Mock Version: 1.2.17
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/epel-1-armhfp-3a14b24069cbceab4ff0529d3e09204f189737a1/root'shell=FalseprintOutput=Falseenv={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0logger=<mockbuild.trace_decorator.getLog object at 0x34a970>uid=996)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False
sh: /usr/bin/python2: No such file or directory
sh: /usr/bin/python2: No such file or directory
sh: /usr/bin/python2: No such file or directory
Building target platforms: armv7hl
Building for target armv7hl
Wrote: /builddir/build/SRPMS/python-biopython-1.68-1.el7.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', u'/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/epel-1-armhfp-3a14b24069cbceab4ff0529d3e09204f189737a1/root'shell=Falseuid=996env={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0private_network=Truelogger=<mockbuild.trace_decorator.getLog object at 0x34a970>printOutput=False)
Executing command: ['bash', '--login', '-c', u'/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False
Building target platforms: armv7hl
Building for target armv7hl
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.8AoRnH
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf python-biopython-1.68
+ /usr/bin/mkdir -p python-biopython-1.68
+ cd python-biopython-1.68
+ /usr/bin/gzip -dc /builddir/build/SOURCES/biopython-1.68.tar.gz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ mv biopython-1.68 python2
~/build/BUILD/python-biopython-1.68/python2 ~/build/BUILD/python-biopython-1.68
+ pushd python2
+ 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' '{}' ';'
~/build/BUILD/python-biopython-1.68
+ popd
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.YOlMlW
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.68
~/build/BUILD/python-biopython-1.68/python2 ~/build/BUILD/python-biopython-1.68
+ pushd python2
+ CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -march=armv7-a -mfpu=vfpv3-d16  -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now'
+ /usr/bin/python2 setup.py build '--executable=/usr/bin/python2 -s'
running build
running build_py
creating build
creating build/lib.linux-armv7l-2.7
creating build/lib.linux-armv7l-2.7/Bio
copying Bio/MaxEntropy.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/NaiveBayes.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/ParserSupport.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/SeqRecord.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/MarkovModel.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/Seq.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/LogisticRegression.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/triefind.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/File.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/Index.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/_utils.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/__init__.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/pairwise2.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/SeqFeature.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/kNN.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/DocSQL.py -> build/lib.linux-armv7l-2.7/Bio
copying Bio/bgzf.py -> build/lib.linux-armv7l-2.7/Bio
creating build/lib.linux-armv7l-2.7/Bio/Align
copying Bio/Align/AlignInfo.py -> build/lib.linux-armv7l-2.7/Bio/Align
copying Bio/Align/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Align
copying Bio/Align/Generic.py -> build/lib.linux-armv7l-2.7/Bio/Align
creating build/lib.linux-armv7l-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-armv7l-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-armv7l-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-armv7l-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> build/lib.linux-armv7l-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-armv7l-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-armv7l-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-armv7l-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-armv7l-2.7/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-armv7l-2.7/Bio/Align/Applications
creating build/lib.linux-armv7l-2.7/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-armv7l-2.7/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> build/lib.linux-armv7l-2.7/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> build/lib.linux-armv7l-2.7/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-armv7l-2.7/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-armv7l-2.7/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-armv7l-2.7/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> build/lib.linux-armv7l-2.7/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> build/lib.linux-armv7l-2.7/Bio/AlignIO
creating build/lib.linux-armv7l-2.7/Bio/Alphabet
copying Bio/Alphabet/Reduced.py -> build/lib.linux-armv7l-2.7/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Alphabet
copying Bio/Alphabet/IUPAC.py -> build/lib.linux-armv7l-2.7/Bio/Alphabet
creating build/lib.linux-armv7l-2.7/Bio/Application
copying Bio/Application/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Application
creating build/lib.linux-armv7l-2.7/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> build/lib.linux-armv7l-2.7/Bio/Blast
copying Bio/Blast/NCBIXML.py -> build/lib.linux-armv7l-2.7/Bio/Blast
copying Bio/Blast/Record.py -> build/lib.linux-armv7l-2.7/Bio/Blast
copying Bio/Blast/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-armv7l-2.7/Bio/Blast
copying Bio/Blast/NCBIStandalone.py -> build/lib.linux-armv7l-2.7/Bio/Blast
copying Bio/Blast/Applications.py -> build/lib.linux-armv7l-2.7/Bio/Blast
creating build/lib.linux-armv7l-2.7/Bio/CAPS
copying Bio/CAPS/__init__.py -> build/lib.linux-armv7l-2.7/Bio/CAPS
creating build/lib.linux-armv7l-2.7/Bio/codonalign
copying Bio/codonalign/codonseq.py -> build/lib.linux-armv7l-2.7/Bio/codonalign
copying Bio/codonalign/__init__.py -> build/lib.linux-armv7l-2.7/Bio/codonalign
copying Bio/codonalign/chisq.py -> build/lib.linux-armv7l-2.7/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> build/lib.linux-armv7l-2.7/Bio/codonalign
copying Bio/codonalign/codonalphabet.py -> build/lib.linux-armv7l-2.7/Bio/codonalign
creating build/lib.linux-armv7l-2.7/Bio/Compass
copying Bio/Compass/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Compass
creating build/lib.linux-armv7l-2.7/Bio/Crystal
copying Bio/Crystal/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Crystal
creating build/lib.linux-armv7l-2.7/Bio/Data
copying Bio/Data/SCOPData.py -> build/lib.linux-armv7l-2.7/Bio/Data
copying Bio/Data/CodonTable.py -> build/lib.linux-armv7l-2.7/Bio/Data
copying Bio/Data/IUPACData.py -> build/lib.linux-armv7l-2.7/Bio/Data
copying Bio/Data/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Data
creating build/lib.linux-armv7l-2.7/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-armv7l-2.7/Bio/Emboss
copying Bio/Emboss/Primer3.py -> build/lib.linux-armv7l-2.7/Bio/Emboss
copying Bio/Emboss/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Emboss
copying Bio/Emboss/Applications.py -> build/lib.linux-armv7l-2.7/Bio/Emboss
creating build/lib.linux-armv7l-2.7/Bio/Entrez
copying Bio/Entrez/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Entrez
copying Bio/Entrez/Parser.py -> build/lib.linux-armv7l-2.7/Bio/Entrez
creating build/lib.linux-armv7l-2.7/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> build/lib.linux-armv7l-2.7/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> build/lib.linux-armv7l-2.7/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> build/lib.linux-armv7l-2.7/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-armv7l-2.7/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> build/lib.linux-armv7l-2.7/Bio/ExPASy
creating build/lib.linux-armv7l-2.7/Bio/FSSP
copying Bio/FSSP/fssp_rec.py -> build/lib.linux-armv7l-2.7/Bio/FSSP
copying Bio/FSSP/FSSPTools.py -> build/lib.linux-armv7l-2.7/Bio/FSSP
copying Bio/FSSP/__init__.py -> build/lib.linux-armv7l-2.7/Bio/FSSP
creating build/lib.linux-armv7l-2.7/Bio/GA
copying Bio/GA/Evolver.py -> build/lib.linux-armv7l-2.7/Bio/GA
copying Bio/GA/Organism.py -> build/lib.linux-armv7l-2.7/Bio/GA
copying Bio/GA/__init__.py -> build/lib.linux-armv7l-2.7/Bio/GA
creating build/lib.linux-armv7l-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/General.py -> build/lib.linux-armv7l-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/Point.py -> build/lib.linux-armv7l-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/GeneralPoint.py -> build/lib.linux-armv7l-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/TwoPoint.py -> build/lib.linux-armv7l-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/Uniform.py -> build/lib.linux-armv7l-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/__init__.py -> build/lib.linux-armv7l-2.7/Bio/GA/Crossover
creating build/lib.linux-armv7l-2.7/Bio/GA/Mutation
copying Bio/GA/Mutation/General.py -> build/lib.linux-armv7l-2.7/Bio/GA/Mutation
copying Bio/GA/Mutation/Simple.py -> build/lib.linux-armv7l-2.7/Bio/GA/Mutation
copying Bio/GA/Mutation/__init__.py -> build/lib.linux-armv7l-2.7/Bio/GA/Mutation
creating build/lib.linux-armv7l-2.7/Bio/GA/Repair
copying Bio/GA/Repair/__init__.py -> build/lib.linux-armv7l-2.7/Bio/GA/Repair
copying Bio/GA/Repair/Stabilizing.py -> build/lib.linux-armv7l-2.7/Bio/GA/Repair
creating build/lib.linux-armv7l-2.7/Bio/GA/Selection
copying Bio/GA/Selection/Diversity.py -> build/lib.linux-armv7l-2.7/Bio/GA/Selection
copying Bio/GA/Selection/Tournament.py -> build/lib.linux-armv7l-2.7/Bio/GA/Selection
copying Bio/GA/Selection/Abstract.py -> build/lib.linux-armv7l-2.7/Bio/GA/Selection
copying Bio/GA/Selection/__init__.py -> build/lib.linux-armv7l-2.7/Bio/GA/Selection
copying Bio/GA/Selection/RouletteWheel.py -> build/lib.linux-armv7l-2.7/Bio/GA/Selection
creating build/lib.linux-armv7l-2.7/Bio/GenBank
copying Bio/GenBank/utils.py -> build/lib.linux-armv7l-2.7/Bio/GenBank
copying Bio/GenBank/Scanner.py -> build/lib.linux-armv7l-2.7/Bio/GenBank
copying Bio/GenBank/Record.py -> build/lib.linux-armv7l-2.7/Bio/GenBank
copying Bio/GenBank/__init__.py -> build/lib.linux-armv7l-2.7/Bio/GenBank
creating build/lib.linux-armv7l-2.7/Bio/Geo
copying Bio/Geo/Record.py -> build/lib.linux-armv7l-2.7/Bio/Geo
copying Bio/Geo/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Geo
creating build/lib.linux-armv7l-2.7/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-armv7l-2.7/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-armv7l-2.7/Bio/Graphics
copying Bio/Graphics/Comparative.py -> build/lib.linux-armv7l-2.7/Bio/Graphics
copying Bio/Graphics/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-armv7l-2.7/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> build/lib.linux-armv7l-2.7/Bio/Graphics
copying Bio/Graphics/Distribution.py -> build/lib.linux-armv7l-2.7/Bio/Graphics
creating build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram
creating build/lib.linux-armv7l-2.7/Bio/HMM
copying Bio/HMM/Utilities.py -> build/lib.linux-armv7l-2.7/Bio/HMM
copying Bio/HMM/Trainer.py -> build/lib.linux-armv7l-2.7/Bio/HMM
copying Bio/HMM/MarkovModel.py -> build/lib.linux-armv7l-2.7/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-armv7l-2.7/Bio/HMM
copying Bio/HMM/__init__.py -> build/lib.linux-armv7l-2.7/Bio/HMM
creating build/lib.linux-armv7l-2.7/Bio/KEGG
copying Bio/KEGG/REST.py -> build/lib.linux-armv7l-2.7/Bio/KEGG
copying Bio/KEGG/__init__.py -> build/lib.linux-armv7l-2.7/Bio/KEGG
creating build/lib.linux-armv7l-2.7/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-armv7l-2.7/Bio/KEGG/Compound
creating build/lib.linux-armv7l-2.7/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-armv7l-2.7/Bio/KEGG/Enzyme
creating build/lib.linux-armv7l-2.7/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> build/lib.linux-armv7l-2.7/Bio/KEGG/Map
creating build/lib.linux-armv7l-2.7/Bio/PDB
creating build/lib.linux-armv7l-2.7/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-armv7l-2.7/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-armv7l-2.7/Bio/PDB/mmtf
creating build/lib.linux-armv7l-2.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-armv7l-2.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-armv7l-2.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-armv7l-2.7/Bio/KEGG/KGML
creating build/lib.linux-armv7l-2.7/Bio/Medline
copying Bio/Medline/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Medline
creating build/lib.linux-armv7l-2.7/Bio/motifs
copying Bio/motifs/mast.py -> build/lib.linux-armv7l-2.7/Bio/motifs
copying Bio/motifs/matrix.py -> build/lib.linux-armv7l-2.7/Bio/motifs
copying Bio/motifs/thresholds.py -> build/lib.linux-armv7l-2.7/Bio/motifs
copying Bio/motifs/transfac.py -> build/lib.linux-armv7l-2.7/Bio/motifs
copying Bio/motifs/__init__.py -> build/lib.linux-armv7l-2.7/Bio/motifs
copying Bio/motifs/meme.py -> build/lib.linux-armv7l-2.7/Bio/motifs
copying Bio/motifs/alignace.py -> build/lib.linux-armv7l-2.7/Bio/motifs
creating build/lib.linux-armv7l-2.7/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-armv7l-2.7/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> build/lib.linux-armv7l-2.7/Bio/motifs/applications
creating build/lib.linux-armv7l-2.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> build/lib.linux-armv7l-2.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-armv7l-2.7/Bio/motifs/jaspar
creating build/lib.linux-armv7l-2.7/Bio/NeuralNetwork
copying Bio/NeuralNetwork/Training.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork
copying Bio/NeuralNetwork/StopTraining.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork
copying Bio/NeuralNetwork/__init__.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork
creating build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/BackPropagation
copying Bio/NeuralNetwork/BackPropagation/Layer.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/BackPropagation
copying Bio/NeuralNetwork/BackPropagation/Network.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/BackPropagation
copying Bio/NeuralNetwork/BackPropagation/__init__.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/BackPropagation
creating build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene
copying Bio/NeuralNetwork/Gene/Motif.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene
copying Bio/NeuralNetwork/Gene/Pattern.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene
copying Bio/NeuralNetwork/Gene/__init__.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene
copying Bio/NeuralNetwork/Gene/Schema.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene
copying Bio/NeuralNetwork/Gene/Signature.py -> build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene
creating build/lib.linux-armv7l-2.7/Bio/Nexus
copying Bio/Nexus/Nodes.py -> build/lib.linux-armv7l-2.7/Bio/Nexus
copying Bio/Nexus/StandardData.py -> build/lib.linux-armv7l-2.7/Bio/Nexus
copying Bio/Nexus/Trees.py -> build/lib.linux-armv7l-2.7/Bio/Nexus
copying Bio/Nexus/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Nexus
copying Bio/Nexus/Nexus.py -> build/lib.linux-armv7l-2.7/Bio/Nexus
creating build/lib.linux-armv7l-2.7/Bio/NMR
copying Bio/NMR/xpktools.py -> build/lib.linux-armv7l-2.7/Bio/NMR
copying Bio/NMR/NOEtools.py -> build/lib.linux-armv7l-2.7/Bio/NMR
copying Bio/NMR/__init__.py -> build/lib.linux-armv7l-2.7/Bio/NMR
creating build/lib.linux-armv7l-2.7/Bio/Pathway
copying Bio/Pathway/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Pathway
creating build/lib.linux-armv7l-2.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-armv7l-2.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-armv7l-2.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Pathway/Rep
copying Bio/PDB/NACCESS.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/PDBIO.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/PDBList.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Atom.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Selection.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/DSSP.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Model.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/PSEA.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/HSExposure.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Chain.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Superimposer.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Dice.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/__init__.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Polypeptide.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Structure.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Vector.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Residue.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/Entity.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/PDBParser.py -> build/lib.linux-armv7l-2.7/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> build/lib.linux-armv7l-2.7/Bio/PDB
creating build/lib.linux-armv7l-2.7/Bio/PopGen
copying Bio/PopGen/__init__.py -> build/lib.linux-armv7l-2.7/Bio/PopGen
creating build/lib.linux-armv7l-2.7/Bio/PopGen/Async
copying Bio/PopGen/Async/Local.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/Async
copying Bio/PopGen/Async/__init__.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/Async
creating build/lib.linux-armv7l-2.7/Bio/PopGen/FDist
copying Bio/PopGen/FDist/__init__.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/FDist
copying Bio/PopGen/FDist/Utils.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/FDist
copying Bio/PopGen/FDist/Controller.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/FDist
copying Bio/PopGen/FDist/Async.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/FDist
creating build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Utils.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop
creating build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal
copying Bio/PopGen/SimCoal/Template.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal
copying Bio/PopGen/SimCoal/__init__.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal
copying Bio/PopGen/SimCoal/Controller.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal
copying Bio/PopGen/SimCoal/Async.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal
copying Bio/PopGen/SimCoal/Cache.py -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal
creating build/lib.linux-armv7l-2.7/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> build/lib.linux-armv7l-2.7/Bio/Restriction
copying Bio/Restriction/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Restriction
copying Bio/Restriction/RanaConfig.py -> build/lib.linux-armv7l-2.7/Bio/Restriction
copying Bio/Restriction/Restriction.py -> build/lib.linux-armv7l-2.7/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-armv7l-2.7/Bio/Restriction
creating build/lib.linux-armv7l-2.7/Bio/SCOP
copying Bio/SCOP/Residues.py -> build/lib.linux-armv7l-2.7/Bio/SCOP
copying Bio/SCOP/Raf.py -> build/lib.linux-armv7l-2.7/Bio/SCOP
copying Bio/SCOP/Cla.py -> build/lib.linux-armv7l-2.7/Bio/SCOP
copying Bio/SCOP/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SCOP
copying Bio/SCOP/Des.py -> build/lib.linux-armv7l-2.7/Bio/SCOP
copying Bio/SCOP/Dom.py -> build/lib.linux-armv7l-2.7/Bio/SCOP
copying Bio/SCOP/Hie.py -> build/lib.linux-armv7l-2.7/Bio/SCOP
creating build/lib.linux-armv7l-2.7/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO
copying Bio/SearchIO/_index.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO
copying Bio/SearchIO/FastaIO.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO
