Mock Version: 3.1 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1660641787.750759/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v4m0tv5f:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=FalseprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v4m0tv5f:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '13e157f88774477d98c6e5812d68f33e', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1660641787.750759/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v4m0tv5f:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1658448000 Wrote: /builddir/build/SRPMS/python-biopython-1.79-4.fc38.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1660641787.750759/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v4m0tv5f:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=FalseprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v4m0tv5f:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '33ecd07eea974e209cb1ccdba7b99cb0', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1660641787.750759/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.v4m0tv5f:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1658448000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.x50Swm + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf python-biopython-1.79 + /usr/bin/mkdir -p python-biopython-1.79 + cd python-biopython-1.79 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.79.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + pushd biopython-1.79 ~/build/BUILD/python-biopython-1.79/biopython-1.79 ~/build/BUILD/python-biopython-1.79 + find Scripts -type f -exec chmod -x '{}' ';' + find Doc -type f -exec chmod -x '{}' ';' + find Doc -type f -exec sed -i 's/\r//' '{}' ';' + find Bio -type f -exec chmod -x '{}' ';' + find Bio -type f -name '*.py' -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' '{}' ';' + popd ~/build/BUILD/python-biopython-1.79 + cp -a biopython-1.79 python3 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.BmhXEW + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh python-biopython 1.79-4.fc38 x86_64 + cd python-biopython-1.79 + pushd python3 ~/build/BUILD/python-biopython-1.79/python3 ~/build/BUILD/python-biopython-1.79 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP' running build running build_py creating build creating build/lib.linux-x86_64-cpython-311 creating build/lib.linux-x86_64-cpython-311/Bio copying Bio/File.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/LogisticRegression.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/MarkovModel.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/MaxEntropy.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/NaiveBayes.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/Seq.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/SeqFeature.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/SeqRecord.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/_utils.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/bgzf.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/kNN.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/pairwise2.py -> build/lib.linux-x86_64-cpython-311/Bio creating build/lib.linux-x86_64-cpython-311/Bio/Affy copying Bio/Affy/CelFile.py -> build/lib.linux-x86_64-cpython-311/Bio/Affy copying Bio/Affy/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Affy creating build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Align creating build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications creating build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices creating build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO creating build/lib.linux-x86_64-cpython-311/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Alphabet creating build/lib.linux-x86_64-cpython-311/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Application creating build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/NCBIXML.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/Record.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast creating build/lib.linux-x86_64-cpython-311/Bio/CAPS copying Bio/CAPS/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/CAPS creating build/lib.linux-x86_64-cpython-311/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Cluster creating build/lib.linux-x86_64-cpython-311/Bio/codonalign copying Bio/codonalign/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/codonalign copying Bio/codonalign/chisq.py -> build/lib.linux-x86_64-cpython-311/Bio/codonalign copying Bio/codonalign/codonalignment.py -> build/lib.linux-x86_64-cpython-311/Bio/codonalign copying Bio/codonalign/codonseq.py -> build/lib.linux-x86_64-cpython-311/Bio/codonalign creating build/lib.linux-x86_64-cpython-311/Bio/Compass copying Bio/Compass/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Compass creating build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/SCOPData.py -> build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Data creating build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/Primer3.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss creating build/lib.linux-x86_64-cpython-311/Bio/Entrez copying Bio/Entrez/Parser.py -> build/lib.linux-x86_64-cpython-311/Bio/Entrez copying Bio/Entrez/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Entrez creating build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy creating build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/Scanner.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank creating build/lib.linux-x86_64-cpython-311/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-x86_64-cpython-311/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Geo creating build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics creating build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram creating build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM creating build/lib.linux-x86_64-cpython-311/Bio/KEGG copying Bio/KEGG/REST.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Compound creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Enzyme creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Gene creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Map creating build/lib.linux-x86_64-cpython-311/Bio/PDB creating build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML creating build/lib.linux-x86_64-cpython-311/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Medline creating build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/alignace.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/clusterbuster.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/mast.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/matrix.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/meme.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/minimal.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/pfm.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/thresholds.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/transfac.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/xms.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs creating build/lib.linux-x86_64-cpython-311/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/applications creating build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar creating build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/Nexus.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/Nodes.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/StandardData.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/Trees.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus creating build/lib.linux-x86_64-cpython-311/Bio/NMR copying Bio/NMR/NOEtools.py -> build/lib.linux-x86_64-cpython-311/Bio/NMR copying Bio/NMR/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/NMR copying Bio/NMR/xpktools.py -> build/lib.linux-x86_64-cpython-311/Bio/NMR creating build/lib.linux-x86_64-cpython-311/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway creating build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/DSSP.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Dice.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/FragmentMapper.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/HSExposure.