embl14 (test_SeqIO.TestSeqIO)
Test parsing file with features over-indented for EMBL. ... ok
test_embl2 (test_SeqIO.TestSeqIO) ... ok
test_embl3 (test_SeqIO.TestSeqIO) ... ok
test_embl4 (test_SeqIO.TestSeqIO) ... ok
test_embl5 (test_SeqIO.TestSeqIO) ... ok
test_embl6 (test_SeqIO.TestSeqIO) ... ok
test_embl7 (test_SeqIO.TestSeqIO) ... ok
test_embl8 (test_SeqIO.TestSeqIO) ... ok
test_embl9 (test_SeqIO.TestSeqIO) ... ok
test_emboss1 (test_SeqIO.TestSeqIO) ... ok
test_emboss2 (test_SeqIO.TestSeqIO) ... ok
test_emboss3 (test_SeqIO.TestSeqIO) ... ok
test_empty_file (test_SeqIO.TestSeqIO)
Check parsers can cope with an empty file. ... ok
test_fasta1 (test_SeqIO.TestSeqIO) ... ok
test_fasta10 (test_SeqIO.TestSeqIO) ... ok
test_fasta11 (test_SeqIO.TestSeqIO) ... ok
test_fasta12 (test_SeqIO.TestSeqIO) ... ok
test_fasta13 (test_SeqIO.TestSeqIO) ... ok
test_fasta14 (test_SeqIO.TestSeqIO) ... ok
test_fasta15 (test_SeqIO.TestSeqIO) ... ok
test_fasta16 (test_SeqIO.TestSeqIO) ... ok
test_fasta17 (test_SeqIO.TestSeqIO) ... ok
test_fasta18 (test_SeqIO.TestSeqIO) ... ok
test_fasta19 (test_SeqIO.TestSeqIO) ... ok
test_fasta2 (test_SeqIO.TestSeqIO) ... ok
test_fasta20 (test_SeqIO.TestSeqIO) ... ok
test_fasta21 (test_SeqIO.TestSeqIO) ... ok
test_fasta22 (test_SeqIO.TestSeqIO) ... ok
test_fasta23 (test_SeqIO.TestSeqIO) ... ok
test_fasta24 (test_SeqIO.TestSeqIO) ... ok
test_fasta3 (test_SeqIO.TestSeqIO) ... ok
test_fasta4 (test_SeqIO.TestSeqIO) ... ok
test_fasta5 (test_SeqIO.TestSeqIO) ... ok
test_fasta6 (test_SeqIO.TestSeqIO) ... ok
test_fasta7 (test_SeqIO.TestSeqIO) ... ok
test_fasta8 (test_SeqIO.TestSeqIO) ... ok
test_fasta9 (test_SeqIO.TestSeqIO) ... ok
test_fasta_2line1 (test_SeqIO.TestSeqIO) ... ok
test_fastq1 (test_SeqIO.TestSeqIO) ... ok
test_fastq2 (test_SeqIO.TestSeqIO) ... ok
test_fastq3 (test_SeqIO.TestSeqIO) ... ok
test_fastq4 (test_SeqIO.TestSeqIO) ... ok
test_fastq5 (test_SeqIO.TestSeqIO) ... ok
test_fastq_illumina1 (test_SeqIO.TestSeqIO) ... ok
test_fastq_solexa1 (test_SeqIO.TestSeqIO) ... ok
test_fastq_solexa2 (test_SeqIO.TestSeqIO) ... ok
test_genbank1 (test_SeqIO.TestSeqIO) ... ok
test_genbank10 (test_SeqIO.TestSeqIO) ... ok
test_genbank11 (test_SeqIO.TestSeqIO) ... ok
test_genbank12 (test_SeqIO.TestSeqIO) ... ok
test_genbank13 (test_SeqIO.TestSeqIO) ... ok
test_genbank14 (test_SeqIO.TestSeqIO) ... ok
test_genbank15 (test_SeqIO.TestSeqIO) ... ok
test_genbank16 (test_SeqIO.TestSeqIO)
Test parsing Genbank file from Vector NTI with an odd LOCUS line. ... ok
test_genbank17 (test_SeqIO.TestSeqIO) ... ok
test_genbank18 (test_SeqIO.TestSeqIO) ... ok
test_genbank19 (test_SeqIO.TestSeqIO) ... ok
test_genbank2 (test_SeqIO.TestSeqIO) ... ok
test_genbank20 (test_SeqIO.TestSeqIO)
Test parsing GenPept file with nasty bond locations. ... ok
test_genbank21 (test_SeqIO.TestSeqIO) ... ok
test_genbank3 (test_SeqIO.TestSeqIO) ... ok
test_genbank4 (test_SeqIO.TestSeqIO) ... ok
test_genbank5 (test_SeqIO.TestSeqIO) ... ok
test_genbank6 (test_SeqIO.TestSeqIO) ... ok
test_genbank7 (test_SeqIO.TestSeqIO) ... ok
test_genbank8 (test_SeqIO.TestSeqIO) ... ok
test_genbank9 (test_SeqIO.TestSeqIO) ... ok
test_ig1 (test_SeqIO.TestSeqIO) ... ok
test_ig2 (test_SeqIO.TestSeqIO) ... ok
test_ig3 (test_SeqIO.TestSeqIO)
Test parsing a MASE alignment with sequence O_ANT70 being shorter. ... ok
test_imgt1 (test_SeqIO.TestSeqIO)
Test parsing file with features over-indented for EMBL. ... ok
test_imgt2 (test_SeqIO.TestSeqIO) ... ok
test_nexus1 (test_SeqIO.TestSeqIO) ... ok
test_pdb_atom1 (test_SeqIO.TestSeqIO) ... ok
test_pdb_atom2 (test_SeqIO.TestSeqIO) ... ok
test_pdb_atom3 (test_SeqIO.TestSeqIO) ... ok
test_pdb_seqres1 (test_SeqIO.TestSeqIO) ... ok
test_pdb_seqres2 (test_SeqIO.TestSeqIO) ... ok
test_phd1 (test_SeqIO.TestSeqIO) ... ok
test_phd2 (test_SeqIO.TestSeqIO) ... ok
test_phd3 (test_SeqIO.TestSeqIO) ... ok
test_phd4 (test_SeqIO.TestSeqIO) ... ok
test_phylip1 (test_SeqIO.TestSeqIO) ... ok
test_phylip2 (test_SeqIO.TestSeqIO) ... ok
test_phylip3 (test_SeqIO.TestSeqIO) ... ok
test_phylip4 (test_SeqIO.TestSeqIO) ... ok
test_phylip5 (test_SeqIO.TestSeqIO) ... ok
test_phylip6 (test_SeqIO.TestSeqIO) ... ok
test_phylip7 (test_SeqIO.TestSeqIO) ... ok
test_pir1 (test_SeqIO.TestSeqIO) ... ok
test_pir2 (test_SeqIO.TestSeqIO) ... ok
test_pir3 (test_SeqIO.TestSeqIO) ... ok
test_pir4 (test_SeqIO.TestSeqIO) ... ok
test_pir5 (test_SeqIO.TestSeqIO) ... ok
test_qual1 (test_SeqIO.TestSeqIO) ... ok
test_seqxml1 (test_SeqIO.TestSeqIO) ... ok
test_seqxml2 (test_SeqIO.TestSeqIO) ... ok
test_seqxml3 (test_SeqIO.TestSeqIO) ... ok
test_sff1 (test_SeqIO.TestSeqIO) ... ok
test_snapgene1 (test_SeqIO.TestSeqIO) ... ok
test_stockholm1 (test_SeqIO.TestSeqIO) ... ok
test_stockholm2 (test_SeqIO.TestSeqIO) ... ok
test_swiss1 (test_SeqIO.TestSeqIO) ... ok
test_swiss10 (test_SeqIO.TestSeqIO) ... ok
test_swiss11 (test_SeqIO.TestSeqIO) ... ok
test_swiss12 (test_SeqIO.TestSeqIO) ... ok
test_swiss13 (test_SeqIO.TestSeqIO) ... ok
test_swiss14 (test_SeqIO.TestSeqIO) ... ok
test_swiss15 (test_SeqIO.TestSeqIO) ... ok
test_swiss16 (test_SeqIO.TestSeqIO) ... ok
test_swiss17 (test_SeqIO.TestSeqIO) ... ok
test_swiss18 (test_SeqIO.TestSeqIO) ... ok
test_swiss19 (test_SeqIO.TestSeqIO) ... ok
test_swiss2 (test_SeqIO.TestSeqIO) ... ok
test_swiss20 (test_SeqIO.TestSeqIO) ... ok
test_swiss3 (test_SeqIO.TestSeqIO) ... ok
test_swiss4 (test_SeqIO.TestSeqIO) ... ok
test_swiss5 (test_SeqIO.TestSeqIO) ... ok
test_swiss6 (test_SeqIO.TestSeqIO) ... ok
test_swiss7 (test_SeqIO.TestSeqIO) ... ok
test_swiss8 (test_SeqIO.TestSeqIO) ... ok
test_swiss9 (test_SeqIO.TestSeqIO) ... ok
test_tab1 (test_SeqIO.TestSeqIO) ... ok
test_uniprot_xml1 (test_SeqIO.TestSeqIO) ... ok
test_uniprot_xml2 (test_SeqIO.TestSeqIO) ... ok
test_uniprot_xml3 (test_SeqIO.TestSeqIO) ... ok
test_uniprot_xml4 (test_SeqIO.TestSeqIO) ... ok
test_uniprot_xml5 (test_SeqIO.TestSeqIO) ... ok
test_xdna1 (test_SeqIO.TestSeqIO) ... ok
test_gzip_fasta (test_SeqIO.TestZipped)
Testing FASTA with gzip. ... ok
test_gzip_fastq (test_SeqIO.TestZipped)
Testing FASTQ with gzip. ... ok
test_gzip_genbank (test_SeqIO.TestZipped)
Testing GenBank with gzip. ... ok
----------------------------------------------------------------------
Ran 1 test in 532.335 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_AbiIO.py
test_SeqIO_AbiIO ... ok
test_file_type (test_SeqIO_AbiIO.TestAbi)
Test if filetype is ABIF. ... ok
test_no_smpl1 (test_SeqIO_AbiIO.TestAbi)
Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok
test_raw (test_SeqIO_AbiIO.TestAbi)
Test access to raw ABIF tags. ... ok
test_seqrecord (test_SeqIO_AbiIO.TestAbi)
Test if the extracted seqrecords data are equal to expected values. ... ok
test_trim (test_SeqIO_AbiIO.TestAbi)
Test if trim works. ... ok
test_file_type (test_SeqIO_AbiIO.TestAbiFake)
Test if error is raised if filetype is not ABIF. ... ok
test_nonascii_tag (test_SeqIO_AbiIO.TestAbiNonAscii)
Test that we can handle non-ascii tags. ... ok
test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode)
Test if exception is raised if file is not opened in 'rb' mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.534 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_FastaIO.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SeqIO_FastaIO ... ok
test_edgecases_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
Test FastaTwoLineParser edge-cases. ... ok
test_edgecases_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
Test SimpleFastaParser edge-cases. ... ok
test_exceptions_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
Test FastaTwoLineParser exceptions. ... ok
test_regular_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
Test regular FastaTwoLineParser cases. ... ok
test_regular_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers)
Test regular SimpleFastaParser cases. ... ok
test_mutli_dna_Quality/example (test_SeqIO_FastaIO.TitleFunctions)
Checking multi DNA file Quality/example.fasta ... ok
test_mutli_pro_Fasta/f002 (test_SeqIO_FastaIO.TitleFunctions)
Checking multi protein file Fasta/f002 ... ok
test_mutli_pro_Fasta/fa01 (test_SeqIO_FastaIO.TitleFunctions)
Checking multi protein file Fasta/fa01 ... ok
test_no_name (test_SeqIO_FastaIO.TitleFunctions)
Test FASTA record with no identifier. ... ok
test_nuc_Fasta/centaurea (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/centaurea.nu ... ok
test_nuc_Fasta/elderberry (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/elderberry.nu ... ok
test_nuc_Fasta/f001 (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/f001 ... ok
test_nuc_Fasta/lavender (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/lavender.nu ... ok
test_nuc_Fasta/lupine (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/lupine.nu ... ok
test_nuc_Fasta/phlox (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/phlox.nu ... ok
test_nuc_Fasta/sweetpea (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/sweetpea.nu ... ok
test_nuc_Fasta/wisteria (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/wisteria.nu ... ok
test_pro_Fasta/aster (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/aster.pro ... ok
test_pro_Fasta/loveliesbleeding (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/loveliesbleeding.pro ... ok
test_pro_Fasta/rose (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/rose.pro ... ok
test_pro_Fasta/rosemary (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/rosemary.pro ... ok
test_fails (test_SeqIO_FastaIO.Wrapping)
Test case which should fail. ... ok
test_passes (test_SeqIO_FastaIO.Wrapping)
Test case which should pass. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.473 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Gck.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SeqIO_Gck ... ok
test_conflicting_lengths (test_SeqIO_Gck.TestGckWithArtificialData)
Read a file with incorrect length. ... ok
test_read (test_SeqIO_Gck.TestGckWithArtificialData)
Read an artificial sample file. ... ok
test_read (test_SeqIO_Gck.TestGckWithDGVC)
Read sample files. ... skipped 'Sample files missing and no Internet access'
test_read (test_SeqIO_Gck.TestGckWithImproperHeader)
Read a file with an incomplete header. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.490 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Insdc.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SeqIO_Insdc ... /builddir/build/BUILD/python-biopython-1.75/python3/build/lib.linux-armv7l-3.7/Bio/GenBank/Scanner.py:304: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
  BiopythonParserWarning,
ok
test_annotation1 (test_SeqIO_Insdc.TestEmbl)
Check parsing of annotation from EMBL files (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmbl)
Check parsing of annotation from EMBL files (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmbl)
Check parsing of annotation from EMBL files (3). ... ok
test_annotation4 (test_SeqIO_Insdc.TestEmbl)
Check parsing of annotation from EMBL files (4). ... ok
test_writing_empty_qualifiers (test_SeqIO_Insdc.TestEmbl) ... ok
test_annotation1 (test_SeqIO_Insdc.TestEmblRewrite)
Check writing-and-parsing EMBL file (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmblRewrite)
Check writing-and-parsing EMBL file (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmblRewrite)
Check writing-and-parsing EMBL file (3). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.656 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_NibIO.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SeqIO_NibIO ... ok
test_read_even (test_SeqIO_NibIO.TestNibReaderWriter) ... ok
test_read_odd (test_SeqIO_NibIO.TestNibReaderWriter) ... ok
test_write_even (test_SeqIO_NibIO.TestNibReaderWriter) ... ok
test_write_odd (test_SeqIO_NibIO.TestNibReaderWriter) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.411 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_PdbIO.py
test_SeqIO_PdbIO ... ok
test_atom_parse (test_SeqIO_PdbIO.TestCifAtom)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestCifAtom)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom)
Read a single-chain CIF without a header by ATOM entries. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres)
Read a single-chain structure by sequence entries. ... ok
test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom)
Parse a PDB with no HEADER line. ... ok
test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestPdbAtom)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom)
Read a single-chain PDB without a header by ATOM entries. ... ok
test_atom_with_insertion (test_SeqIO_PdbIO.TestPdbAtom)
Read a PDB with residue insertion code. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres)
Read a single-chain structure by sequence entries. ... ok
----------------------------------------------------------------------
Ran 1 test in 79.550 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_QualityIO.py
test_SeqIO_QualityIO ... ok
test_illumina_to_sanger (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62). ... ok
test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests)
Mapping check for function phred_quality_from_solexa. ... ok
test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62). ... ok
test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62). ... ok
test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests)
Mapping check for function solexa_quality_from_phred. ... ok
test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62). ... ok
test_fasta_as_fastq (test_SeqIO_QualityIO.NonFastqTests) ... ok
test_sff_as_fastq (test_SeqIO_QualityIO.NonFastqTests) ... ok
test_diff_ids (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with diff ids ... ok
test_double_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with double qual ... ok
test_double_seq (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with double seq ... ok
test_long_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with long qual ... ok
test_no_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with no qual ... ok
test_qual_del (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with del in quality ... ok
test_qual_escape (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with escape in quality ... ok
test_qual_null (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with null in quality ... ok
test_qual_space (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with space in quality ... ok
test_qual_tab (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with tab in quality ... ok
test_qual_unit_sep (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with unit sep in quality ... ok
test_qual_vtab (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with vtab in quality ... ok
test_short_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with short qual ... ok
test_spaces (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with spaces ... ok
test_tabs (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with tabs ... ok
test_trunc_at_plus (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc at plus ... ok
test_trunc_at_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc at qual ... ok
test_trunc_at_seq (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc at seq ... ok
test_trunc_in_plus (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in plus ... ok
test_trunc_in_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in qual ... ok
test_trunc_in_seq (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in seq ... ok
test_trunc_in_title (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in title ... ok
test_fasta (test_SeqIO_QualityIO.TestQual)
Check FASTQ parsing matches FASTA parsing. ... ok
test_fasta_out (test_SeqIO_QualityIO.TestQual)
Check FASTQ to FASTA output. ... ok
test_paired (test_SeqIO_QualityIO.TestQual)
Check FASTQ parsing matches FASTA+QUAL parsing. ... ok
test_qual (test_SeqIO_QualityIO.TestQual)
Check FASTQ parsing matches QUAL parsing. ... ok
test_qual_negative (test_SeqIO_QualityIO.TestQual)
Check QUAL negative scores mapped to PHRED zero. ... ok
test_qual_out (test_SeqIO_QualityIO.TestQual)
Check FASTQ to QUAL output. ... ok
test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with mixed case 1000bp read. ... ok
test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with upper case 2000bp read. ... ok
test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with ambiguous DNA. ... ok
test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with ambiguous RNA. ... ok
test_illumina_full_range_illumina (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of illumina file illumina_full_range ... ok