copying Bio/SearchIO/BlatIO.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO
creating build/lib.linux-armv7l-2.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/_base.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/_model
creating build/lib.linux-armv7l-2.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/BlastIO
creating build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO
creating build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO
creating build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/_index.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/AceIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
copying Bio/SeqIO/_convert.py -> build/lib.linux-armv7l-2.7/Bio/SeqIO
creating build/lib.linux-armv7l-2.7/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-armv7l-2.7/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-armv7l-2.7/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-armv7l-2.7/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-armv7l-2.7/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> build/lib.linux-armv7l-2.7/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-armv7l-2.7/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-armv7l-2.7/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-armv7l-2.7/Bio/SeqUtils
creating build/lib.linux-armv7l-2.7/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> build/lib.linux-armv7l-2.7/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> build/lib.linux-armv7l-2.7/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Sequencing
creating build/lib.linux-armv7l-2.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-armv7l-2.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-armv7l-2.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-armv7l-2.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Sequencing/Applications
creating build/lib.linux-armv7l-2.7/Bio/Statistics
copying Bio/Statistics/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Statistics
copying Bio/Statistics/lowess.py -> build/lib.linux-armv7l-2.7/Bio/Statistics
creating build/lib.linux-armv7l-2.7/Bio/SubsMat
copying Bio/SubsMat/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SubsMat
copying Bio/SubsMat/MatrixInfo.py -> build/lib.linux-armv7l-2.7/Bio/SubsMat
copying Bio/SubsMat/FreqTable.py -> build/lib.linux-armv7l-2.7/Bio/SubsMat
creating build/lib.linux-armv7l-2.7/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SVDSuperimposer
creating build/lib.linux-armv7l-2.7/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.linux-armv7l-2.7/Bio/PDB/QCPSuperimposer
creating build/lib.linux-armv7l-2.7/Bio/SwissProt
copying Bio/SwissProt/KeyWList.py -> build/lib.linux-armv7l-2.7/Bio/SwissProt
copying Bio/SwissProt/__init__.py -> build/lib.linux-armv7l-2.7/Bio/SwissProt
creating build/lib.linux-armv7l-2.7/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> build/lib.linux-armv7l-2.7/Bio/TogoWS
creating build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/_io.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/NeXML.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/Newick.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/Consensus.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/_utils.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/CDAO.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/BaseTree.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-armv7l-2.7/Bio/Phylo
creating build/lib.linux-armv7l-2.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/Applications
creating build/lib.linux-armv7l-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-armv7l-2.7/Bio/Phylo/PAML
creating build/lib.linux-armv7l-2.7/Bio/UniGene
copying Bio/UniGene/__init__.py -> build/lib.linux-armv7l-2.7/Bio/UniGene
creating build/lib.linux-armv7l-2.7/Bio/UniProt
copying Bio/UniProt/GOA.py -> build/lib.linux-armv7l-2.7/Bio/UniProt
copying Bio/UniProt/__init__.py -> build/lib.linux-armv7l-2.7/Bio/UniProt
creating build/lib.linux-armv7l-2.7/Bio/Wise
copying Bio/Wise/psw.py -> build/lib.linux-armv7l-2.7/Bio/Wise
copying Bio/Wise/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Wise
copying Bio/Wise/dnal.py -> build/lib.linux-armv7l-2.7/Bio/Wise
creating build/lib.linux-armv7l-2.7/Bio/_py3k
copying Bio/_py3k/__init__.py -> build/lib.linux-armv7l-2.7/Bio/_py3k
copying Bio/_py3k/_ordereddict.py -> build/lib.linux-armv7l-2.7/Bio/_py3k
creating build/lib.linux-armv7l-2.7/BioSQL
copying BioSQL/Loader.py -> build/lib.linux-armv7l-2.7/BioSQL
copying BioSQL/BioSeq.py -> build/lib.linux-armv7l-2.7/BioSQL
copying BioSQL/BioSeqDatabase.py -> build/lib.linux-armv7l-2.7/BioSQL
copying BioSQL/DBUtils.py -> build/lib.linux-armv7l-2.7/BioSQL
copying BioSQL/__init__.py -> build/lib.linux-armv7l-2.7/BioSQL
creating build/lib.linux-armv7l-2.7/Bio/Affy
copying Bio/Affy/CelFile.py -> build/lib.linux-armv7l-2.7/Bio/Affy
copying Bio/Affy/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Affy
creating build/lib.linux-armv7l-2.7/Bio/Cluster
copying Bio/Cluster/__init__.py -> build/lib.linux-armv7l-2.7/Bio/Cluster
creating build/lib.linux-armv7l-2.7/Bio/KDTree
copying Bio/KDTree/__init__.py -> build/lib.linux-armv7l-2.7/Bio/KDTree
copying Bio/KDTree/KDTree.py -> build/lib.linux-armv7l-2.7/Bio/KDTree
creating build/lib.linux-armv7l-2.7/Bio/phenotype
copying Bio/phenotype/phen_micro.py -> build/lib.linux-armv7l-2.7/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> build/lib.linux-armv7l-2.7/Bio/phenotype
copying Bio/phenotype/__init__.py -> build/lib.linux-armv7l-2.7/Bio/phenotype
creating build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs
creating build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/ssm_2d.par -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/ssm_1d.par -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/split_island.par -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/split_ssm_2d.par -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/bottle.par -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/decline_lambda.par -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/simple.par -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/island.par -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/decline_split.par -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/split_ssm_1d.par -> build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data
running build_ext
building 'Bio.cpairwise2' extension
creating build/temp.linux-armv7l-2.7
creating build/temp.linux-armv7l-2.7/Bio
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.linux-armv7l-2.7/Bio/cpairwise2module.o
In file included from /usr/include/python2.7/Python.h:100:0,
                 from Bio/cpairwise2module.c:14:
Bio/cpairwise2module.c: In function 'cpairwise2__make_score_matrix_fast':
/usr/include/python2.7/listobject.h:62:58: warning: 'py_trace_row' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define PyList_SET_ITEM(op, i, v) (((PyListObject *)(op))->ob_item[i] = (v))
                                                          ^
Bio/cpairwise2module.c:343:34: note: 'py_trace_row' was declared here
         PyObject *py_score_row, *py_trace_row;
                                  ^
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now build/temp.linux-armv7l-2.7/Bio/cpairwise2module.o -L/usr/lib -lpython2.7 -o build/lib.linux-armv7l-2.7/Bio/cpairwise2.so
building 'Bio.trie' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now -fPIC -IBio -I/usr/include/python2.7 -c Bio/triemodule.c -o build/temp.linux-armv7l-2.7/Bio/triemodule.o
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now -fPIC -IBio -I/usr/include/python2.7 -c Bio/trie.c -o build/temp.linux-armv7l-2.7/Bio/trie.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now build/temp.linux-armv7l-2.7/Bio/triemodule.o build/temp.linux-armv7l-2.7/Bio/trie.o -L/usr/lib -lpython2.7 -o build/lib.linux-armv7l-2.7/Bio/trie.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-armv7l-2.7/Bio/Nexus
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/include/python2.7 -c Bio/Nexus/cnexus.c -o build/temp.linux-armv7l-2.7/Bio/Nexus/cnexus.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now build/temp.linux-armv7l-2.7/Bio/Nexus/cnexus.o -L/usr/lib -lpython2.7 -o build/lib.linux-armv7l-2.7/Bio/Nexus/cnexus.so
building 'Bio.Cluster.cluster' extension
creating build/temp.linux-armv7l-2.7/Bio/Cluster
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/Cluster/clustermodule.c -o build/temp.linux-armv7l-2.7/Bio/Cluster/clustermodule.o
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/Cluster/cluster.c -o build/temp.linux-armv7l-2.7/Bio/Cluster/cluster.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now build/temp.linux-armv7l-2.7/Bio/Cluster/clustermodule.o build/temp.linux-armv7l-2.7/Bio/Cluster/cluster.o -L/usr/lib -lpython2.7 -o build/lib.linux-armv7l-2.7/Bio/Cluster/cluster.so
building 'Bio.KDTree._CKDTree' extension
creating build/temp.linux-armv7l-2.7/Bio/KDTree
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/KDTree/KDTree.c -o build/temp.linux-armv7l-2.7/Bio/KDTree/KDTree.o
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-armv7l-2.7/Bio/KDTree/KDTreemodule.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now build/temp.linux-armv7l-2.7/Bio/KDTree/KDTree.o build/temp.linux-armv7l-2.7/Bio/KDTree/KDTreemodule.o -L/usr/lib -lpython2.7 -o build/lib.linux-armv7l-2.7/Bio/KDTree/_CKDTree.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-armv7l-2.7/Bio/motifs
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/motifs/_pwm.c -o build/temp.linux-armv7l-2.7/Bio/motifs/_pwm.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now build/temp.linux-armv7l-2.7/Bio/motifs/_pwm.o -L/usr/lib -lpython2.7 -o build/lib.linux-armv7l-2.7/Bio/motifs/_pwm.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-armv7l-2.7/Bio/PDB
creating build/temp.linux-armv7l-2.7/Bio/PDB/QCPSuperimposer
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-armv7l-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o
In file included from /usr/include/python2.7/pyconfig.h:4:0,
                 from /usr/include/python2.7/Python.h:8,
                 from Bio/PDB/QCPSuperimposer/qcprotmodule.c:43:
/usr/include/python2.7/pyconfig-32.h:1188:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
 #define _POSIX_C_SOURCE 200112L
 ^
In file included from /usr/include/stdio.h:27:0,
                 from Bio/PDB/QCPSuperimposer/qcprotmodule.c:40:
/usr/include/features.h:168:0: note: this is the location of the previous definition
 # define _POSIX_C_SOURCE 200809L
 ^
In file included from /usr/include/python2.7/pyconfig.h:4:0,
                 from /usr/include/python2.7/Python.h:8,
                 from Bio/PDB/QCPSuperimposer/qcprotmodule.c:43:
/usr/include/python2.7/pyconfig-32.h:1210:0: warning: "_XOPEN_SOURCE" redefined [enabled by default]
 #define _XOPEN_SOURCE 600
 ^
In file included from /usr/include/stdio.h:27:0,
                 from Bio/PDB/QCPSuperimposer/qcprotmodule.c:40:
/usr/include/features.h:170:0: note: this is the location of the previous definition
 # define _XOPEN_SOURCE 700
 ^
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -Wl,-z,relro -Wl,-z,now build/temp.linux-armv7l-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib -lpython2.7 -o build/lib.linux-armv7l-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.so
~/build/BUILD/python-biopython-1.68
+ popd
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.v0koVd
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm
++ dirname /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm
+ cd python-biopython-1.68
+ pushd python2
~/build/BUILD/python-biopython-1.68/python2 ~/build/BUILD/python-biopython-1.68
+ /usr/bin/python2 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm --install-data=/usr/share/python-biopython
running install
running install_lib
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL
copying build/lib.linux-armv7l-2.7/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL
copying build/lib.linux-armv7l-2.7/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL
copying build/lib.linux-armv7l-2.7/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL
copying build/lib.linux-armv7l-2.7/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL
copying build/lib.linux-armv7l-2.7/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Compass
copying build/lib.linux-armv7l-2.7/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Compass
copying build/lib.linux-armv7l-2.7/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
copying build/lib.linux-armv7l-2.7/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA
copying build/lib.linux-armv7l-2.7/Bio/GA/Evolver.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Repair
copying build/lib.linux-armv7l-2.7/Bio/GA/Repair/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Repair
copying build/lib.linux-armv7l-2.7/Bio/GA/Repair/Stabilizing.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Repair
copying build/lib.linux-armv7l-2.7/Bio/GA/Organism.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-armv7l-2.7/Bio/GA/Crossover/General.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-armv7l-2.7/Bio/GA/Crossover/Point.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-armv7l-2.7/Bio/GA/Crossover/GeneralPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-armv7l-2.7/Bio/GA/Crossover/TwoPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-armv7l-2.7/Bio/GA/Crossover/Uniform.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-armv7l-2.7/Bio/GA/Crossover/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Mutation
copying build/lib.linux-armv7l-2.7/Bio/GA/Mutation/General.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Mutation
copying build/lib.linux-armv7l-2.7/Bio/GA/Mutation/Simple.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Mutation
copying build/lib.linux-armv7l-2.7/Bio/GA/Mutation/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Mutation
copying build/lib.linux-armv7l-2.7/Bio/GA/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-armv7l-2.7/Bio/GA/Selection/Diversity.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-armv7l-2.7/Bio/GA/Selection/Tournament.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-armv7l-2.7/Bio/GA/Selection/Abstract.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-armv7l-2.7/Bio/GA/Selection/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-armv7l-2.7/Bio/GA/Selection/RouletteWheel.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-armv7l-2.7/Bio/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/UniGene
copying build/lib.linux-armv7l-2.7/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/UniGene
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-2.7/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-2.7/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-2.7/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-2.7/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-2.7/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-armv7l-2.7/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Data
copying build/lib.linux-armv7l-2.7/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Data
copying build/lib.linux-armv7l-2.7/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Data
copying build/lib.linux-armv7l-2.7/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Data
copying build/lib.linux-armv7l-2.7/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Data
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/_py3k
copying build/lib.linux-armv7l-2.7/Bio/_py3k/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/_py3k
copying build/lib.linux-armv7l-2.7/Bio/_py3k/_ordereddict.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/_py3k
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-armv7l-2.7/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-armv7l-2.7/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-armv7l-2.7/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-armv7l-2.7/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/Compound
copying build/lib.linux-armv7l-2.7/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/Compound
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/Map
copying build/lib.linux-armv7l-2.7/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/Map
copying build/lib.linux-armv7l-2.7/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/Enzyme
copying build/lib.linux-armv7l-2.7/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/Enzyme
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Emboss
copying build/lib.linux-armv7l-2.7/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Emboss
copying build/lib.linux-armv7l-2.7/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Emboss
copying build/lib.linux-armv7l-2.7/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Emboss
copying build/lib.linux-armv7l-2.7/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Emboss
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs/applications
copying build/lib.linux-armv7l-2.7/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs/applications
copying build/lib.linux-armv7l-2.7/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs/applications
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-armv7l-2.7/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-armv7l-2.7/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-armv7l-2.7/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-2.7/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-2.7/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-2.7/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-2.7/Bio/motifs/_pwm.so -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-2.7/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-2.7/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-armv7l-2.7/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-armv7l-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.so -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-armv7l-2.7/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-armv7l-2.7/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-armv7l-2.7/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-armv7l-2.7/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB/mmtf
copying build/lib.linux-armv7l-2.7/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Vector.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-armv7l-2.7/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/phenotype
copying build/lib.linux-armv7l-2.7/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/phenotype
copying build/lib.linux-armv7l-2.7/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/phenotype
copying build/lib.linux-armv7l-2.7/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/phenotype
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-2.7/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-2.7/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-2.7/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-2.7/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-2.7/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-armv7l-2.7/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-armv7l-2.7/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align
copying build/lib.linux-armv7l-2.7/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align
copying build/lib.linux-armv7l-2.7/Bio/Align/Generic.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-2.7/Bio/KDTree/_CKDTree.so -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-2.7/Bio/KDTree/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KDTree