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/MMCIFParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/NACCESS.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBList.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PICIO.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PSEA.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/ResidueDepth.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/SASA.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/SCADIO.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/StructureAlignment.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Superimposer.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/ic_data.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/ic_rebuild.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/internal_coords.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/mmcifio.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/vectors.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB creating build/lib.linux-x86_64-cpython-311/Bio/phenotype copying Bio/phenotype/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/phenotype copying Bio/phenotype/phen_micro.py -> build/lib.linux-x86_64-cpython-311/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> build/lib.linux-x86_64-cpython-311/Bio/phenotype creating build/lib.linux-x86_64-cpython-311/Bio/PopGen copying Bio/PopGen/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen creating build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop creating build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/Restriction.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction creating build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/_index.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/_utils.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO creating build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/_index.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO creating build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils creating build/lib.linux-x86_64-cpython-311/Bio/Sequencing copying Bio/Sequencing/Ace.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing copying Bio/Sequencing/Phd.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing copying Bio/Sequencing/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing creating build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications creating build/lib.linux-x86_64-cpython-311/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> build/lib.linux-x86_64-cpython-311/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> build/lib.linux-x86_64-cpython-311/Bio/SubsMat copying Bio/SubsMat/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SubsMat creating build/lib.linux-x86_64-cpython-311/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SVDSuperimposer creating build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer creating build/lib.linux-x86_64-cpython-311/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-x86_64-cpython-311/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SwissProt creating build/lib.linux-x86_64-cpython-311/Bio/TogoWS copying Bio/TogoWS/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/TogoWS creating build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/BaseTree.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/CDAO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/Consensus.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NeXML.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/Newick.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NewickIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NexusIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/_io.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/_utils.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo creating build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications creating build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML creating build/lib.linux-x86_64-cpython-311/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/UniGene creating build/lib.linux-x86_64-cpython-311/Bio/UniProt copying Bio/UniProt/GOA.py -> build/lib.linux-x86_64-cpython-311/Bio/UniProt copying Bio/UniProt/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/UniProt creating build/lib.linux-x86_64-cpython-311/Bio/Wise copying Bio/Wise/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Wise copying Bio/Wise/dnal.py -> build/lib.linux-x86_64-cpython-311/Bio/Wise copying Bio/Wise/psw.py -> build/lib.linux-x86_64-cpython-311/Bio/Wise creating build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/__init__.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/Loader.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-x86_64-cpython-311/BioSQL running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Align.substitution_matrices.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'Bio.Align.substitution_matrices.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'Bio.Align.substitution_matrices.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Entrez.DTDs' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.DTDs' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'Bio.Entrez.DTDs' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'Bio.Entrez.DTDs' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Entrez.XSDs' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.XSDs' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'Bio.Entrez.XSDs' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'Bio.Entrez.XSDs' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying Bio/cpairwise2module.c -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/Align/_aligners.c -> build/lib.linux-x86_64-cpython-311/Bio/Align creating build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> build/lib.linux-x86_64-cpython-311/Bio/Cluster copying Bio/Cluster/cluster.h -> build/lib.linux-x86_64-cpython-311/Bio/Cluster copying Bio/Cluster/clustermodule.c -> build/lib.linux-x86_64-cpython-311/Bio/Cluster creating build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs creating build/lib.linux-x86_64-cpython-311/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/Nexus/cnexus.c -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/PDB/kdtrees.c -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer running build_ext building 'Bio.Align._aligners' extension creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/Bio creating build/temp.linux-x86_64-cpython-311/Bio/Align gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Align/_aligners.c -o build/temp.linux-x86_64-cpython-311/Bio/Align/_aligners.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/Align/_aligners.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/Align/_aligners.cpython-311-x86_64-linux-gnu.so building 'Bio.cpairwise2' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/cpairwise2module.c -o build/temp.linux-x86_64-cpython-311/Bio/cpairwise2module.o Bio/cpairwise2module.c: In function ‘_get_match_score’: Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 60 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist))) | ^~ In file included from /usr/include/python3.11/Python.h:95, from Bio/cpairwise2module.c:16: /usr/include/python3.11/ceval.h:27:43: note: declared here 27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/cpairwise2.cpython-311-x86_64-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-x86_64-cpython-311/Bio/Nexus gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Nexus/cnexus.c -o build/temp.linux-x86_64-cpython-311/Bio/Nexus/cnexus.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/Nexus/cnexus.cpython-311-x86_64-linux-gnu.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-x86_64-cpython-311/Bio/PDB creating build/temp.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-x86_64-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-x86_64-cpython-311/Bio/motifs gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/motifs/_pwm.c -o build/temp.linux-x86_64-cpython-311/Bio/motifs/_pwm.