test_longreads_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file longreads ... ok
test_misc_dna_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file misc_dna ... ok
test_misc_rna_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file misc_rna ... ok
test_sanger_full_range_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file sanger_full_range ... ok
test_solexa_full_range_solexa (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of solexa file solexa_full_range ... ok
test_wrapping_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file wrapping ... ok
test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL. ... ok
test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL. ... ok
test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL. ... ok
test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_index_in_middle into FASTA+QUAL. ... ok
test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_index_at_start into FASTA+QUAL. ... ok
test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL. ... ok
test_original (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL. ... ok
test_negative_clip (test_SeqIO_QualityIO.TestSFF) ... ok
test_overlapping_clip (test_SeqIO_QualityIO.TestSFF) ... ok
test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_random_10_reads.sff. ... ok
test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_alt_index_at_end.sff. ... ok
test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_alt_index_at_start.sff. ... ok
test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_alt_index_in_middle.sff. ... ok
test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_index_at_start.sff. ... ok
test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_index_in_middle.sff. ... ok
test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_no_manifest.sff. ... ok
test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_random_10_reads.sff (trimmed). ... ok
test_example_fasta (test_SeqIO_QualityIO.TestWriteRead)
Write and read back example.fasta. ... ok
test_example_fastq (test_SeqIO_QualityIO.TestWriteRead)
Write and read back example.fastq. ... ok
test_example_qual (test_SeqIO_QualityIO.TestWriteRead)
Write and read back example.qual. ... ok
test_generated (test_SeqIO_QualityIO.TestWriteRead)
Write and read back odd SeqRecord objects. ... ok
test_greek_sff (test_SeqIO_QualityIO.TestWriteRead)
Write and read back greek.sff. ... ok
test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead)
Write and read back illumina_faked.fastq. ... ok
test_paired_sff (test_SeqIO_QualityIO.TestWriteRead)
Write and read back paired.sff. ... ok
test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead)
Write and read back sanger_93.fastq. ... ok
test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead)
Write and read back sanger_faked.fastq. ... ok
test_solexa_example (test_SeqIO_QualityIO.TestWriteRead)
Write and read back solexa_example.fastq. ... ok
test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead)
Write and read back solexa_faked.fastq. ... ok
test_tricky (test_SeqIO_QualityIO.TestWriteRead)
Write and read back tricky.fastq. ... ok
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 3.052 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SeqXML.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SeqIO_SeqXML ... ok
test_duplicated_dbxref (test_SeqIO_SeqXML.TestDetailedRead)
Read multiple cross references to a single source. ... ok
test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead)
Read property with multiple values. ... ok
test_empty_description (test_SeqIO_SeqXML.TestDetailedRead)
Check empty description. ... ok
test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead)
Read full characters set for each type. ... ok
test_global_species (test_SeqIO_SeqXML.TestDetailedRead)
Check global species. ... ok
test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead)
Check local source. ... ok
test_local_species (test_SeqIO_SeqXML.TestDetailedRead)
Check local species. ... ok
test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead)
Check minimal record. ... ok
test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead)
Read special XML characters in description. ... ok
test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead)
Test special unicode characters in the description. ... ok
test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write DNA. ... ok
test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write global species. ... ok
test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write protein. ... ok
test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write RNA. ... ok
test_write_species (test_SeqIO_SeqXML.TestReadAndWrite)
Test writing species from annotation tags. ... ok
test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles)
Handling of corrupt files. ... ok
test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead)
Files readable using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.736 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SnapGene.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SeqIO_SnapGene ... ok
test_extra_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene)
Read a file with supernumerary DNA packet. ... ok
test_invalid_cookie (test_SeqIO_SnapGene.TestCorruptedSnapGene)
Read a file with missing or invalid cookie packet. ... ok
test_missing_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene)
Read a file without a DNA packet. ... ok
test_truncated_packet (test_SeqIO_SnapGene.TestCorruptedSnapGene)
Read a file with incomplete packet. ... ok
test_read (test_SeqIO_SnapGene.TestSnapGene)
Read sample files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.434 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Xdna.py
test_SeqIO_Xdna ... ok
test_corrupted_length (test_SeqIO_Xdna.TestInvalidXdna)
Read a file with incorrect length. ... ok
test_invalid_sequence_type (test_SeqIO_Xdna.TestInvalidXdna)
Read a file with an unknown sequence type. ... ok
test_missing_features (test_SeqIO_Xdna.TestInvalidXdna)
Read a file with an incorrect number of features. ... ok
test_unsupported_version (test_SeqIO_Xdna.TestInvalidXdna)
Read a file with unexpected version number. ... ok
test_read (test_SeqIO_Xdna.TestXdna)
Read sample files. ... ok
test_warnings_on_data_loss (test_SeqIO_Xdna.TestXdnaWriter)
Emit warnings when dropping data on write. ... ok
test_write_sequence_type (test_SeqIO_Xdna.TestXdnaWriter)
Write correct sequence type. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.438 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_convert.py
test_SeqIO_convert ... ok
test_EMBL_TRBG361_embl_embl_to_fasta (test_SeqIO_convert.ConvertTests)
Convert EMBL/TRBG361.embl from embl to fasta ... ok
test_EMBL_U87107_embl_embl_to_fasta (test_SeqIO_convert.ConvertTests)
Convert EMBL/U87107.embl from embl to fasta ... ok
test_GenBank_NC_005816_gb_gb_to_fasta (test_SeqIO_convert.ConvertTests)
Convert GenBank/NC_005816.gb from gb to fasta ... ok
test_GenBank_cor6_6_gb_genbank_to_fasta (test_SeqIO_convert.ConvertTests)
Convert GenBank/cor6_6.gb from genbank to fasta ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fasta ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq-illumina ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq-sanger ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq-solexa ... ok
test_Quality_error_diff_ids_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to qual ... ok
test_Quality_error_diff_ids_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to tab ... ok
test_Quality_error_double_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fasta ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_double_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to qual ... ok
test_Quality_error_double_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to tab ... ok
test_Quality_error_double_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fasta ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq-illumina ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq-sanger ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq-solexa ... ok
test_Quality_error_double_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to qual ... ok
test_Quality_error_double_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to tab ... ok
test_Quality_error_long_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fasta ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_long_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to qual ... ok
test_Quality_error_long_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to tab ... ok
test_Quality_error_no_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fasta ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_no_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to qual ... ok
test_Quality_error_no_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to tab ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_del_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to qual ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_escape_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to qual ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_null_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to qual ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_space_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to qual ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_tab_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to qual ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to qual ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to qual ... ok
test_Quality_error_short_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fasta ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_short_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to qual ... ok
test_Quality_error_short_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to tab ... ok
test_Quality_error_spaces_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fasta ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq-illumina ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq-sanger ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq-solexa ... ok
test_Quality_error_spaces_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to qual ... ok
test_Quality_error_spaces_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to tab ... ok
test_Quality_error_tabs_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fasta ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq-illumina ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq-sanger ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq-solexa ... ok
test_Quality_error_tabs_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to qual ... ok
test_Quality_error_tabs_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to tab ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fasta ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to qual ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to tab ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fasta ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to qual ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to tab ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fasta ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to qual ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to tab ... ok
test_Quality_example_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fasta ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq-illumina ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq-sanger ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq-solexa ... ok
test_Quality_example_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to qual ... ok
test_Quality_example_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to tab ... ok
test_Quality_example_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fasta ... ok
test_Quality_example_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq ... ok
test_Quality_example_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq-illumina ... ok
test_Quality_example_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq-sanger ... ok
test_Quality_example_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq-solexa ... ok
test_Quality_example_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to qual ... ok
test_Quality_example_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to tab ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fasta ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-illumina ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-sanger ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-solexa ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to qual ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to tab ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fasta ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq-illumina ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq-sanger ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq-solexa ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to qual ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to tab ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fasta ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-illumina ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-sanger ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-solexa ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to qual ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to tab ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fasta ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-illumina ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-sanger ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-solexa ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to qual ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to tab ... ok
test_Quality_tricky_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fasta ... ok
test_Quality_tricky_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq ... ok
test_Quality_tricky_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq-illumina ... ok
test_Quality_tricky_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq-sanger ... ok
test_Quality_tricky_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq-solexa ... ok
test_Quality_tricky_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to qual ... ok
test_Quality_tricky_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to tab ... ok
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.850 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_features.py
test_SeqIO_features ... ok
test_after (test_SeqIO_features.FeatureWriting)
Features: write/read simple after locations. ... ok
test_before (test_SeqIO_features.FeatureWriting)
Features: write/read simple before locations. ... ok
test_between (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read simple between locations. ... ok
test_exact (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read simple exact locations. ... ok
test_fuzzy_join (test_SeqIO_features.FeatureWriting)
Features: write/read fuzzy join locations. ... ok
test_join (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read simple join locations. ... ok
test_oneof (test_SeqIO_features.FeatureWriting)
Features: write/read simple one-of locations. ... ok
test_unknown (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read with unknown end points. ... ok
test_within (test_SeqIO_features.FeatureWriting)
Features: write/read simple within locations. ... ok
test_mixed_strand (test_SeqIO_features.GenBankLocations) ... ok
test_rev_comp_styles (test_SeqIO_features.GenBankLocations) ... ok
test_CDS (test_SeqIO_features.NC_000932)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_CDS (test_SeqIO_features.NC_005816)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_Features (test_SeqIO_features.NC_005816)
Checking GenBank features sequences vs FASTA ffn file. ... ok
test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816) ... ok
test_Genome (test_SeqIO_features.NC_005816)
Checking GenBank sequence vs FASTA fna file. ... ok
test_Translations (test_SeqIO_features.NC_005816)
Checking translation of FASTA features (faa vs ffn). ... ok
test_qualifiers (test_SeqIO_features.SeqFeatureCreation)
Pass in qualifiers to SeqFeatures. ... ok
test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, mixed strand). ... ok