copying build/lib.linux-armv7l-2.7/Bio/KDTree/KDTree.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KDTree
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-2.7/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-2.7/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-2.7/Bio/codonalign/chisq.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-2.7/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-2.7/Bio/codonalign/codonalphabet.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-armv7l-2.7/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Statistics
copying build/lib.linux-armv7l-2.7/Bio/Statistics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Statistics
copying build/lib.linux-armv7l-2.7/Bio/Statistics/lowess.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Statistics
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GenBank
copying build/lib.linux-armv7l-2.7/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GenBank
copying build/lib.linux-armv7l-2.7/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GenBank
copying build/lib.linux-armv7l-2.7/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GenBank
copying build/lib.linux-armv7l-2.7/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GenBank
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/CAPS
copying build/lib.linux-armv7l-2.7/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/CAPS
copying build/lib.linux-armv7l-2.7/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-2.7/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-2.7/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-2.7/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-2.7/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-2.7/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-2.7/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-2.7/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-armv7l-2.7/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/AlignIO
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-2.7/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-2.7/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-2.7/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-2.7/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-2.7/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-2.7/Bio/Blast/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-2.7/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-armv7l-2.7/Bio/trie.so -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO
copying build/lib.linux-armv7l-2.7/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SearchIO
copying build/lib.linux-armv7l-2.7/Bio/triefind.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/UniProt
copying build/lib.linux-armv7l-2.7/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/UniProt
copying build/lib.linux-armv7l-2.7/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/UniProt
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-2.7/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-2.7/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-2.7/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-2.7/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-2.7/Bio/Nexus/cnexus.so -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-armv7l-2.7/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Nexus
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Cluster
copying build/lib.linux-armv7l-2.7/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Cluster
copying build/lib.linux-armv7l-2.7/Bio/Cluster/cluster.so -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Cluster
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-armv7l-2.7/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-armv7l-2.7/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-armv7l-2.7/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-armv7l-2.7/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-armv7l-2.7/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-armv7l-2.7/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-armv7l-2.7/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-armv7l-2.7/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-armv7l-2.7/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-armv7l-2.7/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-armv7l-2.7/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Sequencing
copying build/lib.linux-armv7l-2.7/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Sequencing
copying build/lib.linux-armv7l-2.7/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-armv7l-2.7/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-armv7l-2.7/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-armv7l-2.7/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-armv7l-2.7/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-armv7l-2.7/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Geo
copying build/lib.linux-armv7l-2.7/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Geo
copying build/lib.linux-armv7l-2.7/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Geo
copying build/lib.linux-armv7l-2.7/Bio/Index.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
copying build/lib.linux-armv7l-2.7/Bio/cpairwise2.so -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NMR
copying build/lib.linux-armv7l-2.7/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NMR
copying build/lib.linux-armv7l-2.7/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NMR
copying build/lib.linux-armv7l-2.7/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NMR
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/SeqIO/_convert.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-armv7l-2.7/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-2.7/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-2.7/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-2.7/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-2.7/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-2.7/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-2.7/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-2.7/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-2.7/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-2.7/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-armv7l-2.7/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Alphabet
copying build/lib.linux-armv7l-2.7/Bio/Alphabet/Reduced.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Alphabet
copying build/lib.linux-armv7l-2.7/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Alphabet
copying build/lib.linux-armv7l-2.7/Bio/Alphabet/IUPAC.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Alphabet
copying build/lib.linux-armv7l-2.7/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-2.7/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-2.7/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-2.7/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-2.7/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-2.7/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-2.7/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-armv7l-2.7/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SCOP
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Wise
copying build/lib.linux-armv7l-2.7/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Wise
copying build/lib.linux-armv7l-2.7/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Wise
copying build/lib.linux-armv7l-2.7/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Wise
copying build/lib.linux-armv7l-2.7/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SubsMat
copying build/lib.linux-armv7l-2.7/Bio/SubsMat/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SubsMat
copying build/lib.linux-armv7l-2.7/Bio/SubsMat/MatrixInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SubsMat
copying build/lib.linux-armv7l-2.7/Bio/SubsMat/FreqTable.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SubsMat
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Affy
copying build/lib.linux-armv7l-2.7/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Affy
copying build/lib.linux-armv7l-2.7/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Affy
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Crystal
copying build/lib.linux-armv7l-2.7/Bio/Crystal/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Crystal
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Restriction
copying build/lib.linux-armv7l-2.7/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Restriction
copying build/lib.linux-armv7l-2.7/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Restriction
copying build/lib.linux-armv7l-2.7/Bio/Restriction/RanaConfig.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Restriction
copying build/lib.linux-armv7l-2.7/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Restriction
copying build/lib.linux-armv7l-2.7/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Restriction
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SwissProt
copying build/lib.linux-armv7l-2.7/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SwissProt
copying build/lib.linux-armv7l-2.7/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SwissProt
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/FSSP
copying build/lib.linux-armv7l-2.7/Bio/FSSP/fssp_rec.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/FSSP
copying build/lib.linux-armv7l-2.7/Bio/FSSP/FSSPTools.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/FSSP
copying build/lib.linux-armv7l-2.7/Bio/FSSP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/FSSP
copying build/lib.linux-armv7l-2.7/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-armv7l-2.7/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez
copying build/lib.linux-armv7l-2.7/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Entrez
copying build/lib.linux-armv7l-2.7/Bio/DocSQL.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Application
copying build/lib.linux-armv7l-2.7/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Application
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Medline
copying build/lib.linux-armv7l-2.7/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Medline
copying build/lib.linux-armv7l-2.7/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-armv7l-2.7/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-2.7/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-2.7/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-2.7/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-2.7/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-2.7/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-armv7l-2.7/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SVDSuperimposer
copying build/lib.linux-armv7l-2.7/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SVDSuperimposer
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/TogoWS
copying build/lib.linux-armv7l-2.7/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/TogoWS
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop/Utils.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-armv7l-2.7/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/Async
copying build/lib.linux-armv7l-2.7/Bio/PopGen/Async/Local.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/Async
copying build/lib.linux-armv7l-2.7/Bio/PopGen/Async/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/Async
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/Template.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data/ssm_2d.par -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data/ssm_1d.par -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data/split_island.par -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data/split_ssm_2d.par -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data/bottle.par -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data/decline_lambda.par -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data/simple.par -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data/island.par -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data/decline_split.par -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/data/split_ssm_1d.par -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/Async.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
copying build/lib.linux-armv7l-2.7/Bio/PopGen/SimCoal/Cache.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
copying build/lib.linux-armv7l-2.7/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/FDist
copying build/lib.linux-armv7l-2.7/Bio/PopGen/FDist/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/FDist
copying build/lib.linux-armv7l-2.7/Bio/PopGen/FDist/Utils.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/FDist
copying build/lib.linux-armv7l-2.7/Bio/PopGen/FDist/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/FDist
copying build/lib.linux-armv7l-2.7/Bio/PopGen/FDist/Async.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/FDist
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene/Motif.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene/Pattern.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene/Schema.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Gene/Signature.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/Training.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/StopTraining.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork
creating /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/BackPropagation
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/BackPropagation/Layer.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/BackPropagation
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/BackPropagation/Network.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/BackPropagation
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/BackPropagation/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/BackPropagation
copying build/lib.linux-armv7l-2.7/Bio/NeuralNetwork/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL/Loader.py to Loader.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL/BioSeq.py to BioSeq.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL/DBUtils.py to DBUtils.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/BioSQL/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Compass/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/MaxEntropy.py to MaxEntropy.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NaiveBayes.py to NaiveBayes.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Evolver.py to Evolver.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Repair/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Repair/Stabilizing.py to Stabilizing.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Organism.py to Organism.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover/General.py to General.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover/Point.py to Point.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover/GeneralPoint.py to GeneralPoint.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover/TwoPoint.py to TwoPoint.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover/Uniform.py to Uniform.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Crossover/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Mutation/General.py to General.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Mutation/Simple.py to Simple.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Mutation/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection/Diversity.py to Diversity.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection/Tournament.py to Tournament.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection/Abstract.py to Abstract.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/GA/Selection/RouletteWheel.py to RouletteWheel.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ParserSupport.py to ParserSupport.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/UniGene/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy/Prosite.py to Prosite.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy/Enzyme.py to Enzyme.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/ExPASy/Prodoc.py to Prodoc.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SeqRecord.py to SeqRecord.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Data/SCOPData.py to SCOPData.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Data/CodonTable.py to CodonTable.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Data/IUPACData.py to IUPACData.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Data/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/_py3k/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/_py3k/_ordereddict.py to _ordereddict.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/KGML/KGML_parser.py to KGML_parser.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/KGML/KGML_pathway.py to KGML_pathway.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/KGML/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/REST.py to REST.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KEGG/Compound/__init__.py to __init__.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/bgzf.py to bgzf.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/Comparative.py to Comparative.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/KGML_vis.py to KGML_vis.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Graphics/Distribution.py to Distribution.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/SVDSuperimposer/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/TogoWS/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop/FileParser.py to FileParser.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop/LargeFileParser.py to LargeFileParser.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop/EasyController.py to EasyController.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop/Utils.py to Utils.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/Controller.py to Controller.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/Cache.py to Cache.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/__init__.py to __init__.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PopGen/FDist/Utils.py to Utils.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene/Pattern.py to Pattern.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene/Schema.py to Schema.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Training.py to Training.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/StopTraining.py to StopTraining.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/__init__.py to __init__.pyc
writing byte-compilation script '/tmp/tmpaLLCyT.py'
/usr/bin/python2 -O /tmp/tmpaLLCyT.py
removing /tmp/tmpaLLCyT.py
running install_egg_info
Writing /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/biopython-1.68-py2.7.egg-info
~/build/BUILD/python-biopython-1.68
+ popd
+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 /builddir/build/BUILD/python-biopython-1.68
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/motifs/_pwm.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/KDTree/_CKDTree.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/trie.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Nexus/cnexus.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/Cluster/cluster.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7/site-packages/Bio/cpairwise2.so
/usr/lib/rpm/sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match.