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/motifs/_pwm.cpython-311-x86_64-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-x86_64-cpython-311/Bio/Cluster gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Cluster/cluster.c -o build/temp.linux-x86_64-cpython-311/Bio/Cluster/cluster.o gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Cluster/clustermodule.c -o build/temp.linux-x86_64-cpython-311/Bio/Cluster/clustermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/Cluster/cluster.o build/temp.linux-x86_64-cpython-311/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/Cluster/_cluster.cpython-311-x86_64-linux-gnu.so building 'Bio.PDB.kdtrees' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/kdtrees.c -o build/temp.linux-x86_64-cpython-311/Bio/PDB/kdtrees.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/PDB/kdtrees.cpython-311-x86_64-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-x86_64-cpython-311/Bio/SeqIO gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-x86_64-linux-gnu.so + popd ~/build/BUILD/python-biopython-1.79 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.kpHZfk + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd python-biopython-1.79 + pushd python3 ~/build/BUILD/python-biopython-1.79/python3 ~/build/BUILD/python-biopython-1.79 + /usr/bin/python3 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64 --install-data=/usr/share/python-biopython running install /usr/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running install_lib creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64 creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11 creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/cpairwise2.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise copying build/lib.linux-x86_64-cpython-311/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise copying build/lib.linux-x86_64-cpython-311/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise copying build/lib.linux-x86_64-cpython-311/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniProt copying build/lib.linux-x86_64-cpython-311/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniProt copying build/lib.linux-x86_64-cpython-311/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniProt creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniGene copying build/lib.linux-x86_64-cpython-311/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniGene creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/TogoWS copying build/lib.linux-x86_64-cpython-311/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/TogoWS creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SwissProt copying build/lib.linux-x86_64-cpython-311/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SwissProt copying build/lib.linux-x86_64-cpython-311/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SwissProt creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SubsMat copying build/lib.linux-x86_64-cpython-311/Bio/SubsMat/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SubsMat copying build/lib.linux-x86_64-cpython-311/Bio/SubsMat/MatrixInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SubsMat copying build/lib.linux-x86_64-cpython-311/Bio/SubsMat/FreqTable.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SubsMat creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.c -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/XdnaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/TwoBitIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SnapGeneIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/NibIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/GckIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype copying build/lib.linux-x86_64-cpython-311/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype copying build/lib.linux-x86_64-cpython-311/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype copying build/lib.linux-x86_64-cpython-311/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR copying build/lib.linux-x86_64-cpython-311/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR copying build/lib.linux-x86_64-cpython-311/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR copying build/lib.linux-x86_64-cpython-311/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/cnexus.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/_pwm.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-311/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-311/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-311/Bio/motifs/xms.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/pfm.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/clusterbuster.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Medline copying build/lib.linux-x86_64-cpython-311/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Medline creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/kdtrees.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/internal_coords.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ic_rebuild.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ic_data.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/SCADIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/SASA.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PICIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf/mmtfio.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Map copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Map creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Geo copying build/lib.linux-x86_64-cpython-311/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Geo copying build/lib.linux-x86_64-cpython-311/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Geo creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/XSDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/XSDs creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Compass copying build/lib.linux-x86_64-cpython-311/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Compass creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign copying build/lib.linux-x86_64-cpython-311/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign copying build/lib.linux-x86_64-cpython-311/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign copying build/lib.linux-x86_64-cpython-311/Bio/codonalign/chisq.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign copying build/lib.linux-x86_64-cpython-311/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/_cluster.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/CAPS copying build/lib.linux-x86_64-cpython-311/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/CAPS creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Application copying build/lib.linux-x86_64-cpython-311/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Application creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Alphabet copying build/lib.linux-x86_64-cpython-311/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Alphabet creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/MsfIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/_aligners.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/_aligners.c -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/TRANS -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/STR -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/SCHNEIDER -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/RISLER -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/RAO -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/PAM70 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/PAM30 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/PAM250 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/NUC.4.4 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/MDM78 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/MCLACHLAN -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/LEVIN -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/JONES -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/JOHNSON -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/HOXD70 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/GONNET1992 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/GENETIC -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/FENG -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/DAYHOFF -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM90 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM80 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM62 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM50 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM45 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BENNER74 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BENNER6 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BENNER22 -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align creating /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Affy copying build/lib.linux-x86_64-cpython-311/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Affy copying build/lib.linux-x86_64-cpython-311/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Affy copying build/lib.linux-x86_64-cpython-311/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL/BioSeq.py to BioSeq.