test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (multi-join, mixed strand). ... ok
test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (between location, zero length). ... ok
test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (join). ... ok
test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (fuzzy join). ... ok
test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (multi-join). ... ok
test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (one-of positions). ... ok
test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (simple). ... ok
test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, default strand). ... ok
test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, strand +1). ... ok
test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, strand -1, after position). ... ok
test_simple_dna_join_before (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, strand -1, before position). ... ok
test_simple_dna_join_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, strand -1). ... ok
test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand 0). ... ok
test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand +1). ... ok
test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand -1). ... ok
test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand None). ... ok
test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on RNA (simple, default strand). ... ok
test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (single letter, default strand). ... ok
test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (between location, zero length, default strand). ... ok
test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (between location at end, zero length, default strand). ... ok
test_AAA03323 (test_SeqIO_features.TestWriteRead)
Write and read back AAA03323.embl. ... ok
test_AE017046 (test_SeqIO_features.TestWriteRead)
Write and read back AE017046.embl. ... ok
test_DD231055_edited (test_SeqIO_features.TestWriteRead)
Write and read back DD231055_edited.embl. ... ok
test_Human_contigs (test_SeqIO_features.TestWriteRead)
Write and read back Human_contigs.embl. ... ok
test_NC_000932 (test_SeqIO_features.TestWriteRead)
Write and read back NC_000932.gb. ... ok
test_NC_005816 (test_SeqIO_features.TestWriteRead)
Write and read back NC_005816.gb. ... ok
test_NT_019265 (test_SeqIO_features.TestWriteRead)
Write and read back NT_019265.gb. ... ok
test_SC10H5 (test_SeqIO_features.TestWriteRead)
Write and read back SC10H5.embl. ... ok
test_TRBG361 (test_SeqIO_features.TestWriteRead)
Write and read back TRBG361.embl. ... ok
test_U87107 (test_SeqIO_features.TestWriteRead)
Write and read back U87107.embl. ... ok
test_arab1 (test_SeqIO_features.TestWriteRead)
Write and read back arab1.gb. ... ok
test_blank_seq (test_SeqIO_features.TestWriteRead)
Write and read back blank_seq.gb. ... ok
test_cor6 (test_SeqIO_features.TestWriteRead)
Write and read back cor6_6.gb. ... ok
test_dbsource_wrap (test_SeqIO_features.TestWriteRead)
Write and read back dbsource_wrap.gb. ... ok
test_extra_keywords (test_SeqIO_features.TestWriteRead)
Write and read back extra_keywords.gb. ... ok
test_gbvrl1_start (test_SeqIO_features.TestWriteRead)
Write and read back gbvrl1_start.seq. ... ok
test_noref (test_SeqIO_features.TestWriteRead)
Write and read back noref.gb. ... ok
test_one_of (test_SeqIO_features.TestWriteRead)
Write and read back of_one.gb. ... ok
test_origin_line (test_SeqIO_features.TestWriteRead)
Write and read back origin_line.gb. ... ok
test_pri1 (test_SeqIO_features.TestWriteRead)
Write and read back pri1.gb. ... ok
test_protein_refseq (test_SeqIO_features.TestWriteRead)
Write and read back protein_refseq.gb. ... ok
test_protein_refseq2 (test_SeqIO_features.TestWriteRead)
Write and read back protein_refseq2.gb. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.648 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_index.py
test_SeqIO_index ... ok
test_ace_Ace_consed_sample_ace_get_raw (test_SeqIO_index.IndexDictTests)
Index ace file Ace/consed_sample.ace get_raw ... ok
test_ace_Ace_consed_sample_ace_keyf (test_SeqIO_index.IndexDictTests)
Index ace file Ace/consed_sample.ace with key function ... ok
test_ace_Ace_consed_sample_ace_simple (test_SeqIO_index.IndexDictTests)
Index ace file Ace/consed_sample.ace defaults ... ok
test_ace_Ace_contig1_ace_get_raw (test_SeqIO_index.IndexDictTests)
Index ace file Ace/contig1.ace get_raw ... ok
test_ace_Ace_contig1_ace_keyf (test_SeqIO_index.IndexDictTests)
Index ace file Ace/contig1.ace with key function ... ok
test_ace_Ace_contig1_ace_simple (test_SeqIO_index.IndexDictTests)
Index ace file Ace/contig1.ace defaults ... ok
test_ace_Ace_seq_cap_ace_get_raw (test_SeqIO_index.IndexDictTests)
Index ace file Ace/seq.cap.ace get_raw ... ok
test_ace_Ace_seq_cap_ace_keyf (test_SeqIO_index.IndexDictTests)
Index ace file Ace/seq.cap.ace with key function ... ok
test_ace_Ace_seq_cap_ace_simple (test_SeqIO_index.IndexDictTests)
Index ace file Ace/seq.cap.ace defaults ... ok
test_duplicates_index (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifiers with Bio.SeqIO.index(). ... ok
test_duplicates_index_db (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifiers with Bio.SeqIO.index_db(). ... ok
test_duplicates_to_dict (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifiers with Bio.SeqIO.to_dict(). ... ok
test_embl_EMBL_A04195_imgt_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/A04195.imgt get_raw ... ok
test_embl_EMBL_A04195_imgt_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/A04195.imgt with key function ... ok
test_embl_EMBL_A04195_imgt_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/A04195.imgt defaults ... ok
test_embl_EMBL_AAA03323_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/AAA03323.embl get_raw ... ok
test_embl_EMBL_AAA03323_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/AAA03323.embl with key function ... ok
test_embl_EMBL_AAA03323_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/AAA03323.embl defaults ... ok
test_embl_EMBL_TRBG361_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/TRBG361.embl get_raw ... ok
test_embl_EMBL_TRBG361_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/TRBG361.embl with key function ... ok
test_embl_EMBL_TRBG361_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/TRBG361.embl defaults ... ok
test_embl_EMBL_U87107_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/U87107.embl get_raw ... ok
test_embl_EMBL_U87107_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/U87107.embl with key function ... ok
test_embl_EMBL_U87107_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/U87107.embl defaults ... ok
test_embl_EMBL_epo_prt_selection_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/epo_prt_selection.embl get_raw ... ok
test_embl_EMBL_epo_prt_selection_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/epo_prt_selection.embl with key function ... ok
test_embl_EMBL_epo_prt_selection_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/epo_prt_selection.embl defaults ... ok
test_embl_EMBL_kipo_prt_sample_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/kipo_prt_sample.embl get_raw ... ok
test_embl_EMBL_kipo_prt_sample_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/kipo_prt_sample.embl with key function ... ok
test_embl_EMBL_kipo_prt_sample_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/kipo_prt_sample.embl defaults ... ok
test_embl_EMBL_patents_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/patents.embl get_raw ... ok
test_embl_EMBL_patents_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/patents.embl with key function ... ok
test_embl_EMBL_patents_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/patents.embl defaults ... ok
test_fasta_GenBank_NC_000932_faa_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_000932.faa get_raw ... ok
test_fasta_GenBank_NC_000932_faa_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_000932.faa with key function ... ok
test_fasta_GenBank_NC_000932_faa_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_000932.faa defaults ... ok
test_fasta_GenBank_NC_005816_faa_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.faa get_raw ... ok
test_fasta_GenBank_NC_005816_faa_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.faa with key function ... ok
test_fasta_GenBank_NC_005816_faa_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.faa defaults ... ok
test_fasta_GenBank_NC_005816_ffn_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.ffn get_raw ... ok
test_fasta_GenBank_NC_005816_ffn_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.ffn with key function ... ok
test_fasta_GenBank_NC_005816_ffn_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.ffn defaults ... ok
test_fasta_GenBank_NC_005816_fna_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.fna get_raw ... ok
test_fasta_GenBank_NC_005816_fna_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.fna with key function ... ok
test_fasta_GenBank_NC_005816_fna_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.fna defaults ... ok
test_fasta_SwissProt_multi_ex_fasta_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file SwissProt/multi_ex.fasta get_raw ... ok
test_fasta_SwissProt_multi_ex_fasta_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file SwissProt/multi_ex.fasta with key function ... ok
test_fasta_SwissProt_multi_ex_fasta_simple (test_SeqIO_index.IndexDictTests)
Index fasta file SwissProt/multi_ex.fasta defaults ... ok
test_fastq-illumina_Quality_illumina_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-illumina file Quality/illumina_faked.fastq get_raw ... ok
test_fastq-illumina_Quality_illumina_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-illumina file Quality/illumina_faked.fastq with key function ... ok
test_fastq-illumina_Quality_illumina_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-illumina file Quality/illumina_faked.fastq defaults ... ok
test_fastq-sanger_Quality_example_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq get_raw ... ok
test_fastq-sanger_Quality_example_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq with key function ... ok
test_fastq-sanger_Quality_example_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq defaults ... ok
test_fastq-sanger_Quality_sanger_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/sanger_faked.fastq get_raw ... ok
test_fastq-sanger_Quality_sanger_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/sanger_faked.fastq with key function ... ok
test_fastq-sanger_Quality_sanger_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/sanger_faked.fastq defaults ... ok
test_fastq-solexa_Quality_solexa_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-solexa file Quality/solexa_faked.fastq get_raw ... ok
test_fastq-solexa_Quality_solexa_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-solexa file Quality/solexa_faked.fastq with key function ... ok
test_fastq-solexa_Quality_solexa_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-solexa file Quality/solexa_faked.fastq defaults ... ok
test_fastq_Quality_example_dos_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example_dos.fastq get_raw ... ok
test_fastq_Quality_example_dos_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example_dos.fastq with key function ... ok
test_fastq_Quality_example_dos_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example_dos.fastq defaults ... ok
test_fastq_Quality_example_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq get_raw ... ok
test_fastq_Quality_example_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq with key function ... ok
test_fastq_Quality_example_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq defaults ... ok
test_fastq_Quality_tricky_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/tricky.fastq get_raw ... ok
test_fastq_Quality_tricky_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/tricky.fastq with key function ... ok
test_fastq_Quality_tricky_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/tricky.fastq defaults ... ok
test_fastq_Quality_wrapping_original_sanger_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/wrapping_original_sanger.fastq get_raw ... ok
test_fastq_Quality_wrapping_original_sanger_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/wrapping_original_sanger.fastq with key function ... ok
test_fastq_Quality_wrapping_original_sanger_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/wrapping_original_sanger.fastq defaults ... ok
test_fastq_Quality_zero_length_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/zero_length.fastq get_raw ... ok
test_fastq_Quality_zero_length_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/zero_length.fastq with key function ... ok
test_fastq_Quality_zero_length_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/zero_length.fastq defaults ... ok
test_gb_GenBank_NC_005816_gb_get_raw (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/NC_005816.gb get_raw ... ok
test_gb_GenBank_NC_005816_gb_keyf (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/NC_005816.gb with key function ... ok
test_gb_GenBank_NC_005816_gb_simple (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/NC_005816.gb defaults ... ok
test_gb_GenBank_empty_accession_gbk_get_raw (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_accession.gbk get_raw ... ok
test_gb_GenBank_empty_accession_gbk_keyf (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_accession.gbk with key function ... ok
test_gb_GenBank_empty_accession_gbk_simple (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_accession.gbk defaults ... ok
test_gb_GenBank_empty_version_gbk_get_raw (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_version.gbk get_raw ... ok
test_gb_GenBank_empty_version_gbk_keyf (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_version.gbk with key function ... ok
test_gb_GenBank_empty_version_gbk_simple (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/empty_version.gbk defaults ... ok
test_genbank_GenBank_cor6_6_gb_get_raw (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb get_raw ... ok
test_genbank_GenBank_cor6_6_gb_keyf (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb with key function ... ok
test_genbank_GenBank_cor6_6_gb_simple (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb defaults ... ok
test_ig_IntelliGenetics_TAT_mase_nuc_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/TAT_mase_nuc.txt get_raw ... ok
test_ig_IntelliGenetics_TAT_mase_nuc_txt_keyf (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/TAT_mase_nuc.txt with key function ... ok
test_ig_IntelliGenetics_TAT_mase_nuc_txt_simple (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/TAT_mase_nuc.txt defaults ... ok
test_ig_IntelliGenetics_VIF_mase-pro_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/VIF_mase-pro.txt get_raw ... ok
test_ig_IntelliGenetics_VIF_mase-pro_txt_keyf (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/VIF_mase-pro.txt with key function ... ok
test_ig_IntelliGenetics_VIF_mase-pro_txt_simple (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/VIF_mase-pro.txt defaults ... ok
test_ig_IntelliGenetics_vpu_nucaligned_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/vpu_nucaligned.txt get_raw ... ok
test_ig_IntelliGenetics_vpu_nucaligned_txt_keyf (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/vpu_nucaligned.txt with key function ... ok
test_ig_IntelliGenetics_vpu_nucaligned_txt_simple (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/vpu_nucaligned.txt defaults ... ok
test_imgt_EMBL_A04195_imgt_get_raw (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/A04195.imgt get_raw ... ok
test_imgt_EMBL_A04195_imgt_keyf (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/A04195.imgt with key function ... ok
test_imgt_EMBL_A04195_imgt_simple (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/A04195.imgt defaults ... ok
test_imgt_EMBL_hla_3260_sample_imgt_get_raw (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/hla_3260_sample.imgt get_raw ... ok
test_imgt_EMBL_hla_3260_sample_imgt_keyf (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/hla_3260_sample.imgt with key function ... ok
test_imgt_EMBL_hla_3260_sample_imgt_simple (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/hla_3260_sample.imgt defaults ... ok
test_phd_Phd_phd1_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd1 get_raw ... ok
test_phd_Phd_phd1_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd1 with key function ... ok