732 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/python2.7 using /usr/bin/python2.7
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/lib/debug/usr/lib/python2.7 using /usr/bin/python2.7
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.mvPHJl
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.68
~/build/BUILD/python-biopython-1.68/python2/Tests ~/build/BUILD/python-biopython-1.68
+ pushd python2/Tests
+ find . -name run_tests.py
+ xargs sed -i '1s|^#!/usr/bin/env python|#!/usr/bin/python2|'
++ grep -v Tutorial
++ ls test_Ace.py test_AlignIO.py test_AlignIO_ClustalIO.py test_AlignIO_EmbossIO.py test_AlignIO_FastaIO.py test_AlignIO_PhylipIO.py test_AlignIO_convert.py test_AlignInfo.py test_Application.py test_BWA_tool.py test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb_online.py test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector_online.py test_BioSQL_psycopg2.py test_BioSQL_psycopg2_online.py test_BioSQL_sqlite3.py test_BioSQL_sqlite3_online.py test_CAPS.py test_CelFile.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_CodonUsage.py test_ColorSpiral.py test_Compass.py test_Consensus.py test_Crystal.py test_DSSP_tool.py test_Dialign_tool.py test_DocSQL.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_FSSP.py test_Fasttree_tool.py test_File.py test_GACrossover.py test_GAMutation.py test_GAOrganism.py test_GAQueens.py test_GARepair.py test_GASelection.py test_GenBank.py test_GenBank_unittest.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_Location.py test_LogisticRegression.py test_MMCIF.py test_MSAProbs_tool.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_NNExclusiveOr.py test_NNGene.py test_NNGeneral.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_PDB_KDTree.py test_ParserSupport.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_DFDist.py test_PopGen_FDist.py test_PopGen_FDist_nodepend.py test_PopGen_FastSimCoal.py test_PopGen_GenePop.py test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_nodepend.py test_PopGen_SimCoal.py test_PopGen_SimCoal_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_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_model.py test_SearchIO_write.py test_SeqFeature.py test_SeqIO.py test_SeqIO_AbiIO.py test_SeqIO_FastaIO.py test_SeqIO_Insdc.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_convert.py test_SeqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SubsMat.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_Uniprot.py test_Wise.py test_XXmotif_tool.py test_align.py test_bgzf.py test_codonalign.py test_geo.py test_kNN.py test_lowess.py test_mmtf.py test_motifs.py test_motifs_online.py test_pairwise2.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_py3k.py test_raxml_tool.py test_samtools_tool.py test_seq.py test_translate.py test_trie.py
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Ace.py
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 0.755 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_AlignIO.py
test_AlignIO ... ok
runTest (__main__.ComparisonTestCase)
test_AlignIO ... ok
----------------------------------------------------------------------
Ran 1 test in 28.657 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 0.964 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 0.950 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_AlignIO_FastaIO.py
test_AlignIO_FastaIO ... ok
runTest (__main__.ComparisonTestCase)
test_AlignIO_FastaIO ... ok
----------------------------------------------------------------------
Ran 1 test in 1.650 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_AlignIO_PhylipIO.py
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 0.949 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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_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_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_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_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_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_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_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_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
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
----------------------------------------------------------------------
Ran 1 test in 4.642 seconds
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_AlignInfo.py
test_AlignInfo ... ok
test_nucleotides (test_AlignInfo.AlignInfoTests) ... ok
test_proteins (test_AlignInfo.AlignInfoTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.304 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Application.py
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 0.420 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BWA_tool.py
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 0.335 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_MySQLdb.py
test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 1.501 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_MySQLdb_online.py
test_BioSQL_MySQLdb_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 1.279 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_mysql_connector.py
test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 1.268 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_mysql_connector_online.py
test_BioSQL_mysql_connector_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 1.270 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_psycopg2.py
test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 1.263 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_psycopg2_online.py
test_BioSQL_psycopg2_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 1.274 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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)
GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok
test_NC_005816 (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok
test_NT_019265 (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok
test_arab1 (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, arab1. ... ok
test_cor6_6 (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok
test_no_ref (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, noref. ... ok
test_one_of (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, one_of. ... ok
test_protein_refseq2 (common_BioSQL.ClosedLoopTest)
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_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_NC_000932 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok
test_NC_005816 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok
test_NT_019265 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok
test_arab1 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, arab1. ... ok
test_cor6_6 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok
test_no_ref (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, noref. ... ok
test_one_of (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, one_of. ... ok
test_protein_refseq2 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
----------------------------------------------------------------------
Ran 1 test in 116.535 seconds
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_sqlite3_online.py
test_BioSQL_sqlite3_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 1.265 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 4.785 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_CelFile.py
test_CelFile ... ok
test_read (test_CelFile.testCelFile) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.062 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Chi2.py
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 2.361 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 1.380 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Clustalw_tool.py
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 1.323 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Cluster.py
test_Cluster ... ok
test_clusterdistance (test_Cluster.TestCluster) ... ok
test_distancematrix_kmedoids (test_Cluster.TestCluster) ... ok
test_kcluster (test_Cluster.TestCluster) ... ok
test_matrix_parse (test_Cluster.TestCluster) ... ok
test_median_mean (test_Cluster.TestCluster) ... ok
test_pca (test_Cluster.TestCluster) ... ok
test_somcluster (test_Cluster.TestCluster) ... ok
test_treecluster (test_Cluster.TestCluster) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.183 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_CodonTable.py
test_CodonTable ... ok
runTest (__main__.ComparisonTestCase)
test_CodonTable ... ok
----------------------------------------------------------------------
Ran 1 test in 0.780 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_CodonUsage.py
test_CodonUsage ... ok
runTest (__main__.ComparisonTestCase)
test_CodonUsage ... ok
----------------------------------------------------------------------
Ran 1 test in 1.470 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 0.651 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Compass.py
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 0.102 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Consensus.py
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 38.611 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 0.429 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 1.254 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 0.941 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_DocSQL.py
test_DocSQL ... ok
runTest (__main__.ComparisonTestCase)
test_DocSQL ... ok
----------------------------------------------------------------------
Ran 1 test in 0.071 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 an AssertionError is thrown by content after a CO line ... ok
----------------------------------------------------------------------
Ran 1 test in 1.248 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Emboss.py
test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss.
----------------------------------------------------------------------
Ran 1 test in 1.458 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_EmbossPhylipNew.py
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 1.084 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_EmbossPrimer.py
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 0.185 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Entrez.py
test_Entrez ... 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 0.213 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Entrez_online.py
test_Entrez_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.040 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Entrez_parser.py
test_Entrez_parser ... 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_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_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
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
----------------------------------------------------------------------
Ran 1 test in 3.163 seconds
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Enzyme.py
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_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 0.216 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_FSSP.py
test_FSSP ... ok
runTest (__main__.ComparisonTestCase)
test_FSSP ... ok
----------------------------------------------------------------------
Ran 1 test in 38.387 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 2.429 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_File.py
test_File ... ok
test_handle (test_File.AsHandleTestCase)
Test as_handle with a file-like object argument ... ok
test_path (test_File.AsHandleTestCase)
Test as_handle with a path argument ... ok
test_stringio (test_File.AsHandleTestCase) ... ok
test_one (test_File.UndoHandleTests) ... ok
test_read (test_File.UndoHandleTests)
test read method ... ok
test_undohandle_read_block (test_File.UndoHandleTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.220 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GACrossover.py
test_GACrossover ... ok
test_basic_asym_crossover (test_GACrossover.FourPointTest)
Test basic asymmetric 2-point crossover functionality. ... ok
test_basic_crossover (test_GACrossover.FourPointTest)
Test basic 4-point crossover functionality. ... ok
test_prop_sym_crossover (test_GACrossover.FourPointTest)
Test properties of symmetric 4-point crossover. ... ok
test_basic_crossover (test_GACrossover.InterleaveTest)
Test basic interleave crossover functionality. ... ok
test_prop_asym_crossover (test_GACrossover.InterleaveTest)
Test basic interleave crossover with asymmetric genomes. ... ok
test_prop_sym_crossover (test_GACrossover.InterleaveTest)
Test properties of interleave point crossover. ... ok
test_keep_higher (test_GACrossover.SafeFitnessTest)
Make sure we always keep higher fitness when specified. ... ok
test_keep_lower (test_GACrossover.SafeFitnessTest)
Make sure we do normal crossover functionality when specified. ... ok
test_basic_crossover (test_GACrossover.SinglePointTest)
Test basic point crossover functionality. ... ok
test_basic_asym_crossover (test_GACrossover.TwoPointTest)
Test basic asymmetric 2-point crossover functionality. ... ok
test_basic_crossover (test_GACrossover.UniformTest)
Test basic uniform crossover functionality. ... ok
test_ds_prop_uniform_crossover (test_GACrossover.UniformTest)
Test properties of differing genome length, uniform crossovers. ... ok
test_ss_prop_uniform_crossover (test_GACrossover.UniformTest)
Test properties of equal genome length, uniform crossovers. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.975 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GAMutation.py
test_GAMutation ... ok
test_always_mutate (test_GAMutation.ConversionTest)
Test ability to cause mutations. ... ok
test_never_mutate (test_GAMutation.ConversionTest)
Make sure we do not mutate at unexpected times. ... ok
test_keep_higher (test_GAMutation.SafeFitnessTest)
Make sure we always keep the higher fitness. ... ok
test_keep_new (test_GAMutation.SafeFitnessTest)
Make sure we always keep the new organism when specified. ... ok
test_always_mutate (test_GAMutation.SinglePositionTest)
Test ability to cause mutations. ... ok
test_never_mutate (test_GAMutation.SinglePositionTest)
Make sure we do not mutate at unexpected times. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.133 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GAOrganism.py
test_GAOrganism ... ok
test_function_population (test_GAOrganism.CreatePopulationTest)
Create a population using a function to generate genomes. ... ok
test_random_population (test_GAOrganism.CreatePopulationTest)
Create a population randomly from a alphabet. ... ok
test_random_population_types (test_GAOrganism.CreatePopulationTest)
Creating a random population with different types of alphabets. ... ok
test_organism_basic (test_GAOrganism.OrganismTest)
Exercise basic organism functionality. ... ok
test_organism_copy (test_GAOrganism.OrganismTest)
Test copying of organisms. ... ok
test_organism_fitness (test_GAOrganism.OrganismTest)
Test the ability to deal with the fitness of the genome. ... ok
test_provide_fitness (test_GAOrganism.OrganismTest)
Test that providing a pre-calculated fitness works. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.909 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GAQueens.py
test_GAQueens ... ok
test_queens (test_GAQueens.QueensTest)
Place five queens with a GA ... ok
----------------------------------------------------------------------
Ran 1 test in 1.815 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GARepair.py
test_GARepair ... ok
test_multiple_repair (test_GARepair.AmbiguousRepairTest)
Test repair of multiple ambiguous positions in a genome. ... ok
test_single_repair (test_GARepair.AmbiguousRepairTest)
Test repair of a single ambiguous position in a genome. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.951 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GASelection.py
test_GASelection ... ok
test_get_new_organism (test_GASelection.DiversitySelectionTest)
Getting a new organism not in the new population. ... ok
test_no_retrieve_organism (test_GASelection.DiversitySelectionTest)
Test not getting an organism already in the new population. ... ok
test_selection (test_GASelection.DiversitySelectionTest)
Test basic selection on a small population. ... ok
test_select_best (test_GASelection.RouletteWheelSelectionTest)
Ensure selection of a best organism in a population of 2. ... ok
test_selection (test_GASelection.RouletteWheelSelectionTest)
Test basic selection on a small population. ... ok
test_select_best (test_GASelection.TournamentSelectionTest)
Ensure selection of the best organism in a population of 2. ... ok
test_selection (test_GASelection.TournamentSelectionTest)
Test basic selection on a small population. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.223 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GenBank.py
test_GenBank ... ok
runTest (__main__.ComparisonTestCase)
test_GenBank ... ok
----------------------------------------------------------------------
Ran 1 test in 4.302 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GenBank_unittest.py
test_GenBank_unittest ... ok
test_000_genbank_bad_loc_wrap_warning (test_GenBank_unittest.GenBankTests)
Feature line wrapping warning. ... ok
test_001_negative_location_warning (test_GenBank_unittest.GenBankTests)
Un-parsable feature location warning. ... ok
test_dbline_embl_gb (test_GenBank_unittest.GenBankTests)
GenBank / EMBL paired records with PR project entry: EMBL ... ok
test_dbline_gb_embl (test_GenBank_unittest.GenBankTests)
GenBank / EMBL paired records with PR project entry: GenBank ... ok
test_dblink (test_GenBank_unittest.GenBankTests)
GenBank record with old DBLINK project entry. ... ok
test_dblink_two (test_GenBank_unittest.GenBankTests)
GenBank record with old and new DBLINK project entries. ... ok
test_dot_lineage (test_GenBank_unittest.GenBankTests)
Missing taxonomy lineage. ... ok
test_genbank_bad_loc_wrap_parsing (test_GenBank_unittest.GenBankTests)
Bad location wrapping. ... ok
test_genbank_read (test_GenBank_unittest.GenBankTests)
GenBank.read(...) simple test. ... ok
test_genbank_read_invalid (test_GenBank_unittest.GenBankTests)
GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok
test_genbank_read_multirecord (test_GenBank_unittest.GenBankTests)
GenBank.read(...) error on multiple record input. ... ok
test_genbank_read_no_origin_no_end (test_GenBank_unittest.GenBankTests)
GenBank.read(...) error on malformed file. ... ok
test_invalid_product_line_raises_value_error (test_GenBank_unittest.GenBankTests)
Parsing invalid product line. ... ok
test_locus_line_topogoly (test_GenBank_unittest.GenBankTests)
Test if chromosome topology is conserved ... ok
test_long_names (test_GenBank_unittest.GenBankTests)
Various GenBank names which push the column based LOCUS line. ... ok
test_negative_location (test_GenBank_unittest.GenBankTests)
Negative feature locations. ... ok
test_structured_comment_parsing (test_GenBank_unittest.GenBankTests)
Structued comment parsing. ... ok
test_mad_dots (test_GenBank_unittest.OutputTests)
Writing and reading back accesssion.version variants. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.871 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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) ... ok
test_add_track_error (test_GenomeDiagram.DiagramTest)
Test adding unspecified track. ... ok
test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest) ... ok
test_del_tracks (test_GenomeDiagram.DiagramTest) ... 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) ... ok
test_move_track (test_GenomeDiagram.DiagramTest) ... 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_small_arrow_heads (test_GenomeDiagram.SigilsTest)
Feature arrow sigil heads within bounding box. ... ok
----------------------------------------------------------------------
Ran 1 test in 59.887 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 <type 'exceptions.TypeError'>: makeT1Font() argument 2 must be string, not None
----------------------------------------------------------------------
Ran 1 test in 1.019 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GraphicsChromosome.py
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 23.110 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GraphicsDistribution.py
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 2.885 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GraphicsGeneral.py
test_GraphicsGeneral ... ok
test_simple_scatter_plot (test_GraphicsGeneral.ComparativeTest)
Test creation of a simple ScatterPlot. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.797 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_HMMCasino.py
test_HMMCasino ... ok
runTest (__main__.ComparisonTestCase)
test_HMMCasino ... ok
----------------------------------------------------------------------
Ran 1 test in 20.686 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_HMMGeneral.py
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)
Test a non-ergodic model (meaning that some transitions are not ... 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
----------------------------------------------------------------------
Ran 1 test in 0.949 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KDTree.py
test_KDTree ... ok
test_KDTree (test_KDTree.KDTreeTest) ... ok
test_KDTree_neighbour (test_KDTree.KDTreeTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 15.705 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KEGG.py
test_KEGG ... ok
runTest (__main__.ComparisonTestCase)
test_KEGG ... ok
----------------------------------------------------------------------
Ran 1 test in 0.299 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KEGG_online.py
test_KEGG_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.042 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KGML_graphics.py
test_KGML_graphics ... skipping. Install at least reportlab 2.7 for transparency support.