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL/DBUtils.py to DBUtils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL/Loader.py to Loader.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise/psw.py to psw.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise/dnal.py to dnal.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniProt/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniProt/GOA.py to GOA.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniGene/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_parse_yn00.py to _parse_yn00.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_parse_codeml.py to _parse_codeml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_parse_baseml.py to _parse_baseml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/_Raxml.py to _Raxml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/_Phyml.py to _Phyml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/_Fasttree.py to _Fasttree.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/_utils.py to _utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/_io.py to _io.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Newick.py to Newick.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/NeXML.py to NeXML.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Consensus.py to Consensus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/CDAO.py to CDAO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/TogoWS/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SwissProt/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SubsMat/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SubsMat/MatrixInfo.py to MatrixInfo.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SubsMat/FreqTable.py to FreqTable.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/_bwa.py to _bwa.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Phd.py to Phd.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Ace.py to Ace.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/lcc.py to lcc.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/CodonUsageIndices.py to CodonUsageIndices.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/CodonUsage.py to CodonUsage.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/_index.py to _index.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/XdnaIO.py to XdnaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/TwoBitIO.py to TwoBitIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SnapGeneIO.py to SnapGeneIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/GckIO.py to GckIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py to hhsuite2_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO/blast_xml.py to blast_xml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO/blast_text.py to blast_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO/blast_tab.py to blast_tab.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/query.py to query.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/hsp.py to hsp.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/hit.py to hit.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/_base.py to _base.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy/ParserSupport.py to ParserSupport.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy/NCBIStandalone.py to NCBIStandalone.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_utils.py to _utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_index.py to _index.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlatIO.py to BlatIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Residues.py to Residues.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Raf.py to Raf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Hie.py to Hie.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Dom.py to Dom.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Des.py to Des.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Cla.py to Cla.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction/Restriction_Dictionary.py to Restriction_Dictionary.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction/Restriction.py to Restriction.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction/PrintFormat.py to PrintFormat.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/LargeFileParser.py to LargeFileParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/FileParser.py to FileParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/EasyController.py to EasyController.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/Controller.py to Controller.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype/pm_fitting.py to pm_fitting.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype/phen_micro.py to phen_micro.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep/MultiGraph.py to MultiGraph.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep/Graph.py to Graph.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR/xpktools.py to xpktools.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR/NOEtools.py to NOEtools.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/Trees.py to Trees.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/StandardData.py to StandardData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/Nodes.py to Nodes.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/Nexus.py to Nexus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar/db.py to db.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/applications/_xxmotif.py to _xxmotif.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/applications/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/xms.py to xms.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/transfac.py to transfac.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/thresholds.py to thresholds.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/pfm.py to pfm.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/minimal.py to minimal.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/meme.py to meme.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/matrix.py to matrix.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/mast.py to mast.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/clusterbuster.py to clusterbuster.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/alignace.py to alignace.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Medline/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/vectors.py to vectors.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/parse_pdb_header.py to parse_pdb_header.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmcifio.py to mmcifio.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/internal_coords.py to internal_coords.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/ic_rebuild.py to ic_rebuild.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/ic_data.py to ic_data.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Superimposer.py to Superimposer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/StructureBuilder.py to StructureBuilder.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/StructureAlignment.py to StructureAlignment.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Structure.py to Structure.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Selection.py to Selection.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/SCADIO.py to SCADIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/SASA.py to SASA.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/ResidueDepth.py to ResidueDepth.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Residue.py to Residue.