test_phd_Phd_phd1_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd1 defaults ... ok
test_phd_Phd_phd2_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd2 get_raw ... ok
test_phd_Phd_phd2_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd2 with key function ... ok
test_phd_Phd_phd2_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd2 defaults ... ok
test_phd_Phd_phd_454_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_454 get_raw ... ok
test_phd_Phd_phd_454_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_454 with key function ... ok
test_phd_Phd_phd_454_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_454 defaults ... ok
test_phd_Phd_phd_solexa_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_solexa get_raw ... ok
test_phd_Phd_phd_solexa_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_solexa with key function ... ok
test_phd_Phd_phd_solexa_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_solexa defaults ... ok
test_pir_NBRF_B_nuc_pir_get_raw (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/B_nuc.pir get_raw ... ok
test_pir_NBRF_B_nuc_pir_keyf (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/B_nuc.pir with key function ... ok
test_pir_NBRF_B_nuc_pir_simple (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/B_nuc.pir defaults ... ok
test_pir_NBRF_Cw_prot_pir_get_raw (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/Cw_prot.pir get_raw ... ok
test_pir_NBRF_Cw_prot_pir_keyf (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/Cw_prot.pir with key function ... ok
test_pir_NBRF_Cw_prot_pir_simple (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/Cw_prot.pir defaults ... ok
test_pir_NBRF_clustalw_pir_get_raw (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/clustalw.pir get_raw ... ok
test_pir_NBRF_clustalw_pir_keyf (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/clustalw.pir with key function ... ok
test_pir_NBRF_clustalw_pir_simple (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/clustalw.pir defaults ... ok
test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff get_raw ... ok
test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff with key function ... ok
test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff defaults ... ok
test_sff-trim_Roche_greek_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/greek.sff get_raw ... ok
test_sff-trim_Roche_greek_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/greek.sff with key function ... ok
test_sff-trim_Roche_greek_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/greek.sff defaults ... ok
test_sff-trim_Roche_paired_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/paired.sff get_raw ... ok
test_sff-trim_Roche_paired_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/paired.sff with key function ... ok
test_sff-trim_Roche_paired_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/paired.sff defaults ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_end.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_end.sff with key function ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_end.sff defaults ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_start.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_start.sff with key function ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_start.sff defaults ... ok
test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff with key function ... ok
test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff defaults ... ok
test_sff_Roche_E3MFGYR02_index_at_start_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_at_start.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_index_at_start_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_at_start.sff with key function ... ok
test_sff_Roche_E3MFGYR02_index_at_start_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_at_start.sff defaults ... ok
test_sff_Roche_E3MFGYR02_index_in_middle_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_in_middle.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_index_in_middle_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_in_middle.sff with key function ... ok
test_sff_Roche_E3MFGYR02_index_in_middle_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_in_middle.sff defaults ... ok
test_sff_Roche_E3MFGYR02_no_manifest_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_no_manifest.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_no_manifest_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_no_manifest.sff with key function ... ok
test_sff_Roche_E3MFGYR02_no_manifest_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_no_manifest.sff defaults ... ok
test_sff_Roche_E3MFGYR02_random_10_reads_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_random_10_reads.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_random_10_reads_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_random_10_reads.sff with key function ... ok
test_sff_Roche_E3MFGYR02_random_10_reads_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_random_10_reads.sff defaults ... ok
test_sff_Roche_greek_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/greek.sff get_raw ... ok
test_sff_Roche_greek_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/greek.sff with key function ... ok
test_sff_Roche_greek_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/greek.sff defaults ... ok
test_sff_Roche_paired_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/paired.sff get_raw ... ok
test_sff_Roche_paired_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/paired.sff with key function ... ok
test_sff_Roche_paired_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/paired.sff defaults ... ok
test_swiss_SwissProt_multi_ex_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/multi_ex.txt get_raw ... ok
test_swiss_SwissProt_multi_ex_txt_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/multi_ex.txt with key function ... ok
test_swiss_SwissProt_multi_ex_txt_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/multi_ex.txt defaults ... ok
test_swiss_SwissProt_sp001_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp001 get_raw ... ok
test_swiss_SwissProt_sp001_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp001 with key function ... ok
test_swiss_SwissProt_sp001_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp001 defaults ... ok
test_swiss_SwissProt_sp010_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp010 get_raw ... ok
test_swiss_SwissProt_sp010_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp010 with key function ... ok
test_swiss_SwissProt_sp010_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp010 defaults ... ok
test_swiss_SwissProt_sp016_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp016 get_raw ... ok
test_swiss_SwissProt_sp016_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp016 with key function ... ok
test_swiss_SwissProt_sp016_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp016 defaults ... ok
test_tab_GenBank_NC_005816_tsv_get_raw (test_SeqIO_index.IndexDictTests)
Index tab file GenBank/NC_005816.tsv get_raw ... ok
test_tab_GenBank_NC_005816_tsv_keyf (test_SeqIO_index.IndexDictTests)
Index tab file GenBank/NC_005816.tsv with key function ... ok
test_tab_GenBank_NC_005816_tsv_simple (test_SeqIO_index.IndexDictTests)
Index tab file GenBank/NC_005816.tsv defaults ... ok
test_uniprot-xml_SwissProt_multi_ex_xml_get_raw (test_SeqIO_index.IndexDictTests)
Index uniprot-xml file SwissProt/multi_ex.xml get_raw ... ok
test_uniprot-xml_SwissProt_multi_ex_xml_keyf (test_SeqIO_index.IndexDictTests)
Index uniprot-xml file SwissProt/multi_ex.xml with key function ... ok
test_uniprot-xml_SwissProt_multi_ex_xml_simple (test_SeqIO_index.IndexDictTests)
Index uniprot-xml file SwissProt/multi_ex.xml defaults ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingManyFiles)
Check index_db preserves order in multiple indexed files. ... ok
test_order_index (test_SeqIO_index.IndexOrderingSingleFile)
Check index preserves order in indexed file. ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingSingleFile)
Check index_db preserves ordering indexed file. ... ok
test_order_to_dict (test_SeqIO_index.IndexOrderingSingleFile)
Check to_dict preserves order in indexed file. ... ok
test_child_folder_rel (test_SeqIO_index.NewIndexTest)
Check relative links to child folder. ... ok
test_same_folder (test_SeqIO_index.NewIndexTest)
Check relative links in same folder. ... ok
test_some_abs (test_SeqIO_index.NewIndexTest)
Check absolute filenames in index. ... ok
test_old (test_SeqIO_index.OldIndexTest)
Load existing index with no options (from parent directory). ... ok
test_old_check_same_thread (test_SeqIO_index.OldIndexTest)
Setting check_same_thread to False doesn't raise an exception. ... ok
test_old_contents (test_SeqIO_index.OldIndexTest)
Check actual filenames in existing indexes. ... ok
test_old_files (test_SeqIO_index.OldIndexTest)
Load existing index with correct files (from parent directory). ... ok
test_old_files_same_dir (test_SeqIO_index.OldIndexTest)
Load existing index with correct files (from same directory). ... ok
test_old_files_wrong (test_SeqIO_index.OldIndexTest)
Load existing index with wrong files. ... ok
test_old_files_wrong2 (test_SeqIO_index.OldIndexTest)
Load existing index with wrong number of files. ... ok
test_old_format (test_SeqIO_index.OldIndexTest)
Load existing index with correct format. ... ok
test_old_format_wrong (test_SeqIO_index.OldIndexTest)
Load existing index with wrong format. ... ok
test_old_rel (test_SeqIO_index.OldIndexTest)
Load existing index (with relative paths) with no options (from parent directory). ... ok
test_old_same_dir (test_SeqIO_index.OldIndexTest)
Load existing index with no options (from same directory). ... ok
test_old_same_dir_rel (test_SeqIO_index.OldIndexTest)
Load existing index (with relative paths) with no options (from same directory). ... ok
----------------------------------------------------------------------
Ran 1 test in 94.542 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_online.py
test_SeqIO_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.465 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_write.py
test_SeqIO_write ... ok
test_bad_handle (test_SeqIO_write.WriterTests) ... ok
test_clustal_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
clustal for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_clustal_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
clustal for alignment with repeated record ... ok
test_clustal_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
clustal for three DNA sequence alignment ... ok
test_clustal_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
clustal for three peptides of different lengths ... ok
test_clustal_three_proteins_alignment (test_SeqIO_write.WriterTests)
clustal for three proteins alignment ... ok
test_clustal_zero_records (test_SeqIO_write.WriterTests)
clustal for zero records ... ok
test_embl_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
embl for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_embl_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
embl for alignment with repeated record ... ok
test_embl_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
embl for three DNA sequence alignment ... ok
test_embl_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
embl for three peptides of different lengths ... ok
test_embl_three_proteins_alignment (test_SeqIO_write.WriterTests)
embl for three proteins alignment ... ok
test_embl_zero_records (test_SeqIO_write.WriterTests)
embl for zero records ... ok
test_fasta-2line_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fasta-2line for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fasta-2line_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fasta-2line for alignment with repeated record ... ok
test_fasta-2line_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fasta-2line for three DNA sequence alignment ... ok
test_fasta-2line_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fasta-2line for three peptides of different lengths ... ok
test_fasta-2line_three_proteins_alignment (test_SeqIO_write.WriterTests)
fasta-2line for three proteins alignment ... ok
test_fasta-2line_zero_records (test_SeqIO_write.WriterTests)
fasta-2line for zero records ... ok
test_fasta_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fasta for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fasta_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fasta for alignment with repeated record ... ok
test_fasta_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fasta for three DNA sequence alignment ... ok
test_fasta_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fasta for three peptides of different lengths ... ok
test_fasta_three_proteins_alignment (test_SeqIO_write.WriterTests)
fasta for three proteins alignment ... ok
test_fasta_zero_records (test_SeqIO_write.WriterTests)
fasta for zero records ... ok
test_fastq-illumina_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fastq-illumina for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fastq-illumina_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fastq-illumina for alignment with repeated record ... ok
test_fastq-illumina_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fastq-illumina for three DNA sequence alignment ... ok
test_fastq-illumina_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fastq-illumina for three peptides of different lengths ... ok
test_fastq-illumina_three_proteins_alignment (test_SeqIO_write.WriterTests)
fastq-illumina for three proteins alignment ... ok
test_fastq-illumina_zero_records (test_SeqIO_write.WriterTests)
fastq-illumina for zero records ... ok
test_fastq-solexa_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fastq-solexa for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fastq-solexa_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fastq-solexa for alignment with repeated record ... ok
test_fastq-solexa_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fastq-solexa for three DNA sequence alignment ... ok
test_fastq-solexa_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fastq-solexa for three peptides of different lengths ... ok
test_fastq-solexa_three_proteins_alignment (test_SeqIO_write.WriterTests)
fastq-solexa for three proteins alignment ... ok
test_fastq-solexa_zero_records (test_SeqIO_write.WriterTests)
fastq-solexa for zero records ... ok
test_fastq_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fastq for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fastq_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fastq for alignment with repeated record ... ok
test_fastq_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fastq for three DNA sequence alignment ... ok
test_fastq_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fastq for three peptides of different lengths ... ok
test_fastq_three_proteins_alignment (test_SeqIO_write.WriterTests)
fastq for three proteins alignment ... ok
test_fastq_zero_records (test_SeqIO_write.WriterTests)
fastq for zero records ... ok
test_genbank_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
genbank for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_genbank_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
genbank for alignment with repeated record ... ok
test_genbank_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
genbank for three DNA sequence alignment ... ok
test_genbank_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
genbank for three peptides of different lengths ... ok
test_genbank_three_proteins_alignment (test_SeqIO_write.WriterTests)
genbank for three proteins alignment ... ok
test_genbank_zero_records (test_SeqIO_write.WriterTests)
genbank for zero records ... ok
test_imgt_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
imgt for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_imgt_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
imgt for alignment with repeated record ... ok
test_imgt_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
imgt for three DNA sequence alignment ... ok
test_imgt_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
imgt for three peptides of different lengths ... ok
test_imgt_three_proteins_alignment (test_SeqIO_write.WriterTests)
imgt for three proteins alignment ... ok
test_imgt_zero_records (test_SeqIO_write.WriterTests)
imgt for zero records ... ok
test_maf_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