----------------------------------------------------------------------
Ran 1 test in 0.320 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KGML_graphics_online.py
test_KGML_graphics_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.027 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 34.371 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KeyWList.py
test_KeyWList ... ok
test_parse (test_KeyWList.KeyWListTest)
Parsing keywlist.txt ... ok
test_parse2 (test_KeyWList.KeyWListTest)
Parsing keywlist2.txt (without header and footer) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.208 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Location.py
test_Location ... ok
runTest (__main__.ComparisonTestCase)
test_Location ... ok
----------------------------------------------------------------------
Ran 1 test in 0.876 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_LogisticRegression.py
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 1.620 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_MMCIF.py
test_MMCIF ... ok
testModels (test_MMCIF.ParseReal)
Test file with multiple models ... ok
test_filehandle (test_MMCIF.ParseReal)
Test if the parser can handle file handle as well as filename ... ok
test_insertions (test_MMCIF.ParseReal)
Test file with residue insertion codes ... ok
test_parsers (test_MMCIF.ParseReal)
Extract polypeptides from 1A80. ... ok
----------------------------------------------------------------------
Ran 1 test in 54.064 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_MSAProbs_tool.py
test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython.
----------------------------------------------------------------------
Ran 1 test in 1.397 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Mafft_tool.py
test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.941 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_MarkovModel.py
test_MarkovModel ... ok
test_baum_welch (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_visible (test_MarkovModel.TestMarkovModel) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.174 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 0.068 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Muscle_tool.py
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 1.325 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NACCESS_tool.py
test_NACCESS_tool ... skipping. Install naccess if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.982 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NCBITextParser.py
test_NCBITextParser ... ok
test_conversion (test_NCBITextParser.TestBlastRecord)
Test converting a Blast record multiple alignment ... ok
test_text_2010L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output (text_2010L_blastn_001) ... ok
test_text_2010L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output without alignments (text_2010L_blastn_002) ... ok
test_text_2010L_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output without descriptions (text_2010L_blastn_003) ... ok
test_text_2010L_blastn_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output (text_2010L_blastn_004) ... ok
test_text_2010L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_001) ... ok
test_text_2010L_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output without hits (text_2010L_blastp_002) ... ok
test_text_2010L_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_003) ... ok
test_text_2010L_blastp_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output without descriptions (text_2010L_blastp_004) ... ok
test_text_2010L_blastp_005 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output without alignments (text_2010L_blastp_005) ... ok
test_text_2010L_blastp_006 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_006) ... ok
test_text_2010L_blastp_007 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_007) ... ok
test_text_2010L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.10 output (text_2010L_blastx_001) ... ok
test_text_2010L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.10 output without hits (text_2010L_blastx_002) ... ok
test_text_2010L_phiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.10 output, one round (text_2010L_phiblast_001) ... ok
test_text_2010L_phiblast_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (text_2010L_phiblast_002) ... ok
test_text_2010L_phiblast_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (text_2010L_phiblast_003) ... ok
test_text_2010L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.10 output (text_2010L_tblastn_001) ... ok
test_text_2010L_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.10 output without hits (text_2010L_tblastn_002) ... ok
test_text_2010L_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.0.10 output (text_2010L_tblastx_001) ... ok
test_text_2011L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output (text_2011L_blastn_001) ... ok
test_text_2011L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output without alignments (text_2011L_blastn_002) ... ok
test_text_2011L_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output without descriptions (text_2011L_blastn_003) ... ok
test_text_2011L_blastn_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output (text_2011L_blastn_004) ... ok
test_text_2011L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_001) ... ok
test_text_2011L_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output without hits (text_2011L_blastp_002) ... ok
test_text_2011L_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_003) ... ok
test_text_2011L_blastp_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output without descriptions (text_2011L_blastp_004) ... ok
test_text_2011L_blastp_005 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output without alignments (text_2011L_blastp_005) ... ok
test_text_2011L_blastp_006 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_006) ... ok
test_text_2011L_blastp_007 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_007) ... ok
test_text_2011L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.11 output (text_2011L_blastx_001) ... ok
test_text_2011L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.11 output without hits (text_2011L_blastx_002) ... ok
test_text_2011L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_001) ... ok
test_text_2011L_psiblast_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_002) ... ok
test_text_2011L_psiblast_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_psiblast_003) ... ok
test_text_2011L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.11 output (text_2011L_tblastn_001) ... ok
test_text_2011L_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.11 output without hits (text_2011L_tblastn_002) ... ok
test_text_2011L_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.0.11 output (text_2011L_tblastx_001) ... ok
test_text_2012L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.12 output (text_2012L_psiblast_001) ... ok
test_text_2014L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.14 output (text_2014L_blastn_001) ... ok
test_text_2014L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.14 output (text_2014L_psiblast_001) ... ok
test_text_2201L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.1 output (text_2201L_blastx_001) ... ok
test_text_2202L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.2 output with error messages (text_2202L_blastn_001) ... ok
test_text_2202L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.2 output with missing error messages (text_2202L_blastn_002) ... ok
test_text_2202L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.2 output with multiple records (text_2202L_blastp_001) ... ok
test_text_2208L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.8 output (text_2208L_psiblast_001) ... ok
test_text_2215L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.15 output with no hits (text_2215L_blastx_001) ... ok
test_text_2216L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.16 output (text_2216L_tblastn_001) ... ok
test_text_2220L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.20 output (text_2220L_blastx_001) ... ok
test_text_2220L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.20 output with multiple queries (text_2220L_blastx_002) ... ok
test_text_2221L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.21 output with multiple queries (text_2221L_blastp_001) ... ok
test_text_2222L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.22 output with multiple queries (text_2222L_blastx_001) ... ok
test_text_2222_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.22+ output with multiple queries (text_2222_blastx_001) ... ok
test_text_2226_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.26+ output with no results. ... ok
test_text_2226_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with no results. ... ok
test_text_2226_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with single hsp results. ... ok
test_text_2226_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.26+ with no results. ... ok
test_text_2226_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.26+ with single hsp results. ... ok
test_text_2226_blastx_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.26+ output with no results. ... ok
test_text_2226_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.2.26+ output with no results. ... ok
test_text_2226_tblastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastx_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.2.26+ output with multiple hsp results present. ... ok
test_text_2230_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.30+ output with line of dashes. ... ok
----------------------------------------------------------------------
Ran 1 test in 8.135 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NCBIXML.py
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
----------------------------------------------------------------------
Ran 1 test in 8.317 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NCBI_BLAST_tools.py
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 0.294 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NCBI_qblast.py
test_NCBI_qblast ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.898 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NNExclusiveOr.py
test_NNExclusiveOr ... ok
runTest (__main__.ComparisonTestCase)
test_NNExclusiveOr ... ok
----------------------------------------------------------------------
Ran 1 test in 6.770 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NNGene.py
test_NNGene ... ok
test_representation (test_NNGene.MotifCoderTest)
Convert a sequence into its motif representation. ... ok
test_find (test_NNGene.MotifFinderTest)
Find all motifs in a set of sequences. ... ok
test_find_differences (test_NNGene.MotifFinderTest)
Find the difference in motif counts between two sets of sequences. ... ok
test_motif (test_NNGene.PatternIOTest)
Reading and writing motifs to a file ... ok
test_schema (test_NNGene.PatternIOTest)
Reading and writing schemas to a file. ... ok
test_signature (test_NNGene.PatternIOTest)
Reading and writing signatures to a file. ... ok
test_count (test_NNGene.PatternRepositoryTest)
Retrieve counts for particular patterns in the repository. ... ok
test_get_all (test_NNGene.PatternRepositoryTest)
Retrieve all patterns from a repository. ... ok
test_get_differing (test_NNGene.PatternRepositoryTest)
Retrieve patterns from both sides of the list (top and bottom). ... ok
test_get_random (test_NNGene.PatternRepositoryTest)
Retrieve random patterns from the repository. ... ok
test_get_top (test_NNGene.PatternRepositoryTest)
Retrieve a certain number of the top patterns. ... ok
test_get_top_percentage (test_NNGene.PatternRepositoryTest)
Retrieve the top percentge of patterns from the repository. ... ok
test_remove_polyA (test_NNGene.PatternRepositoryTest)
Test the ability to remove A rich patterns from the repository. ... ok
test_representation (test_NNGene.SchemaCoderTest)
Convert a string into a representation of motifs. ... ok
test_easy_from_motifs (test_NNGene.SchemaFactoryTest)
Generating schema from a simple list of motifs. ... ok
test_hard_from_motifs (test_NNGene.SchemaFactoryTest)
Generating schema from a real life set of motifs. ... ok
test_schema_representation (test_NNGene.SchemaFactoryTest)
Convert sequences into schema representations. ... ok
test_find (test_NNGene.SchemaFinderTest)
Find schemas from sequence inputs. ... ok
test_find_differences (test_NNGene.SchemaFinderTest)
Find schemas that differentiate between two sets of sequences. ... ok
runTest (test_NNGene.SchemaMatchingTest)
SchemaMatchingTest:Matching schema to strings works correctly. ... ok
test_all_unambiguous (test_NNGene.SchemaTest)
Return all unambiguous characters that can be in a motif. ... ok
test_find_ambiguous (test_NNGene.SchemaTest)
Find the positions of ambiguous items in a sequence. ... ok
test_find_matches (test_NNGene.SchemaTest)
Find all matches in a sequence. ... ok
test_motif_cache (test_NNGene.SchemaTest)
Make sure motif compiled regular expressions are cached properly. ... ok
test_num_ambiguous (test_NNGene.SchemaTest)
Find the number of ambiguous items in a sequence. ... ok
test_num_matches (test_NNGene.SchemaTest)
Find how many matches are present in a sequence. ... ok
test_representation (test_NNGene.SignatureCoderTest)
Convert a sequence into its signature representation. ... ok
test_find (test_NNGene.SignatureFinderTest)
Find signatures from sequence inputs. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.365 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NNGeneral.py
test_NNGeneral ... ok
test_adding_examples (test_NNGeneral.ExampleManagerTest)
Make sure test examples are added properly. ... ok
test_partioning_examples (test_NNGeneral.ExampleManagerTest)
Test that we can change how to partition the test examples. ... ok
test_validation_increase_stop (test_NNGeneral.StopTrainingTest)
Stop training when the ValidationExamples increase. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.217 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NaiveBayes.py
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 0.081 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Nexus.py
test_Nexus ... ok
test_NexusTest1 (test_Nexus.NexusTest1)
Test Nexus module ... ok
test_TreeTest1 (test_Nexus.NexusTest1)
Test Tree module. ... ok
test_WriteToFileName (test_Nexus.NexusTest1)
Test writing to a given filename. ... ok
test_internal_node_labels (test_Nexus.NexusTest1)
Handle text labels on internal nodes. ... ok
test_large_newick (test_Nexus.NexusTest1) ... ok
test_write_with_dups (test_Nexus.NexusTest1) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.826 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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