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Polypeptide.py to Polypeptide.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PSEA.py to PSEA.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PICIO.py to PICIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBParser.py to PDBParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBList.py to PDBList.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBIO.py to PDBIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBExceptions.py to PDBExceptions.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/NeighborSearch.py to NeighborSearch.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/NACCESS.py to NACCESS.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Model.py to Model.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/MMCIFParser.py to MMCIFParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/MMCIF2Dict.py to MMCIF2Dict.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/HSExposure.py to HSExposure.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/FragmentMapper.py to FragmentMapper.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Entity.py to Entity.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Dice.py to Dice.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/DSSP.py to DSSP.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Chain.py to Chain.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Atom.py to Atom.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/AbstractPropertyMap.py to AbstractPropertyMap.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf/mmtfio.py to mmtfio.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf/DefaultParser.py to DefaultParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML/KGML_pathway.py to KGML_pathway.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML/KGML_parser.py to KGML_parser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Map/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/REST.py to REST.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM/Utilities.py to Utilities.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM/Trainer.py to Trainer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM/MarkovModel.py to MarkovModel.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM/DynamicProgramming.py to DynamicProgramming.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/Distribution.py to Distribution.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/Comparative.py to Comparative.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Geo/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Geo/Record.py to Record.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank/utils.py to utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank/Scanner.py to Scanner.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank/Record.py to Record.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/cellosaurus.py to cellosaurus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/Prosite.py to Prosite.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/Prodoc.py to Prodoc.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/Enzyme.py to Enzyme.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/Parser.py to Parser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss/Primer3.py to Primer3.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss/Applications.py to Applications.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data/SCOPData.py to SCOPData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data/IUPACData.py to IUPACData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data/CodonTable.py to CodonTable.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Compass/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/codonseq.py to codonseq.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/codonalignment.py to codonalignment.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/chisq.py to chisq.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/CAPS/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/Record.py to Record.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/ParseBlastTable.py to ParseBlastTable.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/NCBIXML.py to NCBIXML.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/NCBIWWW.py to NCBIWWW.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/Applications.py to Applications.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Application/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Alphabet/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/StockholmIO.py to StockholmIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/PhylipIO.py to PhylipIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/NexusIO.py to NexusIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/MsfIO.py to MsfIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/MauveIO.py to MauveIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/MafIO.py to MafIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/Interfaces.py to Interfaces.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/EmbossIO.py to EmbossIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/ClustalIO.py to ClustalIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_TCoffee.py to _TCoffee.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Probcons.py to _Probcons.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Prank.py to _Prank.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Muscle.py to _Muscle.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Mafft.py to _Mafft.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_MSAProbs.py to _MSAProbs.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Dialign.py to _Dialign.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Clustalw.py to _Clustalw.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_ClustalOmega.py to _ClustalOmega.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/AlignInfo.py to AlignInfo.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Affy/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Affy/CelFile.py to CelFile.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/pairwise2.py to pairwise2.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/kNN.py to kNN.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/bgzf.py to bgzf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/_utils.py to _utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqRecord.py to SeqRecord.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqFeature.py to SeqFeature.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Seq.py to Seq.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/MarkovModel.py to MarkovModel.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/File.py to File.cpython-311.pyc writing byte-compilation script '/tmp/tmphsb1_s6i.py' /usr/bin/python3 /tmp/tmphsb1_s6i.py removing /tmp/tmphsb1_s6i.py running install_egg_info running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' Copying biopython.egg-info to /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/biopython-1.79-py3.11.egg-info running install_scripts + find Scripts -name '*.py' + xargs pathfix.py -pn -i /usr/bin/python3 Scripts/xbbtools/xbbtools.py: updating Scripts/xbbtools/xbb_widget.py: updating Scripts/xbbtools/xbb_utils.py: updating Scripts/xbbtools/xbb_translations.py: updating Scripts/xbbtools/xbb_search.py: updating Scripts/xbbtools/xbb_help.py: updating Scripts/xbbtools/xbb_blastbg.py: updating Scripts/xbbtools/xbb_blast.py: updating Scripts/xbbtools/nextorf.py: updating Scripts/update_ncbi_codon_table.py: no change Scripts/scop_pdb.py: updating Scripts/query_pubmed.py: updating Scripts/SeqGui/SeqGui.py: no change Scripts/Restriction/rebase_update.py: updating Scripts/Restriction/ranacompiler.py: updating Scripts/Performance/biosql_performance_read.py: updating Scripts/Performance/biosql_performance_load.py: updating Scripts/PDB/hsexpo.py: updating Scripts/PDB/generate_three_to_one_dict.py: no change Scripts/GenBank/check_output_simple.py: updating Scripts/GenBank/check_output.py: updating + popd ~/build/BUILD/python-biopython-1.79 + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.79-4.fc38 --unique-debug-suffix -1.79-4.fc38.x86_64 --unique-debug-src-base python-biopython-1.79-4.