maf for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_maf_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
maf for alignment with repeated record ... ok
test_maf_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
maf for three DNA sequence alignment ... ok
test_maf_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
maf for three peptides of different lengths ... ok
test_maf_three_proteins_alignment (test_SeqIO_write.WriterTests)
maf for three proteins alignment ... ok
test_maf_zero_records (test_SeqIO_write.WriterTests)
maf for zero records ... ok
test_mauve_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
mauve for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_mauve_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
mauve for alignment with repeated record ... ok
test_mauve_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
mauve for three DNA sequence alignment ... ok
test_mauve_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
mauve for three peptides of different lengths ... ok
test_mauve_three_proteins_alignment (test_SeqIO_write.WriterTests)
mauve for three proteins alignment ... ok
test_mauve_zero_records (test_SeqIO_write.WriterTests)
mauve for zero records ... ok
test_nexus_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
nexus for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_nexus_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
nexus for alignment with repeated record ... ok
test_nexus_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
nexus for three DNA sequence alignment ... ok
test_nexus_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
nexus for three peptides of different lengths ... ok
test_nexus_three_proteins_alignment (test_SeqIO_write.WriterTests)
nexus for three proteins alignment ... ok
test_nexus_zero_records (test_SeqIO_write.WriterTests)
nexus for zero records ... ok
test_nib_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
nib for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_nib_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
nib for alignment with repeated record ... ok
test_nib_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
nib for three DNA sequence alignment ... ok
test_nib_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
nib for three peptides of different lengths ... ok
test_nib_three_proteins_alignment (test_SeqIO_write.WriterTests)
nib for three proteins alignment ... ok
test_nib_zero_records (test_SeqIO_write.WriterTests)
nib for zero records ... ok
test_phd_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phd for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phd_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phd for alignment with repeated record ... ok
test_phd_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phd for three DNA sequence alignment ... ok
test_phd_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phd for three peptides of different lengths ... ok
test_phd_three_proteins_alignment (test_SeqIO_write.WriterTests)
phd for three proteins alignment ... ok
test_phd_zero_records (test_SeqIO_write.WriterTests)
phd for zero records ... ok
test_phylip-relaxed_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phylip-relaxed for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phylip-relaxed_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phylip-relaxed for alignment with repeated record ... ok
test_phylip-relaxed_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phylip-relaxed for three DNA sequence alignment ... ok
test_phylip-relaxed_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phylip-relaxed for three peptides of different lengths ... ok
test_phylip-relaxed_three_proteins_alignment (test_SeqIO_write.WriterTests)
phylip-relaxed for three proteins alignment ... ok
test_phylip-relaxed_zero_records (test_SeqIO_write.WriterTests)
phylip-relaxed for zero records ... ok
test_phylip-sequential_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phylip-sequential for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phylip-sequential_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phylip-sequential for alignment with repeated record ... ok
test_phylip-sequential_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phylip-sequential for three DNA sequence alignment ... ok
test_phylip-sequential_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phylip-sequential for three peptides of different lengths ... ok
test_phylip-sequential_three_proteins_alignment (test_SeqIO_write.WriterTests)
phylip-sequential for three proteins alignment ... ok
test_phylip-sequential_zero_records (test_SeqIO_write.WriterTests)
phylip-sequential for zero records ... ok
test_phylip_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phylip for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phylip_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phylip for alignment with repeated record ... ok
test_phylip_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phylip for three DNA sequence alignment ... ok
test_phylip_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phylip for three peptides of different lengths ... ok
test_phylip_three_proteins_alignment (test_SeqIO_write.WriterTests)
phylip for three proteins alignment ... ok
test_phylip_zero_records (test_SeqIO_write.WriterTests)
phylip for zero records ... ok
test_pir_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
pir for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_pir_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
pir for alignment with repeated record ... ok
test_pir_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
pir for three DNA sequence alignment ... ok
test_pir_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
pir for three peptides of different lengths ... ok
test_pir_three_proteins_alignment (test_SeqIO_write.WriterTests)
pir for three proteins alignment ... ok
test_pir_zero_records (test_SeqIO_write.WriterTests)
pir for zero records ... ok
test_qual_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
qual for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_qual_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
qual for alignment with repeated record ... ok
test_qual_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
qual for three DNA sequence alignment ... ok
test_qual_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
qual for three peptides of different lengths ... ok
test_qual_three_proteins_alignment (test_SeqIO_write.WriterTests)
qual for three proteins alignment ... ok
test_qual_zero_records (test_SeqIO_write.WriterTests)
qual for zero records ... ok
test_seqxml_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
seqxml for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_seqxml_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
seqxml for alignment with repeated record ... ok
test_seqxml_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
seqxml for three DNA sequence alignment ... ok
test_seqxml_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
seqxml for three peptides of different lengths ... ok
test_seqxml_three_proteins_alignment (test_SeqIO_write.WriterTests)
seqxml for three proteins alignment ... ok
test_seqxml_zero_records (test_SeqIO_write.WriterTests)
seqxml for zero records ... ok
test_sff_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
sff for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_sff_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
sff for alignment with repeated record ... ok
test_sff_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
sff for three DNA sequence alignment ... ok
test_sff_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
sff for three peptides of different lengths ... ok
test_sff_three_proteins_alignment (test_SeqIO_write.WriterTests)
sff for three proteins alignment ... ok
test_sff_zero_records (test_SeqIO_write.WriterTests)
sff for zero records ... ok
test_stockholm_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
stockholm for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_stockholm_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
stockholm for alignment with repeated record ... ok
test_stockholm_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
stockholm for three DNA sequence alignment ... ok
test_stockholm_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
stockholm for three peptides of different lengths ... ok
test_stockholm_three_proteins_alignment (test_SeqIO_write.WriterTests)
stockholm for three proteins alignment ... ok
test_stockholm_zero_records (test_SeqIO_write.WriterTests)
stockholm for zero records ... ok
test_tab_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
tab for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_tab_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
tab for alignment with repeated record ... ok
test_tab_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
tab for three DNA sequence alignment ... ok
test_tab_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
tab for three peptides of different lengths ... ok
test_tab_three_proteins_alignment (test_SeqIO_write.WriterTests)
tab for three proteins alignment ... ok
test_tab_zero_records (test_SeqIO_write.WriterTests)
tab for zero records ... ok
test_xdna_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
xdna for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_xdna_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
xdna for alignment with repeated record ... ok
test_xdna_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
xdna for three DNA sequence alignment ... ok
test_xdna_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
xdna for three peptides of different lengths ... ok
test_xdna_three_proteins_alignment (test_SeqIO_write.WriterTests)
xdna for three proteins alignment ... ok
test_xdna_zero_records (test_SeqIO_write.WriterTests)
xdna for zero records ... ok
----------------------------------------------------------------------
Ran 1 test in 0.658 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqRecord.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SeqRecord ... ok
test_annotations (test_SeqRecord.SeqRecordCreation)
Pass in annotations to SeqRecords. ... ok
test_letter_annotations (test_SeqRecord.SeqRecordCreation)
Pass in letter annotations to SeqRecords. ... ok
test_replacing_seq (test_SeqRecord.SeqRecordCreation)
Replacing .seq if .letter_annotation present. ... ok
test_valid_annotations (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_description (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_features (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_id (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_name (test_SeqRecord.SeqRecordCreation) ... ok
test_add_seq (test_SeqRecord.SeqRecordMethods)
Simple addition of Seq or string. ... ok
test_add_seq_left (test_SeqRecord.SeqRecordMethods)
Simple left addition of Seq or string. ... ok
test_add_seqrecord (test_SeqRecord.SeqRecordMethods)
Simple left addition of SeqRecord from genbank file. ... ok
test_add_simple (test_SeqRecord.SeqRecordMethods)
Simple addition. ... ok
test_contains (test_SeqRecord.SeqRecordMethods) ... ok
test_format (test_SeqRecord.SeqRecordMethods) ... ok
test_format_spaces (test_SeqRecord.SeqRecordMethods) ... ok
test_iter (test_SeqRecord.SeqRecordMethods) ... ok
test_lower (test_SeqRecord.SeqRecordMethods) ... ok
test_repr (test_SeqRecord.SeqRecordMethods) ... ok
test_slice_add_shift (test_SeqRecord.SeqRecordMethods)
Simple slice and add to shift. ... ok
test_slice_add_simple (test_SeqRecord.SeqRecordMethods)
Simple slice and add. ... ok
test_slice_simple (test_SeqRecord.SeqRecordMethods)
Simple slice. ... ok
test_slice_variants (test_SeqRecord.SeqRecordMethods)
Simple slices using different start/end values. ... ok
test_slice_zero (test_SeqRecord.SeqRecordMethods)
Zero slice. ... ok
test_slicing (test_SeqRecord.SeqRecordMethods) ... ok
test_str (test_SeqRecord.SeqRecordMethods) ... ok
test_upper (test_SeqRecord.SeqRecordMethods) ... ok
test_eq_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_ge_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_gt_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_hash_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_le_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_lt_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_ne_exception (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_reverse_complement_seq (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_translate (test_SeqRecord.SeqRecordMethodsMore) ... ok
test_defaults (test_SeqRecord.TestTranslation) ... ok
test_new_annot (test_SeqRecord.TestTranslation) ... ok
test_preserve (test_SeqRecord.TestTranslation) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.153 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqUtils.py
test_SeqUtils ... ok
test_GC (test_SeqUtils.SeqUtilsTests) ... ok
test_GC_skew (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum1 (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum2 (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum3 (test_SeqUtils.SeqUtilsTests) ... ok
test_codon_adaptation_index (test_SeqUtils.SeqUtilsTests) ... ok
test_codon_usage_custom (test_SeqUtils.SeqUtilsTests)
Test Codon Adaptation Index (CAI) using FASTA file for background. ... ok
test_codon_usage_ecoli (test_SeqUtils.SeqUtilsTests)
Test Codon Adaptation Index (CAI) using default E. coli data. ... ok
test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests) ... ok
test_index (test_SeqUtils.SeqUtilsTests) ... ok
test_seq1_seq3 (test_SeqUtils.SeqUtilsTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 3.505 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Seq_objs.py
test_Seq_objs ... ok
test_unknown_seq_ungap (test_Seq_objs.FileBasedTests)
Test ungap() works properly on UnknownSeq instances. ... ok
test_MutableSeq_init_typeerror (test_Seq_objs.StringMethodTests)
Check MutableSeq __init__ gives TypeError exceptions. ... ok
test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests)
Check our count_overlap method using GG with variable ends and starts. ... ok
test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests)
Check our count_overlap method using NN with variable ends and starts. ... ok
test_init_typeerror (test_Seq_objs.StringMethodTests)
Check Seq __init__ gives TypeError exceptions. ... ok
test_join_MutableSeq (test_Seq_objs.StringMethodTests)
Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok
test_join_MutableSeq_TypeError (test_Seq_objs.StringMethodTests)
Checks that a TypeError is thrown for incompatible alphabets. ... ok
test_join_MutableSeq_ValueError (test_Seq_objs.StringMethodTests)
Checks that a ValueError is thrown for all non-iterable types. ... ok
test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests)
Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok
test_join_Seq (test_Seq_objs.StringMethodTests)
Checks if Seq join correctly concatenates sequence with the spacer. ... ok
test_join_Seq_TypeError (test_Seq_objs.StringMethodTests)
Checks that a TypeError is thrown for incompatible alphabets. ... ok
test_join_Seq_ValueError (test_Seq_objs.StringMethodTests)
Checks that a ValueError is thrown for all non-iterable types. ... ok
test_join_Seq_with_file (test_Seq_objs.StringMethodTests)
Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok
test_join_UnknownSeq (test_Seq_objs.StringMethodTests)
Checks if UnknownSeq join correctly concatenates sequence with the spacer. ... ok
test_join_UnknownSeq_TypeError (test_Seq_objs.StringMethodTests)
Checks that a TypeError is thrown for incompatible alphabets. ... ok
test_join_UnknownSeq_ValueError (test_Seq_objs.StringMethodTests)
Checks that a ValueError is thrown for all non-iterable types. ... ok
test_join_UnknownSeq_with_file (test_Seq_objs.StringMethodTests)
Checks if UnknownSeq join correctly concatenates sequence from a file with the spacer. ... ok
test_str_comparison (test_Seq_objs.StringMethodTests) ... ok
test_str_count (test_Seq_objs.StringMethodTests)
Check matches the python string count method. ... ok
test_str_count_overlap_GG (test_Seq_objs.StringMethodTests)
Check our count_overlap method using GG. ... ok
test_str_count_overlap_NN (test_Seq_objs.StringMethodTests)
Check our count_overlap method using NN. ... ok
test_str_endswith (test_Seq_objs.StringMethodTests)
Check matches the python string endswith method. ... ok
test_str_find (test_Seq_objs.StringMethodTests)