testOutputFileValid (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 3.640 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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
testOutputFileValid (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
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, in response to bug #453, where ... ok
testTreeSpecified (test_PAML_codeml.ModTest) ... ok
testWorkingDirValid (test_PAML_codeml.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 12.259 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 2.117 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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
testOutputFileValid (test_PAML_yn00.ModTest) ... ok
testParseAllVersions (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 2.280 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_atom_copy (test_PDB.CopyTests) ... ok
test_entitity_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) ... 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_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_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_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_transform (test_PDB.TransformTests)
Transform entities (rotation and translation). ... 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 38.442 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PDB_KDTree.py
test_PDB_KDTree ... ok
test_neighbor_search (test_PDB_KDTree.NeighborTest)
NeighborSearch: Find nearby randomly generated coordinates. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.245 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_ParserSupport.py
test_ParserSupport ... ok
runTest (__main__.ComparisonTestCase)
test_ParserSupport ... ok
----------------------------------------------------------------------
Ran 1 test in 0.286 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Pathway.py
test_Pathway ... 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
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 0.079 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phd.py
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 1.508 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phylo.py
test_Phylo ... ok
test_convert (test_Phylo.IOTests)
Convert a tree between all supported formats. ... ok
test_convert_phyloxml_binary (test_Phylo.IOTests)
Try writing phyloxml to a binary handle; fail on Py3. ... ok
test_convert_phyloxml_filename (test_Phylo.IOTests)
Write phyloxml to a given filename. ... ok
test_convert_phyloxml_text (test_Phylo.IOTests)
Write phyloxml to a text handle. ... ok
test_format_branch_length (test_Phylo.IOTests)
Custom format string for Newick branch length serialization. ... ok
test_int_labels (test_Phylo.IOTests)
Read newick formatted tree with numeric labels. ... ok
test_newick_read_multiple (test_Phylo.IOTests)
Parse a Nexus file with multiple trees. ... ok
test_newick_read_scinot (test_Phylo.IOTests)
Parse Newick branch lengths in scientific notation. ... ok
test_newick_read_single1 (test_Phylo.IOTests)
Read first Newick file with one tree. ... ok
test_newick_read_single2 (test_Phylo.IOTests)
Read second Newick file with one tree. ... ok
test_newick_read_single3 (test_Phylo.IOTests)
Read Nexus file with one tree. ... ok
test_newick_write (test_Phylo.IOTests)
Parse a Nexus file with multiple trees. ... ok
test_phylo_read_extra (test_Phylo.IOTests)
Additional tests to check correct parsing ... ok
test_unicode_exception (test_Phylo.IOTests)
Read a Newick file with a unicode byte order mark (BOM). ... ok
test_collapse (test_Phylo.MixinTests)
TreeMixin: collapse() method. ... ok
test_collapse_all (test_Phylo.MixinTests)
TreeMixin: collapse_all() method. ... ok
test_common_ancestor (test_Phylo.MixinTests)
TreeMixin: common_ancestor() method. ... ok
test_depths (test_Phylo.MixinTests)
TreeMixin: depths() method. ... ok
test_distance (test_Phylo.MixinTests)
TreeMixin: distance() method. ... ok
test_find_clades (test_Phylo.MixinTests)
TreeMixin: find_clades() method. ... ok
test_find_elements (test_Phylo.MixinTests)
TreeMixin: find_elements() method. ... ok
test_find_terminal (test_Phylo.MixinTests)
TreeMixin: find_elements() with terminal argument. ... ok
test_get_path (test_Phylo.MixinTests)
TreeMixin: get_path() method. ... ok
test_is_bifurcating (test_Phylo.MixinTests)
TreeMixin: is_bifurcating() method. ... ok
test_is_monophyletic (test_Phylo.MixinTests)
TreeMixin: is_monophyletic() method. ... ok
test_ladderize (test_Phylo.MixinTests)
TreeMixin: ladderize() method. ... ok
test_prune (test_Phylo.MixinTests)
TreeMixin: prune() method. ... ok
test_split (test_Phylo.MixinTests)
TreeMixin: split() method. ... ok
test_total_branch_length (test_Phylo.MixinTests)
TreeMixin: total_branch_length() method. ... ok
test_trace (test_Phylo.MixinTests)
TreeMixin: trace() method. ... ok
test_randomized (test_Phylo.TreeTests)
Tree.randomized: generate a new randomized tree. ... ok
test_root_at_midpoint (test_Phylo.TreeTests)
Tree.root_at_midpoint: reroot at the tree's midpoint. ... ok
test_root_with_outgroup (test_Phylo.TreeTests)
Tree.root_with_outgroup: reroot at a given clade. ... ok
test_str (test_Phylo.TreeTests)
Tree.__str__: pretty-print to a string. ... ok
----------------------------------------------------------------------
Ran 1 test in 10.741 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PhyloXML.py
test_PhyloXML ... ok
test_clade_getitem (test_PhyloXML.MethodTests)
Clade.__getitem__: get sub-clades by extended indexing. ... ok
test_clade_to_phylogeny (test_PhyloXML.MethodTests)
Convert a Clade object to a new Phylogeny. ... ok
test_color_hex (test_PhyloXML.MethodTests)
BranchColor: to_hex() method. ... ok
test_events (test_PhyloXML.MethodTests)
Events: Mapping-type behavior. ... ok
test_phylogeny_to_phyloxml (test_PhyloXML.MethodTests)
Convert a Phylogeny object to a new Phyloxml. ... ok
test_phyloxml_getitem (test_PhyloXML.MethodTests)
Phyloxml.__getitem__: get phylogenies by name or index. ... ok
test_sequence_conversion (test_PhyloXML.MethodTests) ... ok
test_singlular (test_PhyloXML.MethodTests)
Clade, Phylogeny: Singular properties for plural attributes. ... ok
test_to_alignment (test_PhyloXML.MethodTests) ... ok
test_parse_apaf (test_PhyloXML.ParseTests)
Parse the phylogenies in apaf.xml. ... ok
test_parse_bcl2 (test_PhyloXML.ParseTests)
Parse the phylogenies in bcl_2.xml. ... ok
test_parse_dollo (test_PhyloXML.ParseTests)
Parse the phylogenies in o_tol_332_d_dollo.xml. ... ok
test_parse_made (test_PhyloXML.ParseTests)
Parse the phylogenies in made_up.xml. ... ok
test_parse_phylo (test_PhyloXML.ParseTests)
Parse the phylogenies in phyloxml_examples.xml. ... ok
test_read_apaf (test_PhyloXML.ParseTests)
Read apaf.xml to produce a phyloXML object. ... ok
test_read_bcl2 (test_PhyloXML.ParseTests)
Read bcl_2.xml to produce a phyloXML object. ... ok
test_read_dollo (test_PhyloXML.ParseTests)
Read o_tol_332_d_dollo.xml to produce a phyloXML object. ... ok
test_read_made (test_PhyloXML.ParseTests)
Read made_up.xml to produce a phyloXML object. ... ok
test_read_phylo (test_PhyloXML.ParseTests)
Read phyloxml_examples.xml to produce a phyloXML object. ... ok
test_shape_apaf (test_PhyloXML.ParseTests)
Check the branching structure of apaf.xml. ... ok
test_shape_bcl2 (test_PhyloXML.ParseTests)
Check the branching structure of bcl_2.xml. ... ok
test_shape_dollo (test_PhyloXML.ParseTests)
Check the branching structure of o_tol_332_d_dollo.xml. ... ok
test_shape_phylo (test_PhyloXML.ParseTests)
Check the branching structure of phyloxml_examples.xml. ... ok
test_Annotation (test_PhyloXML.TreeTests)
Instantiation of Annotation objects. ... ok
test_BinaryCharacters (test_PhyloXML.TreeTests)
Instantiation of BinaryCharacters objects. ... ok
test_Clade (test_PhyloXML.TreeTests)
Instantiation of Clade objects. ... ok
test_CladeRelation (test_PhyloXML.TreeTests)
Instantiation of CladeRelation objects. ... ok
test_Confidence (test_PhyloXML.TreeTests)
Instantiation of Confidence objects. ... ok
test_Date (test_PhyloXML.TreeTests)
Instantiation of Date objects. ... ok
test_Distribution (test_PhyloXML.TreeTests)
Instantiation of Distribution objects. ... ok
test_DomainArchitecture (test_PhyloXML.TreeTests)
Instantiation of DomainArchitecture objects. ... ok
test_Events (test_PhyloXML.TreeTests)
Instantiation of Events objects. ... ok
test_Other (test_PhyloXML.TreeTests)
Instantiation of Other objects. ... ok
test_Phylogeny (test_PhyloXML.TreeTests)
Instantiation of Phylogeny objects. ... ok
test_Phyloxml (test_PhyloXML.TreeTests)
Instantiation of Phyloxml objects. ... ok
test_Polygon (test_PhyloXML.TreeTests)
Instantiation of Polygon objects. ... ok
test_Property (test_PhyloXML.TreeTests)
Instantiation of Property objects. ... ok
test_Reference (test_PhyloXML.TreeTests)
Instantiation of Reference objects. ... ok
test_Sequence (test_PhyloXML.TreeTests)
Instantiation of Sequence objects. ... ok
test_SequenceRelation (test_PhyloXML.TreeTests)
Instantiation of SequenceRelation objects. ... ok
test_Taxonomy (test_PhyloXML.TreeTests)
Instantiation of Taxonomy objects. ... ok
test_Uri (test_PhyloXML.TreeTests)
Instantiation of Uri objects. ... ok
test_apaf (test_PhyloXML.WriterTests)
Round-trip parsing and serialization of apaf.xml. ... ok
test_bcl2 (test_PhyloXML.WriterTests)
Round-trip parsing and serialization of bcl_2.xml. ... ok
test_dollo (test_PhyloXML.WriterTests)
Round-trip parsing and serialization of o_tol_332_d_dollo.xml. ... ok
test_made (test_PhyloXML.WriterTests)
Round-trip parsing and serialization of made_up.xml. ... ok
test_phylo (test_PhyloXML.WriterTests)
Round-trip parsing and serialization of phyloxml_examples.xml. ... ok
----------------------------------------------------------------------
Ran 1 test in 15.406 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phylo_CDAO.py
test_Phylo_CDAO ... ok
test_parse_0 (test_Phylo_CDAO.ParseTests)
Parse the phylogenies in test.cdao. ... ok
test_write_0 (test_Phylo_CDAO.WriterTests)
Write and re-parse the phylogenies in test.cdao. ... ok
----------------------------------------------------------------------
Ran 1 test in 14.574 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phylo_NeXML.py
test_Phylo_NeXML ... ok
test_parse_0 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in characters.xml. ... ok
test_parse_1 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in edgelabels.xml. ... ok
test_parse_10 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in treebase-record.xml. ... ok
test_parse_11 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in trees-uris.xml. ... ok
test_parse_12 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in trees.xml. ... ok
test_parse_2 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in meta_taxa.xml. ... ok
test_parse_3 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in meta_types.xml. ... ok
test_parse_4 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in nexml.xml. ... ok
test_parse_5 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in phenoscape.xml. ... ok
test_parse_6 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in sets.xml. ... ok
test_parse_7 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in taxa.xml. ... ok
test_parse_8 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in timetree.xml. ... ok
test_parse_9 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in tolweb.xml. ... ok
test_write_1 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in edgelabels.xml. ... ok
test_write_10 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in treebase-record.xml. ... ok
test_write_11 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in trees-uris.xml. ... ok
test_write_12 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in trees.xml. ... ok
test_write_6 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in sets.xml. ... ok
test_write_8 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in timetree.xml. ... ok
test_write_9 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in tolweb.xml. ... ok
----------------------------------------------------------------------
Ran 1 test in 3.676 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phylo_matplotlib.py
test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils.
----------------------------------------------------------------------
Ran 1 test in 2.077 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phylo_networkx.py
test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo
----------------------------------------------------------------------
Ran 1 test in 2.189 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_DFDist.py
test_PopGen_DFDist ... skipping. Install Dfdist, Ddatacal, pv2 and cplot2 if you want to use DFDist with Bio.PopGen.FDist.
----------------------------------------------------------------------
Ran 1 test in 0.119 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_FDist.py
test_PopGen_FDist ... skipping. Install fdist2, datacal, pv and cplot if you want to use FDist2 with Bio.PopGen.FDist.
----------------------------------------------------------------------
Ran 1 test in 0.098 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_FDist_nodepend.py
test_PopGen_FDist_nodepend ... /builddir/build/BUILD/python-biopython-1.68/python2/build/lib.linux-armv7l-2.7/Bio/PopGen/FDist/__init__.py:28: BiopythonDeprecationWarning: Bio.PopGen.FDist has been deprecated, and we intend to remove it in a future release of Biopython. If you would like to continue using it, please contact the Biopython developers via the mailing list.
  " via the mailing list.", BiopythonDeprecationWarning)
ok
test_convert (test_PopGen_FDist_nodepend.ConversionTest)
Basic conversion test. ... ok
test_convert_big (test_PopGen_FDist_nodepend.ConversionTest)
Big interface conversion test. ... ok
test_record_parser (test_PopGen_FDist_nodepend.ParserTest)
Basic operation of the Record Parser. ... ok
test_record_basic (test_PopGen_FDist_nodepend.RecordTest)
Basic test on Record ... ok
----------------------------------------------------------------------
Ran 1 test in 0.107 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_FastSimCoal.py
test_PopGen_FastSimCoal ... skipping. Install fastsimcoal if you want to use Bio.PopGen.SimCoal.Controller.FastSimCoalController.
----------------------------------------------------------------------
Ran 1 test in 0.254 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_GenePop.py
test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.290 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py
test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.255 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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 0.086 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_SimCoal.py
test_PopGen_SimCoal ... skipping. Install SIMCOAL2 if you want to use Bio.PopGen.SimCoal.