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.79 extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/_aligners.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster/_cluster.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/cnexus.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/kdtrees.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/_twoBitIO.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/cpairwise2.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/_pwm.cpython-311-x86_64-linux-gnu.so original debug info size: 916kB, size after compression: 860kB /usr/bin/sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match. 1146 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib/debug/usr/lib64/python3.11 using python3.11 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11 using python3.11 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.5VEqQD + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/python-biopython-1.79/.package_note-python-biopython-1.79-4.fc38.x86_64.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh python-biopython 1.79-4.fc38 x86_64 + cd python-biopython-1.79 + pushd python3/Tests ~/build/BUILD/python-biopython-1.79/python3/Tests ~/build/BUILD/python-biopython-1.79 + find . -name run_tests.py + xargs pathfix.py -pn -i /usr/bin/python3 ./run_tests.py: updating + find ../ -name __init__.py + xargs rm -f ++ ls test_Ace.py test_Affy.py test_AlignIO.py test_AlignIO_ClustalIO.py test_AlignIO_EmbossIO.py test_AlignIO_FastaIO.py test_AlignIO_MauveIO.py test_AlignIO_PhylipIO.py test_AlignIO_convert.py test_AlignInfo.py test_Application.py test_BWA_tool.py test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb_online.py test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector_online.py test_BioSQL_psycopg2.py test_BioSQL_psycopg2_online.py test_BioSQL_sqlite3.py test_BioSQL_sqlite3_online.py test_Blast_Record.py test_CAPS.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_ColorSpiral.py test_Compass.py test_Consensus.py test_Dialign_tool.py test_EMBL_unittest.py test_Emboss.py test_EmbossPhylipNew.py test_EmbossPrimer.py test_Entrez.py test_Entrez_online.py test_Entrez_parser.py test_Enzyme.py test_ExPASy.py test_Fasttree_tool.py test_File.py test_GenBank.py test_GenomeDiagram.py test_GraphicsBitmaps.py test_GraphicsChromosome.py test_GraphicsDistribution.py test_GraphicsGeneral.py test_HMMCasino.py test_HMMGeneral.py test_KEGG.py test_KEGG_online.py test_KGML_graphics.py test_KGML_graphics_online.py test_KGML_nographics.py test_KeyWList.py test_LogisticRegression.py test_MSAProbs_tool.py test_MafIO_index.py test_Mafft_tool.py test_MarkovModel.py test_Medline.py test_Muscle_tool.py test_NCBITextParser.py test_NCBIXML.py test_NCBI_BLAST_tools.py test_NCBI_qblast.py test_NMR.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDBList.py test_PDB_DSSP.py test_PDB_Dice.py test_PDB_Disordered.py test_PDB_Exposure.py test_PDB_FragmentMapper.py test_PDB_KDTree.py test_PDB_MMCIF2Dict.py test_PDB_MMCIFIO.py test_PDB_MMCIFParser.py test_PDB_NACCESS.py test_PDB_PDBIO.py test_PDB_PDBParser.py test_PDB_Polypeptide.py test_PDB_ResidueDepth.py test_PDB_SASA.py test_PDB_SMCRA.py test_PDB_StructureAlignment.py test_PDB_Superimposer.py test_PDB_internal_coords.py test_PDB_parse_pdb_header.py test_PDB_vectors.py test_PQR.py test_Pathway.py test_Phd.py test_Phylo.py test_PhyloXML.py test_Phylo_CDAO.py test_Phylo_NeXML.py test_Phylo_matplotlib.py test_Phylo_networkx.py test_PopGen_GenePop.py test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_nodepend.py test_Prank_tool.py test_Probcons_tool.py test_ProtParam.py test_QCPSuperimposer.py test_RCSBFormats.py test_Restriction.py test_SCOP_Astral.py test_SCOP_Cla.py test_SCOP_Des.py test_SCOP_Dom.py test_SCOP_Hie.py test_SCOP_Raf.py test_SCOP_Residues.py test_SCOP_Scop.py test_SCOP_online.py test_SVDSuperimposer.py test_SearchIO_blast_tab.py test_SearchIO_blast_tab_index.py test_SearchIO_blast_text.py test_SearchIO_blast_xml.py test_SearchIO_blast_xml_index.py test_SearchIO_blat_psl.py test_SearchIO_blat_psl_index.py test_SearchIO_exonerate.py test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_vulgar_index.py test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10_index.py test_SearchIO_hhsuite2_text.py test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text_index.py test_SearchIO_interproscan_xml.py test_SearchIO_legacy.py test_SearchIO_model.py test_SearchIO_write.py test_SeqFeature.py test_SeqIO.py test_SeqIO_AbiIO.py test_SeqIO_FastaIO.py test_SeqIO_Gck.py test_SeqIO_Insdc.py test_SeqIO_NibIO.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_SnapGene.py test_SeqIO_TwoBitIO.py test_SeqIO_Xdna.py test_SeqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SubsMat.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_UniProt_GOA.py test_Uniprot.py test_Wise.py test_XXmotif_tool.py test_align.py test_align_substitution_matrices.py test_bgzf.py test_cellosaurus.py test_codonalign.py test_geo.py test_kNN.py test_mmtf.py test_mmtf_online.py test_motifs.py test_motifs_online.py test_pairwise2.py test_pairwise2_no_C.py test_pairwise_aligner.py test_pairwise_alignment_map.py test_phenotype.py test_phenotype_fit.py test_phyml_tool.py test_prodoc.py test_prosite.py test_psw.py test_raxml_tool.py test_samtools_tool.py test_seq.py test_translate.py ++ grep -v SubsMat ++ grep -v Phylo ++ grep -v Nexus ++ grep -v Tutorial ++ grep -v bgzf ++ grep -v SearchIO_blast ++ grep -v pairwise_aligner + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Ace.py test_Ace ... ok test_check_ACEParser (test_Ace.AceTestOne.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestOne.test_check_record_parser) Test to check that contig parser parses each contig into a contig. ... ok test_check_ACEParser (test_Ace.AceTestThree.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestThree.test_check_record_parser) Test to check that record parser parses each contig into a record. ... ok test_check_ACEParser (test_Ace.AceTestTwo.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestTwo.test_check_record_parser) Test to check that record parser parses each contig into a record. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.052 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Affy.py C test_Affy ... ok testAffy3 (test_Affy.AffyTest.testAffy3) ... ok testAffy4 (test_Affy.AffyTest.testAffy4) ... ok testAffyBadHeader (test_Affy.AffyTest.testAffyBadHeader) ... ok testAffyWrongModeReadV3 (test_Affy.AffyTest.testAffyWrongModeReadV3) ... ok testAffyWrongModeReadV4 (test_Affy.AffyTest.testAffyWrongModeReadV4) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.044 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO.py C test_AlignIO ... ok test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_parsing_empty_files) Check that parsing an empty file returns an empty list. ... ok test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions.test_phylip_reject_duplicate) Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_writing_empty_files) Check that writers can cope with no alignments. ... ok test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions.test_writing_not_alignments) Check that writers reject records that are not alignments. ... ok test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal1) ... ok test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal2) ... ok test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal3) ... ok test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal4) ... ok test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal5) ... ok test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal6) ... ok test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss1) ... ok test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss2) ... ok test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss3) ... ok test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss4) ... ok test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss5) ... ok test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss6) ... ok test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss7) ... ok test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss8) ... ok test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta) ... ok