Check matches the python string find method. ... ok
test_str_getitem (test_Seq_objs.StringMethodTests)
Check slicing and indexing works like a string. ... ok
test_str_hash (test_Seq_objs.StringMethodTests) ... ok
test_str_index (test_Seq_objs.StringMethodTests)
Check matches the python string index method. ... ok
test_str_length (test_Seq_objs.StringMethodTests)
Check matches the python string __len__ method. ... ok
test_str_lower (test_Seq_objs.StringMethodTests)
Check matches the python string lower method. ... ok
test_str_lsplit (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_rfind (test_Seq_objs.StringMethodTests)
Check matches the python string rfind method. ... ok
test_str_rindex (test_Seq_objs.StringMethodTests)
Check matches the python string rindex method. ... ok
test_str_rsplit (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_rstrip (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_split (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_startswith (test_Seq_objs.StringMethodTests)
Check matches the python string startswith method. ... ok
test_str_strip (test_Seq_objs.StringMethodTests)
Check matches the python string strip method. ... ok
test_str_upper (test_Seq_objs.StringMethodTests)
Check matches the python string upper method. ... ok
test_the_back_transcription (test_Seq_objs.StringMethodTests)
Check obj.back_transcribe() method. ... ok
test_the_complement (test_Seq_objs.StringMethodTests)
Check obj.complement() method. ... ok
test_the_reverse_complement (test_Seq_objs.StringMethodTests)
Check obj.reverse_complement() method. ... ok
test_the_transcription (test_Seq_objs.StringMethodTests)
Check obj.transcribe() method. ... ok
test_the_translate (test_Seq_objs.StringMethodTests)
Check obj.translate() method. ... ok
test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests)
Check obj.translate() method with ambiguous codons. ... ok
test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests)
Check obj.translate() method with invalid codons. ... ok
test_the_translation_of_stops (test_Seq_objs.StringMethodTests)
Check obj.translate() method with stop codons. ... ok
test_tomutable (test_Seq_objs.StringMethodTests)
Check obj.tomutable() method. ... ok
test_toseq (test_Seq_objs.StringMethodTests)
Check obj.toseq() method. ... ok
----------------------------------------------------------------------
Ran 1 test in 25.084 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SffIO.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SffIO ... ok
test_alt_index_at_end (test_SffIO.TestAlternativeIndexes) ... ok
test_alt_index_at_start (test_SffIO.TestAlternativeIndexes) ... ok
test_alt_index_in_middle (test_SffIO.TestAlternativeIndexes) ... ok
test_index_at_start (test_SffIO.TestAlternativeIndexes) ... ok
test_index_in_middle (test_SffIO.TestAlternativeIndexes) ... ok
test_trim (test_SffIO.TestAlternativeIndexes) ... ok
test_index1 (test_SffIO.TestConcatenated) ... ok
test_index2 (test_SffIO.TestConcatenated) ... ok
test_parse1 (test_SffIO.TestConcatenated) ... ok
test_parse2 (test_SffIO.TestConcatenated) ... ok
test_parses_gzipped_stream (test_SffIO.TestConcatenated) ... ok
test_30bytes (test_SffIO.TestErrors) ... ok
test_31bytes (test_SffIO.TestErrors) ... ok
test_31bytes_bad_flowgram (test_SffIO.TestErrors) ... ok
test_31bytes_bad_ver (test_SffIO.TestErrors) ... ok
test_31bytes_index_header (test_SffIO.TestErrors) ... ok
test_bad_index_eof (test_SffIO.TestErrors) ... ok
test_bad_index_length (test_SffIO.TestErrors) ... ok
test_bad_index_offset (test_SffIO.TestErrors) ... ok
test_empty (test_SffIO.TestErrors) ... ok
test_index_lengths (test_SffIO.TestErrors) ... ok
test_index_mft_data_size (test_SffIO.TestErrors) ... ok
test_index_mft_version (test_SffIO.TestErrors) ... ok
test_index_name_no_null (test_SffIO.TestErrors) ... ok
test_no_index (test_SffIO.TestErrors) ... ok
test_no_manifest_xml (test_SffIO.TestErrors) ... ok
test_premature_end_of_index (test_SffIO.TestErrors) ... ok
test_unknown_index (test_SffIO.TestErrors) ... ok
test_both_ways (test_SffIO.TestIndex) ... ok
test_manifest (test_SffIO.TestIndex) ... ok
test_index (test_SffIO.TestSelf) ... ok
test_read (test_SffIO.TestSelf) ... ok
test_read_wrong (test_SffIO.TestSelf) ... ok
test_write (test_SffIO.TestSelf) ... ok
test_coords (test_SffIO.TestUAN) ... ok
test_region (test_SffIO.TestUAN) ... ok
test_time (test_SffIO.TestUAN) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.515 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SwissProt.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_SwissProt ... ok
test_sp001 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp001. ... ok
test_sp002 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp002. ... ok
test_sp003 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp003. ... ok
test_sp004 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp004. ... ok
test_sp005 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp005. ... ok
test_sp006 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp006. ... ok
test_sp007 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp007. ... ok
test_sp008 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp008. ... ok
test_sp009 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp009. ... ok
test_sp010 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp010. ... ok
test_sp011 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp011. ... ok
test_sp012 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp012. ... ok
test_sp013 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp013. ... ok
test_sp014 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp014. ... ok
test_sp015 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp015. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.604 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TCoffee_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.437 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TogoWS.py
test_TogoWS ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.489 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TreeConstruction.py
test_TreeConstruction ... ok
test_known_matrices (test_TreeConstruction.DistanceCalculatorTest) ... ok
test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest) ... ok
test_bad_construction (test_TreeConstruction.DistanceMatrixTest) ... ok
test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest) ... ok
test_format_phylip (test_TreeConstruction.DistanceMatrixTest) ... ok
test_good_construction (test_TreeConstruction.DistanceMatrixTest) ... ok
test_good_manipulation (test_TreeConstruction.DistanceMatrixTest) ... ok
test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
test_nj (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
test_upgma (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest) ... ok
test_get_score (test_TreeConstruction.ParsimonyScorerTest) ... ok
test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 13.318 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_UniGene.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_UniGene ... ok
test_parse (test_UniGene.TestUniGene) ... ok
test_read (test_UniGene.TestUniGene) ... ok
test_read_value_error (test_UniGene.TestUniGene) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.121 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_UniProt_GOA.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_UniProt_GOA ... ok
test_gaf_iterator (test_UniProt_GOA.GoaTests)
Test GOA GAF file iterator. ... ok
test_gpa_iterator (test_UniProt_GOA.GoaTests)
Test GOA GPA file iterator. ... ok
test_gpi_iterator (test_UniProt_GOA.GoaTests)
Test GOA GPI file iterator. ... ok
test_selection_writing (test_UniProt_GOA.GoaTests)
Test record_has, and writerec. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.136 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Uniprot.py
test_Uniprot ... ok
test_F2CXE6 (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok
test_H2CNN8 (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok
test_P84001 (test_Uniprot.TestUniprot)
Parse mass spec structured comment with unknown loc. ... ok
test_Q13639 (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of Q13639. ... ok
test_multi_ex (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of several examples. ... ok
test_multi_ex_index (test_Uniprot.TestUniprot)
Index SwissProt text and uniprot XML versions of several examples. ... ok
test_sp002 (test_Uniprot.TestUniprot)
Parsing SwissProt file sp002. ... ok
test_sp016 (test_Uniprot.TestUniprot)
Parsing SwissProt file sp016. ... ok
test_submittedName_allowed (test_Uniprot.TestUniprot)
Checks if parser supports new XML Element (submittedName). ... ok
test_uni001 (test_Uniprot.TestUniprot)
Parsing Uniprot file uni001. ... ok
test_uni003 (test_Uniprot.TestUniprot)
Parsing Uniprot file uni003. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.109 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Wise.py
test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
----------------------------------------------------------------------
Ran 1 test in 0.412 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_XXmotif_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.408 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_align.py
test_align ... ok
test_basic_alignment (test_align.TestBasics)
Basic tests on a simple alignment of three sequences. ... ok
test_empty_alignment (test_align.TestBasics)
Very simple tests on an empty alignment. ... ok
test_format_conversion (test_align.TestReading)
Parse the alignment file and get an aligment object. ... ok
test_read_clustal1 (test_align.TestReading)
Parse an alignment file and get an aligment object. ... ok
test_read_clustal2 (test_align.TestReading)
Parse an alignment file and get an aligment object. ... ok
test_read_fasta (test_align.TestReading) ... ok
test_read_write_clustal (test_align.TestReading)
Test the base alignment stuff. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.557 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_align_substitution_matrices.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_align_substitution_matrices ... /builddir/build/BUILD/python-biopython-1.75/python3/build/lib.linux-armv7l-3.7/Bio/Align/substitution_matrices/__init__.py:21: BiopythonExperimentalWarning: Bio.Align.substitution_matrices is an experimental module which may still undergo significant changes. In particular, the location of this module may change, and the Array class defined in this module may be moved to other existing or new modules in Biopython.
  BiopythonExperimentalWarning)
ok
test1_observed_frequencies (test_align_substitution_matrices.TestScoringMatrices) ... ok
test2_observed_probabilities (test_align_substitution_matrices.TestScoringMatrices) ... ok
test3_observed_symmetric_probabilities (test_align_substitution_matrices.TestScoringMatrices) ... ok
test4_aminoacid_probabilities (test_align_substitution_matrices.TestScoringMatrices) ... ok
test5_expected_probabilities (test_align_substitution_matrices.TestScoringMatrices) ... ok
test6_scores (test_align_substitution_matrices.TestScoringMatrices) ... ok
test_ident (test_align_substitution_matrices.TestScoringMatrices) ... ok
test_basics_matrix (test_align_substitution_matrices.Test_basics) ... ok
test_basics_vector (test_align_substitution_matrices.Test_basics) ... ok
test_nucleotide_freq (test_align_substitution_matrices.Test_basics) ... ok
test_protein_freq (test_align_substitution_matrices.Test_basics) ... ok
test_read_write (test_align_substitution_matrices.Test_basics) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.208 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_cellosaurus.py
test_cellosaurus ... ok
test__str__ (test_cellosaurus.TestCellosaurus)
Test string function. ... ok
test_parse (test_cellosaurus.TestCellosaurus)
Test parsing function. ... ok
test_read (test_cellosaurus.TestCellosaurus)
Test read function. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.048 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_codonalign.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_codonalign ... /builddir/build/BUILD/python-biopython-1.75/python3/build/lib.linux-armv7l-3.7/Bio/Seq.py:2728: 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.
  BiopythonWarning)
ok
test_TypeError (test_codonalign.TestAddition)
Check that TypeError is thrown for non CodonAlignment/MultipleSequenceAlignment objects. ... ok
test_ValueError (test_codonalign.TestAddition)
Check that ValueError is thrown for Alignments of different lengths. ... ok
test_addition_CodonAlignment (test_codonalign.TestAddition)
Check addition of CodonAlignment and CodonAlignment. ... ok
test_addition_MultipleSeqAlignment (test_codonalign.TestAddition)
Check addition of CodonAlignment and MultipleSeqAlignment. ... ok
test_IO (test_codonalign.TestBuildAndIO) ... ok
test_align (test_codonalign.TestCodonAlignment) ... ok
test_seq (test_codonalign.TestCodonSeq) ... ok
test_mk (test_codonalign.Test_MK) ... ok
test_build (test_codonalign.Test_build) ... ok
test_dn_ds (test_codonalign.Test_dn_ds) ... ok
test_dn_ds_matrix (test_codonalign.Test_dn_ds) ... ok
----------------------------------------------------------------------
Ran 1 test in 46.241 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_geo.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_geo ... ok
test_GSE16 (test_geo.TestGeo) ... ok
test_GSM645 (test_geo.TestGeo) ... ok
test_GSM691 (test_geo.TestGeo) ... ok
test_GSM700 (test_geo.TestGeo) ... ok
test_GSM804 (test_geo.TestGeo) ... ok
test_record_str (test_geo.TestGeo) ... ok
test_soft_ex_affy (test_geo.TestGeo) ... ok
test_soft_ex_affy_chp (test_geo.TestGeo) ... ok
test_soft_ex_dual (test_geo.TestGeo) ... ok
test_soft_ex_family (test_geo.TestGeo) ... ok
test_soft_ex_platform (test_geo.TestGeo) ... ok
test_soft_ex_series (test_geo.TestGeo) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.258 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_kNN.py
test_kNN ... ok
test_calculate_model (test_kNN.TestKNN) ... ok
test_calculate_probability (test_kNN.TestKNN) ... ok
test_classify (test_kNN.TestKNN) ... ok
test_leave_one_out (test_kNN.TestKNN) ... ok
test_model_accuracy (test_kNN.TestKNN) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.060 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_lowess.py
test_lowess ... ok
test_Precomputed (test_lowess.test_lowess) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.049 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_mmtf.py
test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.291 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_mmtf_online.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.290 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_motifs.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_motifs ... ok
test_mixed_alphabets (test_motifs.MotifTestPWM)
Test creating motif with mixed alphabets. ... ok
test_simple (test_motifs.MotifTestPWM)
Test if Bio.motifs PWM scoring works. ... ok
test_with_alt_alphabet (test_motifs.MotifTestPWM)
Test motif search using alternative instance of alphabet. ... ok
test_with_bad_char (test_motifs.MotifTestPWM)
Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok
test_with_mixed_case (test_motifs.MotifTestPWM)
Test if Bio.motifs PWM scoring works with mixed case. ... ok
test_TFoutput (test_motifs.MotifTestsBasic)
Ensure that we can write proper TransFac output files. ... ok
test_alignace_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse AlignAce output files. ... ok
test_clusterbuster_parsing_and_output (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse and output Cluster Buster PFM files. ... ok
test_format (test_motifs.MotifTestsBasic) ... ok
test_pfm_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse JASPAR-style pfm files. ... ok
test_sites_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse JASPAR-style sites files. ... ok
test_xms_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse and output xms PFM files. ... ok
test_mast_parser_1 (test_motifs.TestMAST)
Parse motifs/mast.crp0.de.oops.txt.xml file. ... ok
test_mast_parser_2 (test_motifs.TestMAST)
Parse motifs/mast.adh.de.oops.html.xml file. ... ok
test_mast_parser_3 (test_motifs.TestMAST)
Parse motifs/mast.Klf1-200.cd.oops.xml.xml file. ... ok
test_meme_parser_1 (test_motifs.TestMEME)
Parsing motifs/meme.out file. ... ok
test_meme_parser_2 (test_motifs.TestMEME)
Parse motifs/meme.dna.oops.txt file. ... ok
test_meme_parser_3 (test_motifs.TestMEME)