----------------------------------------------------------------------
Ran 1 test in 0.237 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_SimCoal_nodepend.py
test_PopGen_SimCoal_nodepend ... ok
test_template_full (test_PopGen_SimCoal_nodepend.TemplateTest)
Full template creation test ... ok
----------------------------------------------------------------------
Ran 1 test in 0.216 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Prank_tool.py
test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 1.300 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Probcons_tool.py
test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 1.299 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_ProtParam.py
test_ProtParam ... ok
test_aromaticity (test_ProtParam.ProtParamTest)
Test calculating protein aromaticity ... ok
test_count_amino_acids (test_ProtParam.ProtParamTest)
Test getting amino acid counts ... ok
test_flexibility (test_ProtParam.ProtParamTest)
Test calculating protein flexibility ... ok
test_get_amino_acids_percent (test_ProtParam.ProtParamTest)
Test getting amino acid percentage ... ok
test_get_molecular_weight (test_ProtParam.ProtParamTest)
Test calculating protein molecular weight ... ok
test_get_molecular_weight_identical (test_ProtParam.ProtParamTest)
Test calculating the protein molecular weight agrees with calculation from Bio.SeqUtils ... ok
test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest)
Test calculating the monoisotopic molecular weight ... ok
test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest)
Test calculating the protein molecular weight agrees with calculation from Bio.SeqUtils ... ok
test_gravy (test_ProtParam.ProtParamTest)
Test calculating gravy ... ok
test_instability_index (test_ProtParam.ProtParamTest)
Test calculating protein instability index ... ok
test_isoelectric_point (test_ProtParam.ProtParamTest)
Test calculating the isoelectric point ... ok
test_protein_scale (test_ProtParam.ProtParamTest)
Test calculating the Kite Doolittle scale ... ok
test_secondary_structure_fraction (test_ProtParam.ProtParamTest)
Test calculating secondary structure fractions ... ok
----------------------------------------------------------------------
Ran 1 test in 1.023 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_QCPSuperimposer.py
test_QCPSuperimposer ... ok
runTest (__main__.ComparisonTestCase)
test_QCPSuperimposer ... ok
----------------------------------------------------------------------
Ran 1 test in 0.984 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 37.216 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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)
Comparison operators between iso and neoschizomers. ... ok
test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest)
Make sure print_as('map'); print_that() does not error on wrap round with no markers. ... ok
test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest)
Make sure print_as('map'); print_that() does not error on wrap round with marker. ... ok
test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest)
Make sure print_as('map'); print_that() does not error on wrap round with marker restricted. ... 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_circular_sequences (test_Restriction.SimpleEnzyme)
Deal with cutting circular sequences. ... ok
test_eco_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with EcoRI. ... ok
----------------------------------------------------------------------
Ran 1 test in 3.856 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 1.424 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 1.289 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Des.py
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 1.252 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Dom.py
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 1.254 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 1.251 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Raf.py
test_SCOP_Raf ... ok
testParse (test_SCOP_Raf.RafTests)
Can we 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 1.346 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 1.264 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Scop.py
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 1.323 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_online.py
test_SCOP_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.024 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SVDSuperimposer.py
test_SVDSuperimposer ... ok
runTest (__main__.ComparisonTestCase)
test_SVDSuperimposer ... ok
----------------------------------------------------------------------
Ran 1 test in 0.041 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blast_tab.py
test_SearchIO_blast_tab ... ok
test_tab_2226_tblastn_001 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_001) ... ok
test_tab_2226_tblastn_002 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_002) ... ok
test_tab_2226_tblastn_003 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_003) ... ok
test_tab_2226_tblastn_004 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_004) ... ok
test_tab_2226_tblastn_005 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_005) ... ok
test_tab_2226_tblastn_006 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_006) ... ok
test_tab_2226_tblastn_007 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_007) ... ok
test_tab_2226_tblastn_008 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_008) ... ok
test_tab_2226_tblastn_009 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_009) ... ok
test_tab_2226_tblastn_010 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_010) ... ok
test_tab_2226_tblastn_011 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_011) ... ok
test_tab_2226_tblastn_012 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_012) ... ok
test_tab_2226_tblastn_013 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_013) ... ok
test_tab_2228_tblastn_001 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.28+ tabular output (tab_2228_tblastn_001) ... ok
test_tab_2228_tblastx_001 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTX 2.2.28+ tabular output (tab_2228_tblastx_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.941 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blast_tab_index.py
test_SearchIO_blast_tab_index ... ok
test_blasttab_2226_tblastn_001 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, multiple queries ... ok
test_blasttab_2226_tblastn_002 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, single query, no hits ... ok
test_blasttab_2226_tblastn_004 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, single query, multiple hits ... ok
test_blasttab_2226_tblastn_005 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, multiple queries, commented ... ok
test_blasttab_2226_tblastn_006 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, single query, no hits, commented ... ok
test_blasttab_2226_tblastn_009 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, custom columns ... ok
test_blasttab_2226_tblastn_010 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, custom columns, commented ... ok
test_blasttab_2226_tblastn_011 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, all columns, commented ... ok
test_blasttab_comment_sing (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, single query, multiple hits, commented ... ok
test_blasttab_2226_multiple_first (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, first (tab_2226_tblastn_001.txt) ... ok
test_blasttab_2226_multiple_first_commented (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, first, commented (tab_2226_tblastn_005.txt) ... ok
test_blasttab_2226_multiple_last (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, last (tab_2226_tblastn_001.txt) ... ok
test_blasttab_2226_multiple_last_commented (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, last, commented (tab_2226_tblastn_005.txt) ... ok
test_blasttab_2226_multiple_middle_commented (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, middle, commented (tab_2226_tblastn_005.txt) ... ok
test_blasttab_2226_single (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt) ... ok
test_blasttab_2226_single_commented (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, single query, commented (tab_2226_tblastn_008.txt) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.204 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blast_text.py
test_SearchIO_blast_text ... ok
test_text_2226_blastn_001 (test_SearchIO_blast_text.BlastnCases)
Test parsing blastn output (text_2226_blastn_001.txt) ... ok
test_text_2226_blastn_002 (test_SearchIO_blast_text.BlastnCases)
Test parsing blastn output (text_2226_blastn_002.txt) ... ok
test_text_2226_blastn_003 (test_SearchIO_blast_text.BlastnCases)
Test parsing blastn output (text_2226_blastn_003.txt) ... ok
test_text_2226_blastn_004 (test_SearchIO_blast_text.BlastnCases)
Test parsing blastn output (text_2226_blastn_004.txt) ... ok
test_text_2226_blastp_001 (test_SearchIO_blast_text.BlastpCases)
Test parsing blastp output (text_2226_blastp_001.txt) ... ok
test_text_2226_blastp_002 (test_SearchIO_blast_text.BlastpCases)
Test parsing blastp output (text_2226_blastp_002.txt) ... ok
test_text_2226_blastp_003 (test_SearchIO_blast_text.BlastpCases)
Test parsing blastp output (text_2226_blastp_003.txt) ... ok
test_text_2226_blastp_004 (test_SearchIO_blast_text.BlastpCases)
Test parsing blastp output (text_2226_blastp_004.txt) ... ok
test_text_2226_blastx_001 (test_SearchIO_blast_text.BlastxCases)
Test parsing blastx output (text_2226_blastx_001.txt) ... ok
test_text_2226_blastx_002 (test_SearchIO_blast_text.BlastxCases)
Test parsing blastx output (text_2226_blastx_002.txt) ... ok
test_text_2226_blastx_003 (test_SearchIO_blast_text.BlastxCases)
Test parsing blastx output (text_2226_blastx_003.txt) ... ok
test_text_2226_blastx_004 (test_SearchIO_blast_text.BlastxCases)
Test parsing blastx output (text_2226_blastx_004.txt) ... ok
test_text_2226_tblastn_001 (test_SearchIO_blast_text.TblastnCases)
Test parsing tblastn output (text_2226_tblastn_001.txt) ... ok
test_text_2226_tblastn_002 (test_SearchIO_blast_text.TblastnCases)
Test parsing tblastn output (text_2226_tblastn_002.txt) ... ok
test_text_2226_tblastn_003 (test_SearchIO_blast_text.TblastnCases)
Test parsing tblastn output (text_2226_tblastn_003.txt) ... ok
test_text_2226_tblastn_004 (test_SearchIO_blast_text.TblastnCases)
Test parsing tblastn output (text_2226_tblastn_004.txt) ... ok
test_text_2226_tblastx_001 (test_SearchIO_blast_text.TblastxCases)
Test parsing tblastx output (text_2226_tblastx_001.txt) ... ok
test_text_2226_tblastx_002 (test_SearchIO_blast_text.TblastxCases)
Test parsing tblastx output (text_2226_tblastx_002.txt) ... ok
test_text_2226_tblastx_003 (test_SearchIO_blast_text.TblastxCases)
Test parsing tblastx output (text_2226_tblastx_003.txt) ... ok
test_text_2226_tblastx_004 (test_SearchIO_blast_text.TblastxCases)
Test parsing tblastx output (text_2226_tblastx_004.txt) ... ok
test_text_2230_blastp_001 (test_SearchIO_blast_text.TblastxCases)
Test parsing blastp output (text_2230_blastp_001.txt) ... ok
----------------------------------------------------------------------
Ran 1 test in 3.464 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blast_xml.py
test_SearchIO_blast_xml ... ok
test_xml_2226_blastn_006 (test_SearchIO_blast_xml.BlastXmlSpecialCases) ... ok
test_xml_2212L_blastn_001 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2226_blastn_001 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2226_blastn_002 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2226_blastn_003 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2226_blastn_004 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2226_blastn_005 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2212L_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2218L_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2218_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2218_blastp_002 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2222_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2226_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2226_blastp_002 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2226_blastp_003 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2226_blastp_004 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2226_blastp_005 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2212L_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2222_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2226_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2226_blastx_002 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2226_blastx_003 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2226_blastx_004 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2212L_tblastn_001 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2226_tblastn_001 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2226_tblastn_002 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2226_tblastn_003 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2226_tblastn_004 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2226_tblastn_005 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2212L_tblastx_001 (test_SearchIO_blast_xml.TblastxXmlCases) ... ok
test_xml_2226_tblastx_001 (test_SearchIO_blast_xml.TblastxXmlCases) ... ok
test_xml_2226_tblastx_002 (test_SearchIO_blast_xml.TblastxXmlCases) ... ok
test_xml_2226_tblastx_003 (test_SearchIO_blast_xml.TblastxXmlCases) ... ok
test_xml_2226_tblastx_004 (test_SearchIO_blast_xml.TblastxXmlCases) ... ok
----------------------------------------------------------------------
Ran 1 test in 5.574 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blast_xml_index.py
test_SearchIO_blast_xml_index ... ok
test_blastxml_2212L_blastp_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BLAST 2.2.12 ... ok
test_blastxml_2218_blastp_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BLAST 2.2.18+ ... ok
test_blastxml_2222_blastx_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BLAST 2.2.22+ ... ok
test_blastxml_2226_tblastn_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BLAST 2.2.26+, multiple queries ... ok
test_blastxml_2226_tblastn_002 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BlAST 2.2.26+, single query, no hits ... ok
test_blastxml_2226_tblastn_004 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BLAST 2.2.26+, single query, multiple hits ... ok
test_blastxml_2226_multiple_first (test_SearchIO_blast_xml_index.BlastXmlRawCases)
Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, first (xml_2226_blastp_001.xml) ... ok
test_blastxml_2226_multiple_last (test_SearchIO_blast_xml_index.BlastXmlRawCases)
Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, last (xml_2226_blastp_001.xml) ... ok
test_blastxml_2226_multiple_middle (test_SearchIO_blast_xml_index.BlastXmlRawCases)
Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, middle (xml_2226_blastp_001.xml) ... ok
test_blastxml_2226_single (test_SearchIO_blast_xml_index.BlastXmlRawCases)
Test blast-xml raw string retrieval, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml) ... ok
----------------------------------------------------------------------
Ran 1 test in 12.821 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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_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
----------------------------------------------------------------------
Ran 1 test in 2.083 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 3.069 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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 2.599 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 1.530 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 1.283 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 2.288 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_fasta_m10_index.py
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 3.323 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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 5.491 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 3.062 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_domtab.py
test_SearchIO_hmmer3_domtab ... ok
test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases)
Test parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001) ... ok
test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases)
Test parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001) ... ok
test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001) ... ok
test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test 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)
Test parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003) ... ok
test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004) ... ok
test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.200 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_domtab_index.py
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 1.459 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_tab.py
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 1.092 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_tab_index.py
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 1.244 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_text.py
test_SearchIO_hmmer3_text ... ok
test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_001) ... ok
test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_002) ... ok
test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_003) ... ok
test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_004) ... ok
test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test 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_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_001) ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_002) ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_003) ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_004) ... ok
test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_005) ... ok
test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_006) ... ok
test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_007) ... ok
test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_008) ... ok
test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_009) ... ok
test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_010) ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.1b1 (text_31b1_hmmscan_001) ... ok
test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases)
Test parsing phmmer 3.1b2 (text_31b2_phmmer_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 3.559 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 2.120 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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_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_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_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: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
----------------------------------------------------------------------
Ran 1 test in 2.133 seconds
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_write.py
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_blatpslx (test_SearchIO_write.BlatPslWriteCases)
Test blat-pslx writing from blat-pslx, single query (pslx_34_004.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 8.112 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqFeature.py
test_SeqFeature ... ok
test_eq_identical (test_SeqFeature.TestReference)
Test two identical references eq() to True ... ok
----------------------------------------------------------------------
Ran 1 test in 1.260 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO.py
test_SeqIO ... ok
runTest (__main__.ComparisonTestCase)
test_SeqIO ... ok
----------------------------------------------------------------------
Ran 1 test in 108.547 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode)
Test if exception is raised if file is not opened in 'rb' mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 3.378 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_FastaIO.py
test_SeqIO_FastaIO ... 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
----------------------------------------------------------------------
Ran 1 test in 1.311 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_Insdc.py
test_SeqIO_Insdc ... /builddir/build/BUILD/python-biopython-1.68/python2/build/lib.linux-armv7l-2.7/Bio/GenBank/Scanner.py:279: 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 1.660 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_PdbIO.py
test_SeqIO_PdbIO ... /builddir/build/BUILD/python-biopython-1.68/python2/build/lib.linux-armv7l-2.7/Bio/SeqIO/PdbIO.py:187: BiopythonWarning: First line is not a 'HEADER'; can't determine PDB ID. Line: 'TITLE     STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND AN\n'
  "Line: %r" % firstline, BiopythonWarning)
/builddir/build/BUILD/python-biopython-1.68/python2/build/lib.linux-armv7l-2.7/Bio/SeqIO/PdbIO.py:187: BiopythonWarning: First line is not a 'HEADER'; can't determine PDB ID. Line: 'REMARK INTRODUCED BUGS IN RESIDUES 2,3,4 AND WAT 67\n'
  "Line: %r" % firstline, BiopythonWarning)
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 PDB by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestPdbAtom)
Read a single-chain PDB by ATOM entries. ... 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 PDB by SEQRES entries. ... ok
----------------------------------------------------------------------
Ran 1 test in 26.733 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
----------------------------------------------------------------------
Ran 1 test in 12.700 seconds
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_SeqXML.py
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 2.872 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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
----------------------------------------------------------------------
Ran 1 test in 2.855 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 14.605 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 identifers with Bio.SeqIO.index() ... ok
test_duplicates_index_db (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifers with Bio.SeqIO.index_db() ... ok
test_duplicates_to_dict (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifers 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_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_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_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_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_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 199.083 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_online.py
test_SeqIO_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.029 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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_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_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_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
----------------------------------------------------------------------
Ran 1 test in 1.853 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqRecord.py
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_eq_exception (test_SeqRecord.SeqRecordMethods) ... ok
test_format (test_SeqRecord.SeqRecordMethods) ... ok
test_ge_exception (test_SeqRecord.SeqRecordMethods) ... ok
test_gt_exception (test_SeqRecord.SeqRecordMethods) ... ok
test_iter (test_SeqRecord.SeqRecordMethods) ... ok
test_le_exception (test_SeqRecord.SeqRecordMethods) ... ok
test_lower (test_SeqRecord.SeqRecordMethods) ... ok
test_ne_exception (test_SeqRecord.SeqRecordMethods) ... ok
test_repr (test_SeqRecord.SeqRecordMethods) ... ok
test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethods) ... ok
test_reverse_complement_seq (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
----------------------------------------------------------------------
Ran 1 test in 4.517 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqUtils.py
test_SeqUtils ... ok
test_GC (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum1 (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum2 (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum3 (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_seq1_seq3 (test_SeqUtils.SeqUtilsTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.462 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Seq_objs.py
test_Seq_objs ... ok
test_init_typeerror (test_Seq_objs.StringMethodTests)
Check Seq __init__ gives TypeError exceptions. ... 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_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_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_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 63.587 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SffIO.py
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_coords (test_SffIO.TestUAN) ... ok
test_region (test_SffIO.TestUAN) ... ok
test_time (test_SffIO.TestUAN) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.621 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SubsMat.py
test_SubsMat ... ok
runTest (__main__.ComparisonTestCase)
test_SubsMat ... ok
----------------------------------------------------------------------
Ran 1 test in 0.745 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SwissProt.py
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 1.989 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_TCoffee_tool.py
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 1.299 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_TogoWS.py
test_TogoWS ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.218 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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 9.223 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_UniGene.py
test_UniGene ... ok
test_parse (test_UniGene.TestUniGene) ... ok
test_read (test_UniGene.TestUniGene) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.218 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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_uni001 (test_Uniprot.TestUniprot)
Parsing Uniprot file uni001 ... ok
test_uni003 (test_Uniprot.TestUniprot)
Parsing Uniprot file uni003 ... ok
----------------------------------------------------------------------
Ran 1 test in 3.627 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Wise.py
test_Wise ... ok
test_align (test_Wise.TestWise)
Call dnal with optional arguments, and do a trivial check on the output. ... ok
test_dnal (test_Wise.TestWiseDryRun)
Call dnal, and do a trivial check on its output. ... ok
test_psw (test_Wise.TestWiseDryRun)
Call psw, and do a trivial check on its output. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.320 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_XXmotif_tool.py
test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython.