test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_1) ... ok test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_2) ... ok test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_3) ... ok test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_4) ... ok test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_5) ... ok test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_6) ... ok test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_7) ... ok test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_8) ... ok test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading.test_reading_alignments_ig) ... ok test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf1) ... ok test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf2) ... ok test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf3) ... ok test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf4) ... ok test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading.test_reading_alignments_mauve) ... ok test_reading_alignments_msf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf1) ... ok test_reading_alignments_msf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf2) ... ok test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus1) ... ok test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus2) ... ok test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip1) ... ok test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip10) ... ok test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip2) ... ok test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip3) ... ok test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip4) ... ok test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip5) ... ok test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip6) ... ok test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip7) ... ok test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip8) ... ok test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip9) ... ok test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading.test_reading_alignments_pir) ... ok test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm1) ... ok test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm2) ... ok ---------------------------------------------------------------------- Ran 1 test in 1.002 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_ClustalIO.py C test_AlignIO_ClustalIO ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO.test_cat_one_two) ... ok test_empy (test_AlignIO_ClustalIO.TestClustalIO.test_empy) Checking empty file. ... ok test_kalign_header (test_AlignIO_ClustalIO.TestClustalIO.test_kalign_header) Make sure we can parse the Kalign header. ... ok test_one (test_AlignIO_ClustalIO.TestClustalIO.test_one) ... ok test_three (test_AlignIO_ClustalIO.TestClustalIO.test_three) ... ok test_two (test_AlignIO_ClustalIO.TestClustalIO.test_two) ... ok test_write_read (test_AlignIO_ClustalIO.TestClustalIO.test_write_read) Checking write/read. ... ok test_write_read_single (test_AlignIO_ClustalIO.TestClustalIO.test_write_read_single) Testing write/read when there is only one sequence. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_EmbossIO.py test_AlignIO_EmbossIO ... ok test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example) ... ok test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example2) ... ok test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example3) ... ok test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_plus_simple) ... ok test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO.test_simple_example) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.096 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_FastaIO.py test_AlignIO_FastaIO ... ok test_output001 (test_AlignIO_FastaIO.FastaIOTests.test_output001) Check output001.m10 file. ... ok test_output002 (test_AlignIO_FastaIO.FastaIOTests.test_output002) Check output002.m10 file. ... ok test_output003 (test_AlignIO_FastaIO.FastaIOTests.test_output003) Check output003.m10 file. ... ok test_output004 (test_AlignIO_FastaIO.FastaIOTests.test_output004) Check output004.m10 file. ... ok test_output005 (test_AlignIO_FastaIO.FastaIOTests.test_output005) Check output005.m10 file. ... ok test_output006 (test_AlignIO_FastaIO.FastaIOTests.test_output006) Check output006.m10 file. ... ok test_output007 (test_AlignIO_FastaIO.FastaIOTests.test_output007) Check output007.m10 file. ... ok test_output008 (test_AlignIO_FastaIO.FastaIOTests.test_output008) Check output008.m10 file. ... ok test_output009 (test_AlignIO_FastaIO.FastaIOTests.test_output009) Check output009.m10 file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.093 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_MauveIO.py test_AlignIO_MauveIO ... ok test_one (test_AlignIO_MauveIO.TestMauveIO.test_one) ... ok test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO.test_sequence_positions) ... ok test_write_read (test_AlignIO_MauveIO.TestMauveIO.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.104 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` C + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_PhylipIO.py test_AlignIO_PhylipIO ... ok test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO.test_concatenation) ... ok test_five (test_AlignIO_PhylipIO.TestPhylipIO.test_five) ... ok test_five_a (test_AlignIO_PhylipIO.TestPhylipIO.test_five_a) ... ok test_four (test_AlignIO_PhylipIO.TestPhylipIO.test_four) ... ok test_one (test_AlignIO_PhylipIO.TestPhylipIO.test_one) ... ok test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO.test_two_and_three) ... ok test_write_read (test_AlignIO_PhylipIO.TestPhylipIO.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.074 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_convert.py test_AlignIO_convert ... ok test_clustal_to_nexus_with_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_with_mol_type) Converting Clustal to NEXUS with a molecule type. ... ok test_clustal_to_nexus_without_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_without_mol_type) Converting Clustal to NEXUS without a molecule type. ... ok test_convert (test_AlignIO_convert.ConvertTests.test_convert) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.232 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignInfo.py test_AlignInfo ... ok test_nucleotides (test_AlignInfo.AlignInfoTests.test_nucleotides) ... ok test_proteins (test_AlignInfo.AlignInfoTests.test_proteins) ... ok test_pseudo_count (test_AlignInfo.AlignInfoTests.test_pseudo_count) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.096 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Application.py test_Application ... ok test_echo (test_Application.TestApp.test_echo) ... ok test_echo_capture_both (test_Application.TestApp.test_echo_capture_both) ... ok test_echo_capture_neither (test_Application.TestApp.test_echo_capture_neither) ... ok test_echo_capture_stderr (test_Application.TestApp.test_echo_capture_stderr) ... ok test_echo_capture_stdout (test_Application.TestApp.test_echo_capture_stdout) ... ok test_echo_file_both (test_Application.TestApp.test_echo_file_both) ... ok test_echo_file_same (test_Application.TestApp.test_echo_file_same) ... ok test_echo_file_stderr (test_Application.TestApp.test_echo_file_stderr) ... ok test_echo_file_stdout (test_Application.TestApp.test_echo_file_stdout) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.028 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BWA_tool.py C 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 0.024 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb.py C test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) ---------------------------------------------------------------------- Ran 1 test in 0.141 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` C + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb_online.py test_BioSQL_MySQLdb_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.107 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector.py C test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) ---------------------------------------------------------------------- Ran 1 test in 0.106 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector_online.py test_BioSQL_mysql_connector_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.097 