Parse motifs/meme.protein.oops.txt file. ... ok
test_meme_parser_4 (test_motifs.TestMEME)
Parse motifs/meme.protein.tcm.txt file. ... ok
test_meme_parser_4_11_4 (test_motifs.TestMEME)
Parse motifs/meme_v_4_11_4.txt file. ... ok
test_meme_parser_rna (test_motifs.TestMEME)
Test if Bio.motifs can parse MEME output files using RNA. ... ok
test_minimal_meme_parser (test_motifs.TestMEME)
Parse motifs/minimal_test.meme file. ... ok
test_permissive_transfac_parser (test_motifs.TestTransfac)
Parse the TRANSFAC-like file motifs/MA0056.1.transfac. ... ok
test_transfac_parser (test_motifs.TestTransfac)
Parse motifs/transfac.dat file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.589 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_motifs_online.py
test_motifs_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.239 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2.py
test_pairwise2 ... ok
test_clean_alignments (pairwise2_testCases.TestOtherFunctions)
``_clean_alignments`` removes redundant and wrong alignments. ... ok
test_print_matrix (pairwise2_testCases.TestOtherFunctions)
``print_matrix`` prints nested lists as nice matrices. ... ok
test_recover_alignments (pairwise2_testCases.TestOtherFunctions)
One possible start position in local alignment is not a match. ... ok
test_function_name (pairwise2_testCases.TestPairwiseErrorConditions)
Test for wrong function names. ... ok
test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions)
Test for number of parameters. ... ok
test_param_names (pairwise2_testCases.TestPairwiseErrorConditions)
Test for unknown parameter in parameter names. ... ok
test_warnings (pairwise2_testCases.TestPairwiseErrorConditions)
Test for warnings. ... ok
test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty)
Test 1. ... ok
test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty)
Test 2. ... ok
test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal)
Test globalxx. ... ok
test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal)
Do the same test with sequence order reversed. ... ok
test_list_input (pairwise2_testCases.TestPairwiseGlobal)
Do a global aligment with sequences supplied as lists. ... ok
test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal)
Test one_alignment_only parameter. ... ok
test_blosum62 (pairwise2_testCases.TestPairwiseLocal)
Test localds with blosum62. ... ok
test_empty_result (pairwise2_testCases.TestPairwiseLocal)
Return no alignment. ... ok
test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal)
Test if alignment is independent on direction of sequence. ... ok
test_localms (pairwise2_testCases.TestPairwiseLocal)
Two different local alignments. ... ok
test_localxs_1 (pairwise2_testCases.TestPairwiseLocal)
Test localxx. ... ok
test_localxs_2 (pairwise2_testCases.TestPairwiseLocal)
Test localxx with ``full_sequences=True``. ... ok
test_localxs_generic (pairwise2_testCases.TestPairwiseLocal)
Test the generic method with local alignments. ... ok
test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary)
Test 1. ... ok
test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary)
Test 2. ... ok
test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary)
Test 3. ... ok
test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter)
Test sequence with only one match. ... ok
test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter)
Test sequences with two possible match positions. ... ok
test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter)
Like test 1, but global alignment. ... ok
test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty)
Test 1. ... ok
test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty)
Test 2. ... ok
test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty)
Test 3. ... ok
test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty)
Test 4. ... ok
test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps)
Turn off end-gap penalties. ... ok
test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps)
Do the same, but use the generic method (with the same result). ... ok
test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps)
Test alignment where end-gaps are differently penalized. ... ok
test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening)
Add gap-extend penalty to gap-opening penalty. ... ok
test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties)
Test 1. ... ok
test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties)
Test 2. ... ok
test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension)
Test separate gap-extension penalties and list input. ... ok
test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties)
Open a gap in second sequence only. ... ok
test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties)
Force a bad alignment. ... ok
test_score_only_global (pairwise2_testCases.TestScoreOnly)
Test ``score_only`` in a global alignment. ... ok
test_score_only_local (pairwise2_testCases.TestScoreOnly)
Test ``score_only`` in a local alignment. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.855 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2_no_C.py
test_pairwise2_no_C ... ok
test_clean_alignments (pairwise2_testCases.TestOtherFunctions)
``_clean_alignments`` removes redundant and wrong alignments. ... ok
test_print_matrix (pairwise2_testCases.TestOtherFunctions)
``print_matrix`` prints nested lists as nice matrices. ... ok
test_recover_alignments (pairwise2_testCases.TestOtherFunctions)
One possible start position in local alignment is not a match. ... ok
test_function_name (pairwise2_testCases.TestPairwiseErrorConditions)
Test for wrong function names. ... ok
test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions)
Test for number of parameters. ... ok
test_param_names (pairwise2_testCases.TestPairwiseErrorConditions)
Test for unknown parameter in parameter names. ... ok
test_warnings (pairwise2_testCases.TestPairwiseErrorConditions)
Test for warnings. ... ok
test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty)
Test 1. ... ok
test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty)
Test 2. ... ok
test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal)
Test globalxx. ... ok
test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal)
Do the same test with sequence order reversed. ... ok
test_list_input (pairwise2_testCases.TestPairwiseGlobal)
Do a global aligment with sequences supplied as lists. ... ok
test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal)
Test one_alignment_only parameter. ... ok
test_blosum62 (pairwise2_testCases.TestPairwiseLocal)
Test localds with blosum62. ... ok
test_empty_result (pairwise2_testCases.TestPairwiseLocal)
Return no alignment. ... ok
test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal)
Test if alignment is independent on direction of sequence. ... ok
test_localms (pairwise2_testCases.TestPairwiseLocal)
Two different local alignments. ... ok
test_localxs_1 (pairwise2_testCases.TestPairwiseLocal)
Test localxx. ... ok
test_localxs_2 (pairwise2_testCases.TestPairwiseLocal)
Test localxx with ``full_sequences=True``. ... ok
test_localxs_generic (pairwise2_testCases.TestPairwiseLocal)
Test the generic method with local alignments. ... ok
test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary)
Test 1. ... ok
test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary)
Test 2. ... ok
test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary)
Test 3. ... ok
test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter)
Test sequence with only one match. ... ok
test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter)
Test sequences with two possible match positions. ... ok
test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter)
Like test 1, but global alignment. ... ok
test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty)
Test 1. ... ok
test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty)
Test 2. ... ok
test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty)
Test 3. ... ok
test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty)
Test 4. ... ok
test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps)
Turn off end-gap penalties. ... ok
test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps)
Do the same, but use the generic method (with the same result). ... ok
test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps)
Test alignment where end-gaps are differently penalized. ... ok
test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening)
Add gap-extend penalty to gap-opening penalty. ... ok
test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties)
Test 1. ... ok
test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties)
Test 2. ... ok
test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension)
Test separate gap-extension penalties and list input. ... ok
test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties)
Open a gap in second sequence only. ... ok
test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties)
Force a bad alignment. ... ok
test_score_only_global (pairwise2_testCases.TestScoreOnly)
Test ``score_only`` in a global alignment. ... ok
test_score_only_local (pairwise2_testCases.TestScoreOnly)
Test ``score_only`` in a local alignment. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.028 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_phenotype ... ok
test_PlateRecord (test_phenotype.TestPhenoMicro)
Test basic functionalities of PlateRecord objects. ... ok
test_PlateRecord_errors (test_phenotype.TestPhenoMicro)
Test bad arguments with PlateRecord objects. ... ok
test_WellRecord (test_phenotype.TestPhenoMicro)
Test basic functionalities of WellRecord objects. ... ok
test_bad_fit_args (test_phenotype.TestPhenoMicro)
Test error handling of the fit method. ... ok
test_phenotype_IO (test_phenotype.TestPhenoMicro)
Test basic functionalities of phenotype IO methods. ... ok
test_phenotype_IO_errors (test_phenotype.TestPhenoMicro)
Test bad arguments to phenotype IO methods. ... ok
----------------------------------------------------------------------
Ran 1 test in 64.841 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype_fit.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality.
----------------------------------------------------------------------
Ran 1 test in 0.041 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_phyml_tool.py
test_phyml_tool ... skipping. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.451 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prodoc.py
test_prodoc ... ok
test_parse_pdoc (test_prodoc.TestProdocParse)
Parsing an excerpt of prosite.doc. ... ok
test_read_pdoc00100 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00100. ... ok
test_read_pdoc00113 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00113. ... ok
test_read_pdoc00144 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00144. ... ok
test_read_pdoc00149 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00149. ... ok
test_read_pdoc00340 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00340. ... ok
test_read_pdoc00424 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00424. ... ok
test_read_pdoc00472 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00472. ... ok
test_read_pdoc00640 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00640. ... ok
test_read_pdoc00787 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00787. ... ok
test_read_pdoc0933 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00933. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prosite1.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_prosite1 ... ok
test_read1 (test_prosite1.TestPrositeRead)
Parsing Prosite record ps00107.txt. ... ok
test_read2 (test_prosite1.TestPrositeRead)
Parsing Prosite record ps00159.txt. ... ok
test_read3 (test_prosite1.TestPrositeRead)
Parsing Prosite record ps00165.txt. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.264 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prosite2.py
test_prosite2 ... ok
test_read4 (test_prosite2.TestPrositeRead)
Parsing Prosite record ps00432.txt. ... ok
test_read5 (test_prosite2.TestPrositeRead)
Parsing Prosite record ps00488.txt. ... ok
test_read6 (test_prosite2.TestPrositeRead)
Parsing Prosite record ps00546.txt. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.099 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_psw.py
test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
----------------------------------------------------------------------
Ran 1 test in 0.617 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_raxml_tool.py
test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.677 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_samtools_tool.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program
        if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
C
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_seq.py
test_seq ... ok
test_ambiguous_values (test_seq.TestAmbiguousComplements)
Test that other tests do not introduce characters to our values. ... ok
test_complement_ambiguous_dna_values (test_seq.TestComplement) ... ok
test_complement_ambiguous_rna_values (test_seq.TestComplement) ... ok
test_complement_incompatible_alphabets (test_seq.TestComplement) ... ok
test_complement_of_dna (test_seq.TestComplement) ... ok
test_complement_of_mixed_dna_rna (test_seq.TestComplement) ... ok
test_complement_of_rna (test_seq.TestComplement) ... ok
test_complement_on_proteins (test_seq.TestComplement)
Check complement fails on a protein. ... ok
test_reverse_complements (test_seq.TestDoubleReverseComplement)
Test double reverse complement preserves the sequence. ... ok
test_add_method (test_seq.TestMutableSeq)
Test adding wrong type to MutableSeq. ... ok
test_appending (test_seq.TestMutableSeq) ... ok
test_as_string (test_seq.TestMutableSeq) ... ok
test_complement (test_seq.TestMutableSeq) ... ok
test_complement_dna_string (test_seq.TestMutableSeq) ... ok
test_complement_mixed_aphabets (test_seq.TestMutableSeq) ... ok
test_complement_rna (test_seq.TestMutableSeq) ... ok
test_complement_rna_string (test_seq.TestMutableSeq) ... ok
test_converting_to_immutable (test_seq.TestMutableSeq) ... ok
test_count (test_seq.TestMutableSeq) ... ok
test_delete_stride_slice (test_seq.TestMutableSeq) ... ok
test_deleting_item (test_seq.TestMutableSeq) ... ok
test_deleting_slice (test_seq.TestMutableSeq) ... ok
test_equal_comparison (test_seq.TestMutableSeq)
Test __eq__ comparison method. ... ok
test_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_extend_method (test_seq.TestMutableSeq) ... ok
test_extend_with_mutable_seq (test_seq.TestMutableSeq) ... ok
test_extract_third_nucleotide (test_seq.TestMutableSeq)
Test extracting every third nucleotide (slicing with stride 3). ... ok
test_first_nucleotide (test_seq.TestMutableSeq) ... ok
test_greater_than_comparison (test_seq.TestMutableSeq)
Test __gt__ comparison method. ... ok
test_greater_than_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_greater_than_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
test_greater_than_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
test_greater_than_or_equal_comparison (test_seq.TestMutableSeq)
Test __ge__ comparison method. ... ok
test_greater_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
test_greater_than_or_equal_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
test_index (test_seq.TestMutableSeq) ... ok
test_inserting (test_seq.TestMutableSeq) ... ok
test_length (test_seq.TestMutableSeq) ... ok
test_less_than_comparison (test_seq.TestMutableSeq)
Test __lt__ comparison method. ... ok
test_less_than_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_less_than_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
test_less_than_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
test_less_than_or_equal_comparison (test_seq.TestMutableSeq)
Test __le__ comparison method. ... ok
test_less_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq) ... ok
test_less_than_or_equal_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
test_mutableseq_creation (test_seq.TestMutableSeq)
Test creating MutableSeqs in multiple ways. ... ok
test_not_equal_comparison (test_seq.TestMutableSeq)
Test __ne__ comparison method. ... ok
test_popping_last_item (test_seq.TestMutableSeq) ... ok
test_radd_method (test_seq.TestMutableSeq) ... ok
test_radd_method_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_radd_method_using_seq_object (test_seq.TestMutableSeq) ... ok
test_radd_method_wrong_type (test_seq.TestMutableSeq) ... ok