----------------------------------------------------------------------
Ran 1 test in 1.301 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_align.py
test_align ... ok
runTest (__main__.ComparisonTestCase)
test_align ... ok
----------------------------------------------------------------------
Ran 1 test in 3.379 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_bgzf.py
test_bgzf ... ok
test_bam_ex1 (test_bgzf.BgzfTests)
Reproduce BGZF compression for BAM file ... ok
test_example_cor6 (test_bgzf.BgzfTests)
Reproduce BGZF compression for cor6_6.gb GenBank file ... ok
test_example_fastq (test_bgzf.BgzfTests)
Reproduce BGZF compression for a FASTQ file ... ok
test_example_gb (test_bgzf.BgzfTests)
Reproduce BGZF compression for NC_000932 GenBank file ... ok
test_example_wnts_xml (test_bgzf.BgzfTests)
Reproduce BGZF compression for wnts.xml BLAST file ... ok
test_iter_bam_ex1 (test_bgzf.BgzfTests)
Check iteration over SamBam/ex1.bam ... ok
test_iter_example_cor6 (test_bgzf.BgzfTests)
Check iteration over GenBank/cor6_6.gb.bgz ... ok
test_iter_example_fastq (test_bgzf.BgzfTests)
Check iteration over Quality/example.fastq.bgz ... ok
test_iter_example_gb (test_bgzf.BgzfTests)
Check iteration over GenBank/NC_000932.gb.bgz ... ok
test_iter_wnts_xml (test_bgzf.BgzfTests)
Check iteration over Blast/wnts.xml.bgz ... ok
test_random_bam_ex1 (test_bgzf.BgzfTests)
Check random access to SamBam/ex1.bam ... ok
test_random_bam_ex1_header (test_bgzf.BgzfTests)
Check random access to SamBam/ex1_header.bam ... ok
test_random_bam_ex1_refresh (test_bgzf.BgzfTests)
Check random access to SamBam/ex1_refresh.bam ... ok
test_random_example_cor6 (test_bgzf.BgzfTests)
Check random access to GenBank/cor6_6.gb.bgz ... ok
test_random_example_dos_fastq (test_bgzf.BgzfTests)
Check random access to Quality/example_dos.fastq.bgz (DOS newlines) ... ok
test_random_example_fastq (test_bgzf.BgzfTests)
Check random access to Quality/example.fastq.bgz (Unix newlines) ... ok
test_random_wnts_xml (test_bgzf.BgzfTests)
Check random access to Blast/wnts.xml.bgz ... ok
test_text_example_fastq (test_bgzf.BgzfTests)
Check text mode access to Quality/example.fastq.bgz ... ok
test_text_wnts_xml (test_bgzf.BgzfTests)
Check text mode access to Blast/wnts.xml.bgz ... ok
test_write_tell (test_bgzf.BgzfTests)
Check offset works during BGZF writing ... ok
----------------------------------------------------------------------
Ran 1 test in 75.548 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_codonalign.py
test_codonalign ... 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
----------------------------------------------------------------------
Ran 1 test in 99.858 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_geo.py
test_geo ... ok
runTest (__main__.ComparisonTestCase)
test_geo ... ok
----------------------------------------------------------------------
Ran 1 test in 0.337 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 0.161 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_lowess.py
test_lowess ... ok
test_Precomputed (test_lowess.test_lowess) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.215 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_mmtf.py
test_mmtf ... skipping. Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.957 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_motifs.py
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_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_mast_parser_1 (test_motifs.TestMAST)
Test if Bio.motifs can parse MAST output files (first test) ... ok
test_mast_parser_2 (test_motifs.TestMAST)
Test if Bio.motifs can parse MAST output files (second test) ... ok
test_mast_parser_3 (test_motifs.TestMAST)
Test if Bio.motifs can parse MAST output files (third test) ... ok
test_meme_parser_1 (test_motifs.TestMEME)
Test if Bio.motifs can parse MEME output files (first test) ... ok
test_meme_parser_2 (test_motifs.TestMEME)
Test if Bio.motifs can parse MEME output files (second test) ... ok
test_meme_parser_3 (test_motifs.TestMEME)
Test if Bio.motifs can parse MEME output files (third test) ... ok
test_meme_parser_4 (test_motifs.TestMEME)
Test if Bio.motifs can parse MEME output files (fourth test) ... ok
test_transfac_parser (test_motifs.TestTransfac)
Test if Bio.motifs can parse TRANSFAC files ... ok
----------------------------------------------------------------------
Ran 1 test in 1.494 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_motifs_online.py
test_motifs_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.868 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_pairwise2.py
test_pairwise2 ... ok
test_clean_alignments (test_pairwise2.TestOtherFunctions)
``_clean_alignments`` removes redundant alignments. ... ok
test_print_matrix (test_pairwise2.TestOtherFunctions)
``print_matrix`` prints nested lists as nice matrices. ... ok
test_function_name (test_pairwise2.TestPairwiseErrorConditions)
Test for wrong function names ... ok
test_function_parameters (test_pairwise2.TestPairwiseErrorConditions)
Test for number of parameteres ... ok
test_extend_penalty1 (test_pairwise2.TestPairwiseExtendPenalty) ... ok
test_extend_penalty2 (test_pairwise2.TestPairwiseExtendPenalty) ... ok
test_globalxx_simple (test_pairwise2.TestPairwiseGlobal) ... ok
test_globalxx_simple2 (test_pairwise2.TestPairwiseGlobal)
Do the same test with sequence order reversed ... ok
test_blosum62 (test_pairwise2.TestPairwiseLocal)
Test localds with blosum62. ... ok
test_localms (test_pairwise2.TestPairwiseLocal)
Two different local alignments ... ok
test_localxs (test_pairwise2.TestPairwiseLocal) ... ok
test_match_dictionary1 (test_pairwise2.TestPairwiseMatchDictionary) ... ok
test_match_dictionary2 (test_pairwise2.TestPairwiseMatchDictionary) ... ok
test_match_dictionary3 (test_pairwise2.TestPairwiseMatchDictionary) ... ok
test_align_one_char1 (test_pairwise2.TestPairwiseOneCharacter) ... ok
test_align_one_char2 (test_pairwise2.TestPairwiseOneCharacter) ... ok
test_align_one_char3 (test_pairwise2.TestPairwiseOneCharacter) ... ok
test_match_score_open_penalty1 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty2 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty3 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty4 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_penalize_end_gaps (test_pairwise2.TestPairwisePenalizeEndgaps) ... ok
test_penalize_end_gaps2 (test_pairwise2.TestPairwisePenalizeEndgaps)
Do the same, but use the generic method (with the same resutlt) ... ok
test_penalize_extend_when_opening (test_pairwise2.TestPairwisePenalizeExtendWhenOpening) ... ok
test_separate_gap_penalties1 (test_pairwise2.TestPairwiseSeparateGapPenalties) ... ok
test_separate_gap_penalties2 (test_pairwise2.TestPairwiseSeparateGapPenalties) ... ok
test_separate_gap_penalties_with_extension (test_pairwise2.TestPairwiseSeparateGapPenaltiesWithExtension) ... ok
test_gap_here_only_1 (test_pairwise2.TestPersiteGapPenalties) ... ok
test_gap_here_only_2 (test_pairwise2.TestPersiteGapPenalties)
Force a bad alignment. ... ok
test_score_only_global (test_pairwise2.TestScoreOnly)
Test ``score_only`` in a global alignment ... ok
test_score_only_local (test_pairwise2.TestScoreOnly)
Test ``score_only`` in a local alignment ... ok
----------------------------------------------------------------------
Ran 1 test in 0.773 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_phenotype.py
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 290.091 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_phenotype_fit.py
test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality.
----------------------------------------------------------------------
Ran 1 test in 0.028 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_phyml_tool.py
test_phyml_tool ... skipping. Install PhyML 3.0 if you want to use the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 2.122 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 0.284 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_prosite1.py
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 0.769 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 0.351 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_psw.py
test_psw ... ok
test_AlignmentColumn_assertions (test_psw.TestPSW) ... ok
test_AlignmentColumn_full (test_psw.TestPSW) ... ok
test_AlignmentColumn_kinds (test_psw.TestPSW) ... ok
test_AlignmentColumn_repr (test_psw.TestPSW) ... ok
test_Alignment_assertions (test_psw.TestPSW) ... ok
test_Alignment_normal (test_psw.TestPSW) ... ok
test_ColumnUnit (test_psw.TestPSW) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.278 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_py3k.py
test_py3k ... ok
test_od (test_py3k.ODTest)
Quick test OrderedDict works. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.191 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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 2.105 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_samtools_tool.py
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 0.259 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 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_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_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_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_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_to_string_method (test_seq.TestMutableSeq)
This method is currently deprecated, probably will need to remove this test soon ... ok
test_truncated_repr (test_seq.TestMutableSeq) ... ok
test_complement_on_proteins (test_seq.TestReverseComplement)
Test complement shouldn't work on a protein! ... 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)
Test reverse complement shouldn't work 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)
Test DNA Seq objects cannot be concatenated with Protein Seq ... ok
test_concatenation_of_ambiguous_and_unambiguous_dna (test_seq.TestSeq)
Test concatenated Seq object with ambiguous and unambiguous DNA ... 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_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition) ... ok
test_addition_dna_with_dna (test_seq.TestSeqAddition) ... ok
test_addition_dna_with_rna (test_seq.TestSeqAddition) ... ok
test_addition_proteins (test_seq.TestSeqAddition) ... ok
test_addition_rna_with_rna (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_more_than_one_stop_codon_type (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_nucletides (test_seq.TestSeqAddition) ... 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_hash (test_seq.TestSeqStringMethods) ... ok
test_less_than_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test __lt__ comparison method ... ok
test_less_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test __lt__ 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_to_string_deprecated_method (test_seq.TestSeqStringMethods) ... ok
test_sequence_alphabets (test_seq.TestSequenceAlphabets)
Sanity test on the test sequence alphabets (see also enhancement ... 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)
Test back-transcription shouldn't work on DNA! ... ok
test_back_transcription_of_proteins (test_seq.TestTranscription)
Test back-transcription shouldn't work 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)
Test transcription shouldn't work on a protein! ... ok
test_transcription_of_rna (test_seq.TestTranscription)
Test transcription shouldn't work on RNA! ... ok
test_alphabet_of_translated_gapped_seq (test_seq.TestTranslating) ... ok
test_alphabets_of_translated_seqs (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_seq_no_gap_char_given (test_seq.TestTranslating) ... ok
test_translation_of_gapped_seq_no_gap_char_given_and_inferred_from_alphabet (test_seq.TestTranslating) ... ok
test_translation_of_gapped_seq_with_gap_char_given (test_seq.TestTranslating) ... ok
test_translation_of_gapped_seq_with_gap_char_given_and_inferred_from_alphabet (test_seq.TestTranslating) ... ok
test_translation_of_gapped_seq_with_gap_char_given_and_inferred_from_alphabet2 (test_seq.TestTranslating)
Test using stop codon in sequence ... ok
test_translation_of_gapped_seq_with_stop_codon_and_gap_char_given (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)
Test translation shouldn't work on a protein! ... ok
test_translation_to_stop (test_seq.TestTranslating) ... ok
test_translation_using_cds (test_seq.TestTranslating) ... 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)
Test reverse complement shouldn't work 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 1.631 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_translate.py
test_translate ... ok
runTest (__main__.ComparisonTestCase)
test_translate ... ok
----------------------------------------------------------------------
Ran 1 test in 0.881 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_trie.py
test_trie ... ok
test_get_approximate (test_trie.TestTrie) ... ok
test_get_set (test_trie.TestTrie) ... 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 0.064 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Aug  5 2017, 23:48:14) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)]
Operating system: posix linux2
~/build/BUILD/python-biopython-1.68
+ popd
+ exit 0
Processing files: python2-biopython-1.68-1.el7.armv7hl
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.y5NC2P
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.68
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python2-biopython-1.68
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python2-biopython-1.68
+ cp -pr python2/Scripts /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python2-biopython-1.68
+ cp -pr python2/CONTRIB /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python2-biopython-1.68
+ cp -pr python2/DEPRECATED /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python2-biopython-1.68
+ cp -pr python2/NEWS /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python2-biopython-1.68
+ cp -pr python2/README /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python2-biopython-1.68
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.urD6er
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.68
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/licenses/python2-biopython-1.68
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/licenses/python2-biopython-1.68
+ cp -pr python2/LICENSE /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/licenses/python2-biopython-1.68
+ exit 0
Provides: python-biopython = 1.68-1.el7 python-biopython(armv7hl-32) = 1.68-1.el7 python2-biopython = 1.68-1.el7 python2-biopython(armv7hl-32) = 1.68-1.el7
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) libpython2.7.so.1.0 python(abi) = 2.7 rtld(GNU_HASH)
Obsoletes: python-biopython < 1.68-1.el7
Processing files: python-biopython-doc-1.68-1.el7.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.XLQaDw
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.68
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python-biopython-doc-1.68
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python-biopython-doc-1.68
+ cp -pr python2/Doc /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python-biopython-doc-1.68
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.wHxXIQ
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.68
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/licenses/python-biopython-doc-1.68
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/licenses/python-biopython-doc-1.68
+ cp -pr python2/LICENSE /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/licenses/python-biopython-doc-1.68
+ exit 0
warning: Recognition of file "/builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm/usr/share/doc/python-biopython-doc-1.68/Doc/examples/ls_orchid.gbk.bgz" failed: mode 100644 zlib: invalid distance too far backempty (gzip compressed data, extra field)
Provides: python-biopython-doc = 1.68-1.el7
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-biopython-debuginfo-1.68-1.el7.armv7hl
Provides: python-biopython-debuginfo = 1.68-1.el7 python-biopython-debuginfo(armv7hl-32) = 1.68-1.el7
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm
Wrote: /builddir/build/RPMS/python2-biopython-1.68-1.el7.armv7hl.rpm
Wrote: /builddir/build/RPMS/python-biopython-doc-1.68-1.el7.noarch.rpm
Wrote: /builddir/build/RPMS/python-biopython-debuginfo-1.68-1.el7.armv7hl.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.05CTXJ
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.68
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.68-1.el7.arm
+ exit 0
Child return code was: 0