test_remove_items (test_seq.TestMutableSeq) ... ok
test_repr (test_seq.TestMutableSeq) ... ok
test_reverse (test_seq.TestMutableSeq)
Test using reverse method. ... ok
test_reverse_complement (test_seq.TestMutableSeq) ... ok
test_reverse_complement_of_protein (test_seq.TestMutableSeq) ... ok
test_reverse_with_stride (test_seq.TestMutableSeq)
Test reverse using -1 stride. ... ok
test_set_wobble_codon_to_n (test_seq.TestMutableSeq)
Test setting wobble codon to N (set slice with stride 3). ... ok
test_setting_item (test_seq.TestMutableSeq) ... ok
test_setting_slices (test_seq.TestMutableSeq) ... ok
test_truncated_repr (test_seq.TestMutableSeq) ... ok
test_reverse_complement (test_seq.TestReverseComplement) ... ok
test_reverse_complement_of_dna (test_seq.TestReverseComplement) ... ok
test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement) ... ok
test_reverse_complement_of_rna (test_seq.TestReverseComplement) ... ok
test_reverse_complement_on_proteins (test_seq.TestReverseComplement)
Check reverse complement fails on a protein. ... ok
test_alphabet (test_seq.TestSeq)
Test alphabet of derived Seq object. ... ok
test_alphabet_letters (test_seq.TestSeq)
Test nucleotides in DNA Seq. ... ok
test_as_string (test_seq.TestSeq)
Test converting Seq to string. ... ok
test_concatenation_error (test_seq.TestSeq)
DNA Seq objects cannot be concatenated with Protein Seq objects. ... ok
test_concatenation_of_ambiguous_and_unambiguous_dna (test_seq.TestSeq)
Concatenate Seq object with ambiguous and unambiguous DNA returns ambiguous Seq. ... ok
test_concatenation_of_seq (test_seq.TestSeq) ... ok
test_construction_using_a_seq_object (test_seq.TestSeq)
Test using a Seq object to initialize another Seq object. ... ok
test_extract_third_nucleotide (test_seq.TestSeq)
Test extracting every third nucleotide (slicing with stride 3). ... ok
test_first_nucleotide (test_seq.TestSeq)
Test getting first nucleotide of Seq. ... ok
test_last_nucleotide (test_seq.TestSeq)
Test getting last nucleotide of Seq. ... ok
test_length (test_seq.TestSeq)
Test len method on Seq object. ... ok
test_length_concatenated_unambiguous_seq (test_seq.TestSeq)
Test length of concatenated Seq object with unambiguous DNA. ... ok
test_repr (test_seq.TestSeq)
Test representation of Seq object. ... ok
test_reverse (test_seq.TestSeq)
Test reverse using -1 stride. ... ok
test_slicing (test_seq.TestSeq)
Test slicing of Seq. ... ok
test_truncated_repr (test_seq.TestSeq) ... ok
test_ungap (test_seq.TestSeq) ... ok
test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition) ... ok
test_adding_generic_nucleotide_with_other_nucleotides_inplace (test_seq.TestSeqAddition) ... ok
test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition) ... ok
test_addition_dna_rna_with_generic_nucleotides_inplace (test_seq.TestSeqAddition) ... ok
test_addition_dna_with_dna (test_seq.TestSeqAddition) ... ok
test_addition_dna_with_dna_inplace (test_seq.TestSeqAddition) ... ok
test_addition_dna_with_rna (test_seq.TestSeqAddition) ... ok
test_addition_proteins (test_seq.TestSeqAddition) ... ok
test_addition_proteins_inplace (test_seq.TestSeqAddition) ... ok
test_addition_rna_with_rna (test_seq.TestSeqAddition) ... ok
test_addition_rna_with_rna_inplace (test_seq.TestSeqAddition) ... ok
test_exception_when_added_protein_has_more_than_one_gap_type (test_seq.TestSeqAddition)
Test resulting protein has gap types '-' and '.'. ... ok
test_exception_when_added_protein_has_several_stop_codon_types (test_seq.TestSeqAddition)
Test resulting protein has stop codon types '*' and '@'. ... ok
test_exception_when_added_rna_has_more_than_one_gap_type (test_seq.TestSeqAddition)
Test resulting sequence has gap types '-' and '.'. ... ok
test_exception_when_adding_protein_with_nucleotides (test_seq.TestSeqAddition) ... ok
test_imul_method (test_seq.TestSeqMultiplication)
Test imul method; relies on addition and mull methods. ... ok
test_imul_method_exceptions (test_seq.TestSeqMultiplication)
Test imul method exceptions. ... ok
test_mul_method (test_seq.TestSeqMultiplication)
Test mul method; relies on addition method. ... ok
test_mul_method_exceptions (test_seq.TestSeqMultiplication)
Test mul method exceptions. ... ok
test_rmul_method (test_seq.TestSeqMultiplication)
Test rmul method; relies on addition method. ... ok
test_rmul_method_exceptions (test_seq.TestSeqMultiplication)
Test rmul method exceptions. ... ok
test_add_method_using_wrong_object (test_seq.TestSeqStringMethods) ... ok
test_append_nucleotides (test_seq.TestSeqStringMethods) ... ok
test_append_proteins (test_seq.TestSeqStringMethods) ... ok
test_contains_method (test_seq.TestSeqStringMethods) ... ok
test_counting_characters (test_seq.TestSeqStringMethods) ... ok
test_endswith (test_seq.TestSeqStringMethods) ... ok
test_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test __eq__ comparison method. ... ok
test_exception_when_clashing_alphabets (test_seq.TestSeqStringMethods)
Test by setting up clashing alphabet sequences. ... ok
test_finding_characters (test_seq.TestSeqStringMethods) ... ok
test_greater_than_comparison (test_seq.TestSeqStringMethods)
Test __gt__ comparison method. ... ok
test_greater_than_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test incompatible alphabet __gt__ comparison method. ... ok
test_greater_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
Test incompatible types __gt__ comparison method. ... ok
test_greater_than_or_equal_comparison (test_seq.TestSeqStringMethods)
Test __ge__ comparison method. ... ok
test_greater_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test incompatible alphabet __ge__ comparison method. ... ok
test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
Test incompatible types __ge__ comparison method. ... ok
test_hash (test_seq.TestSeqStringMethods) ... ok
test_less_than_comparison (test_seq.TestSeqStringMethods)
Test __lt__ comparison method. ... ok
test_less_than_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test incompatible alphabet __lt__ comparison method. ... ok
test_less_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
Test incompatible types __lt__ comparison method. ... ok
test_less_than_or_equal_comparison (test_seq.TestSeqStringMethods)
Test __le__ comparison method. ... ok
test_less_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test incompatible alphabet __le__ comparison method. ... ok
test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods)
Test incompatible types __le__ comparison method. ... ok
test_not_equal_comparsion (test_seq.TestSeqStringMethods)
Test __ne__ comparison method. ... ok
test_radd_method (test_seq.TestSeqStringMethods) ... ok
test_radd_method_using_incompatible_alphabets (test_seq.TestSeqStringMethods) ... ok
test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods) ... ok
test_splits (test_seq.TestSeqStringMethods) ... ok
test_startswith (test_seq.TestSeqStringMethods) ... ok
test_string_methods (test_seq.TestSeqStringMethods) ... ok
test_stripping_characters (test_seq.TestSeqStringMethods) ... ok
test_sequence_alphabets (test_seq.TestSequenceAlphabets)
Sanity test on the test sequence alphabets. ... ok
test_stops (test_seq.TestStopCodons) ... ok
test_translation_of_stops (test_seq.TestStopCodons) ... ok
test_back_transcribe_rna_into_dna (test_seq.TestTranscription) ... ok
test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription) ... ok
test_back_transcription_of_dna (test_seq.TestTranscription)
Check back-transcription fails on DNA. ... ok
test_back_transcription_of_proteins (test_seq.TestTranscription)
Check back-transcription fails on a protein. ... ok
test_seq_object_back_transcription_method (test_seq.TestTranscription) ... ok
test_seq_object_transcription_method (test_seq.TestTranscription) ... ok
test_transcription_dna_into_rna (test_seq.TestTranscription) ... ok
test_transcription_dna_string_into_rna (test_seq.TestTranscription) ... ok
test_transcription_of_proteins (test_seq.TestTranscription)
Check transcription fails on a protein. ... ok
test_transcription_of_rna (test_seq.TestTranscription)
Check transcription fails on RNA. ... ok
test_alphabet_of_translated_gapped_seq (test_seq.TestTranslating) ... ok
test_alphabets_of_translated_seqs (test_seq.TestTranslating) ... ok
test_gapped_seq_no_gap_char_given (test_seq.TestTranslating) ... ok
test_gapped_seq_no_gap_char_given_and_inferred_from_alphabet (test_seq.TestTranslating) ... ok
test_gapped_seq_with_gap_char_given (test_seq.TestTranslating) ... ok
test_gapped_seq_with_gap_char_given_and_inferred_from_alphabet (test_seq.TestTranslating) ... ok
test_gapped_seq_with_gap_char_given_and_inferred_from_alphabet2 (test_seq.TestTranslating)
Test using stop codon in sequence. ... ok
test_gapped_seq_with_stop_codon_and_gap_char_given (test_seq.TestTranslating) ... ok
test_translation (test_seq.TestTranslating) ... ok
test_translation_extra_stop_codon (test_seq.TestTranslating) ... ok
test_translation_incomplete_codon (test_seq.TestTranslating) ... ok
test_translation_of_asparagine (test_seq.TestTranslating) ... ok
test_translation_of_gapped_string_no_gap_char_given (test_seq.TestTranslating) ... ok
test_translation_of_gapped_string_with_gap_char_given (test_seq.TestTranslating) ... ok
test_translation_of_glutamine (test_seq.TestTranslating) ... ok
test_translation_of_invalid_codon (test_seq.TestTranslating) ... ok
test_translation_of_leucine (test_seq.TestTranslating) ... ok
test_translation_of_string (test_seq.TestTranslating) ... ok
test_translation_on_proteins (test_seq.TestTranslating)
Check translation fails on a protein. ... ok
test_translation_to_stop (test_seq.TestTranslating) ... ok
test_translation_using_cds (test_seq.TestTranslating) ... ok
test_translation_using_tables_with_ambiguous_stop_codons (test_seq.TestTranslating)
Check for error and warning messages. ... ok
test_translation_with_bad_table_argument (test_seq.TestTranslating) ... ok
test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating) ... ok
test_translation_wrong_type (test_seq.TestTranslating)
Test translation table cannot be CodonTable. ... ok
test_add_method (test_seq.TestUnknownSeq) ... ok
test_back_transcribe (test_seq.TestUnknownSeq) ... ok
test_complement (test_seq.TestUnknownSeq) ... ok
test_complement_of_protein (test_seq.TestUnknownSeq)
Check reverse complement fails on a protein. ... ok
test_construction (test_seq.TestUnknownSeq) ... ok
test_count (test_seq.TestUnknownSeq) ... ok
test_getitem_method (test_seq.TestUnknownSeq) ... ok
test_length (test_seq.TestUnknownSeq) ... ok
test_lower (test_seq.TestUnknownSeq) ... ok
test_repr (test_seq.TestUnknownSeq) ... ok
test_reverse_complement (test_seq.TestUnknownSeq) ... ok
test_reverse_complement_of_protein (test_seq.TestUnknownSeq) ... ok
test_transcribe (test_seq.TestUnknownSeq) ... ok
test_translation (test_seq.TestUnknownSeq) ... ok
test_translation_of_proteins (test_seq.TestUnknownSeq) ... ok
test_ungap (test_seq.TestUnknownSeq) ... ok
test_upper (test_seq.TestUnknownSeq) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.207 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_translate.py
test_translate ... ok
test_ambiguous (test_translate.TestTranscriptionTranslation) ... ok
test_dna_rna_translation (test_translate.TestTranscriptionTranslation) ... ok
test_transcription (test_translate.TestTranscriptionTranslation) ... ok
test_translation (test_translate.TestTranscriptionTranslation) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.449 seconds
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
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 | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/lib/python3.7/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_trie.py
Skipping any tests requiring internet access
Python version: 3.7.5 (default, Oct 17 2019, 11:41:52) 
[GCC 9.2.1 20190827 (Red Hat 9.2.1-1)]
Operating system: posix linux
test_trie ... ok
test_get_approximate (test_trie.TestTrie) ... ok
test_get_set (test_trie.TestTrie) ... ok
test_large_save_load (test_trie.TestTrie)
Generate random key/val pairs in three length categories. ... ok
test_prefix (test_trie.TestTrie) ... ok
test_save (test_trie.TestTrie) ... ok
test_with_prefix (test_trie.TestTrie) ... ok
test_find (test_trie.TestTrieFind) ... ok
----------------------------------------------------------------------
Ran 1 test in 269.707 seconds
~/build/BUILD/python-biopython-1.75
+ popd
+ exit 0
Processing files: python3-biopython-1.75-2.fc30.armv7hl
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.xFTnZL
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.75
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/doc/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/doc/python3-biopython
+ cp -pr python3/Scripts /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/doc/python3-biopython
+ cp -pr python3/CONTRIB.rst /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/doc/python3-biopython
+ cp -pr python3/DEPRECATED.rst /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/doc/python3-biopython
+ cp -pr python3/NEWS.rst /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/doc/python3-biopython
+ cp -pr python3/README.rst /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/doc/python3-biopython
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.bD5r7P
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.75
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/licenses/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/licenses/python3-biopython
+ cp -pr python3/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/licenses/python3-biopython
+ exit 0
Provides: python3-biopython = 1.75-2.fc30 python3-biopython(armv7hl-32) = 1.75-2.fc30 python3.7dist(biopython) = 1.75 python3dist(biopython) = 1.75
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-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libc.so.6 libc.so.6(GLIBC_2.4) libgcc_s.so.1 libgcc_s.so.1(GCC_3.5) libpthread.so.0 libpthread.so.0(GLIBC_2.4) libpython3.7m.so.1.0 python(abi) = 3.7 python3.7dist(numpy) rtld(GNU_HASH)
Processing files: python-biopython-doc-1.75-2.fc30.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.D3RJFZ
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.75
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/doc/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/doc/python-biopython-doc
+ cp -pr biopython-1.75/Doc /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/doc/python-biopython-doc
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.7gpNgr
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.75
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/licenses/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/licenses/python-biopython-doc
+ cp -pr biopython-1.75/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm/usr/share/licenses/python-biopython-doc
+ exit 0
Provides: python-biopython-doc = 1.75-2.fc30
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-biopython-debugsource-1.75-2.fc30.armv7hl
Provides: python-biopython-debugsource = 1.75-2.fc30 python-biopython-debugsource(armv7hl-32) = 1.75-2.fc30
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python3-biopython-debuginfo-1.75-2.fc30.armv7hl
Provides: debuginfo(build-id) = 0fa90b95f7c809490753a5a65e9538ea55a22e54 debuginfo(build-id) = 176f0893dae3a276867fd3c6733a3ee77cfcc020 debuginfo(build-id) = 2a8f4467fcc3b5e8eec14c79efc8d30c19aeebcc debuginfo(build-id) = 3d6ac95f87280b56d7ddf3cdd70170a0bb4ea8ef debuginfo(build-id) = 4364a5d201d482e78f1cb4c25aed3e3e4bb18820 debuginfo(build-id) = 6afe6ac1f58c0d925cc2fcdca65c02046592e85a debuginfo(build-id) = 787db912fbf61e1f79bc70b82ecdfc36b34e320c debuginfo(build-id) = a8a7dc8cb09e50e6fa9702cf7c60ea27b412736c debuginfo(build-id) = a9bb09e4ddbca23c6cf282a22eec2c3fee61fd12 python3-biopython-debuginfo = 1.75-2.fc30 python3-biopython-debuginfo(armv7hl-32) = 1.75-2.fc30
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: python-biopython-debugsource(armv7hl-32) = 1.75-2.fc30
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm
Wrote: /builddir/build/RPMS/python3-biopython-1.75-2.fc30.armv7hl.rpm
Wrote: /builddir/build/RPMS/python-biopython-doc-1.75-2.fc30.noarch.rpm
Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.75-2.fc30.armv7hl.rpm
Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.75-2.fc30.armv7hl.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.T79fD9
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.75
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.75-2.fc30.arm
+ exit 0
Child return code was: 0