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.095 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` C + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2_online.py test_BioSQL_psycopg2_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.093 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3.py test_BioSQL_sqlite3 ... ok test_SeqIO_loading (common_BioSQL.AutoSeqIOTests.test_SeqIO_loading) ... ok test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest.test_backwards_compatibility) Check can re-use an old BioSQL SQLite3 database. ... ok test_NC_000932 (common_BioSQL.ClosedLoopTest.test_NC_000932) From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok test_NC_005816 (common_BioSQL.ClosedLoopTest.test_NC_005816) From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok test_NT_019265 (common_BioSQL.ClosedLoopTest.test_NT_019265) From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok test_arab1 (common_BioSQL.ClosedLoopTest.test_arab1) From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok test_cor6_6 (common_BioSQL.ClosedLoopTest.test_cor6_6) From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok test_no_ref (common_BioSQL.ClosedLoopTest.test_no_ref) From GenBank file to BioSQL and back to a GenBank file, noref. ... ok test_one_of (common_BioSQL.ClosedLoopTest.test_one_of) From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok test_protein_refseq2 (common_BioSQL.ClosedLoopTest.test_protein_refseq2) From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok test_del_db_items (common_BioSQL.DeleteTest.test_del_db_items) Check all associated data is deleted from an item. ... ok test_server (common_BioSQL.DeleteTest.test_server) Check BioSeqDatabase methods. ... ok test_duplicate_id_load (common_BioSQL.DupLoadTest.test_duplicate_id_load) Make sure can't import records with same ID (in one go). ... ok test_duplicate_load (common_BioSQL.DupLoadTest.test_duplicate_load) Make sure can't import a single record twice (in one go). ... ok test_duplicate_load2 (common_BioSQL.DupLoadTest.test_duplicate_load2) Make sure can't import a single record twice (in steps). ... ok test_record_loading (common_BioSQL.InDepthLoadTest.test_record_loading) Make sure all records are correctly loaded. ... ok test_reload (common_BioSQL.InDepthLoadTest.test_reload) Make sure can't reimport existing records. ... ok test_seq_feature (common_BioSQL.InDepthLoadTest.test_seq_feature) In depth check that SeqFeatures are transmitted through the db. ... ok test_transfer (common_BioSQL.InDepthLoadTest.test_transfer) Make sure can load record into another namespace. ... ok test_load_database (common_BioSQL.LoaderTest.test_load_database) Load SeqRecord objects into a BioSQL database. ... ok test_cross_retrieval_of_items (common_BioSQL.MultiReadTest.test_cross_retrieval_of_items) Test that valid ids can't be retrieved between namespaces. ... ok test_get_db_items (common_BioSQL.MultiReadTest.test_get_db_items) Check list, keys, length etc. ... ok test_server (common_BioSQL.MultiReadTest.test_server) Check BioSeqDatabase methods. ... ok test_get_db_items (common_BioSQL.ReadTest.test_get_db_items) Check list, keys, length etc. ... ok test_lookup_items (common_BioSQL.ReadTest.test_lookup_items) Test retrieval of items using various ids. ... ok test_server (common_BioSQL.ReadTest.test_server) Check BioSeqDatabase methods. ... ok test_addition (common_BioSQL.SeqInterfaceTest.test_addition) Check can add Seq objects from BioSQL together. ... ok test_convert (common_BioSQL.SeqInterfaceTest.test_convert) Check can turn a Seq object from BioSQL into a Seq or MutableSeq. ... ok test_eq (common_BioSQL.SeqInterfaceTest.test_eq) ... ok test_ge (common_BioSQL.SeqInterfaceTest.test_ge) ... ok test_gt (common_BioSQL.SeqInterfaceTest.test_gt) ... ok test_le (common_BioSQL.SeqInterfaceTest.test_le) ... ok test_lt (common_BioSQL.SeqInterfaceTest.test_lt) ... ok test_multiplication (common_BioSQL.SeqInterfaceTest.test_multiplication) Check can multiply Seq objects from BioSQL by integers. ... ok test_ne (common_BioSQL.SeqInterfaceTest.test_ne) ... ok test_record_slicing (common_BioSQL.SeqInterfaceTest.test_record_slicing) Check that slices of DBSeqRecord are retrieved properly. ... ok test_seq (common_BioSQL.SeqInterfaceTest.test_seq) Make sure Seqs from BioSQL implement the right interface. ... ok test_seq_features (common_BioSQL.SeqInterfaceTest.test_seq_features) Check SeqFeatures of a sequence. ... ok test_seq_record (common_BioSQL.SeqInterfaceTest.test_seq_record) Make sure SeqRecords from BioSQL implement the right interface. ... ok test_seq_slicing (common_BioSQL.SeqInterfaceTest.test_seq_slicing) Check that slices of sequences are retrieved properly. ... ok test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest.test_ambiguous_location) Loaded uniprot-xml with ambiguous location in BioSQL. ... ok test_add (common_BioSQL.TestBaseClassMethods.test_add) ... ok test_bytes (common_BioSQL.TestBaseClassMethods.test_bytes) ... ok test_contains (common_BioSQL.TestBaseClassMethods.test_contains) ... ok test_count (common_BioSQL.TestBaseClassMethods.test_count) ... ok test_endswith (common_BioSQL.TestBaseClassMethods.test_endswith) ... ok test_find (common_BioSQL.TestBaseClassMethods.test_find) ... ok test_hash (common_BioSQL.TestBaseClassMethods.test_hash) ... ok test_index (common_BioSQL.TestBaseClassMethods.test_index) ... ok test_lower (common_BioSQL.TestBaseClassMethods.test_lower) ... ok test_lstrip (common_BioSQL.TestBaseClassMethods.test_lstrip) ... ok test_mul (common_BioSQL.TestBaseClassMethods.test_mul) ... ok test_radd (common_BioSQL.TestBaseClassMethods.test_radd) ... ok test_replace (common_BioSQL.TestBaseClassMethods.test_replace) ... ok test_repr (common_BioSQL.TestBaseClassMethods.test_repr) ... ok test_rfind (common_BioSQL.TestBaseClassMethods.test_rfind) ... ok test_rindex (common_BioSQL.TestBaseClassMethods.test_rindex) ... ok test_rsplit (common_BioSQL.TestBaseClassMethods.test_rsplit) ... ok test_rstrip (common_BioSQL.TestBaseClassMethods.test_rstrip) ... ok test_split (common_BioSQL.TestBaseClassMethods.test_split) ... ok test_startswith (common_BioSQL.TestBaseClassMethods.test_startswith) ... ok test_str (common_BioSQL.TestBaseClassMethods.test_str) ... ok test_strip (common_BioSQL.TestBaseClassMethods.test_strip) ... ok test_translate (common_BioSQL.TestBaseClassMethods.test_translate) ... ok test_upper (common_BioSQL.TestBaseClassMethods.test_upper) ... ok test_NC_000932 (common_BioSQL.TransferTest.test_NC_000932) From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok test_NC_005816 (common_BioSQL.TransferTest.test_NC_005816) From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok test_NT_019265 (common_BioSQL.TransferTest.test_NT_019265) From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok test_arab1 (common_BioSQL.TransferTest.test_arab1) From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok test_cor6_6 (common_BioSQL.TransferTest.test_cor6_6) From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok test_no_ref (common_BioSQL.TransferTest.test_no_ref) From GenBank file to BioSQL, then again to a new namespace, noref. ... ok test_one_of (common_BioSQL.TransferTest.test_one_of) From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok test_protein_refseq2 (common_BioSQL.TransferTest.test_protein_refseq2) From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok ---------------------------------------------------------------------- Ran 1 test in 3.694 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3_online.py test_BioSQL_sqlite3_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.091 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Blast_Record.py test_Blast_Record ... ok test_str (test_Blast_Record.TestHsp.test_str) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.056 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_CAPS.py test_CAPS ... ok test (test_CAPS.TestCAPS.test) ... ok testNoCAPS (test_CAPS.TestCAPS.testNoCAPS) ... ok test_trivial (test_CAPS.TestCAPS.test_trivial) ... ok test_uneven (test_CAPS.TestCAPS.test_uneven) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.155 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Chi2.py test_Chi2 ... ok test_cdf_chi2 (test_Chi2.ModTest.test_cdf_chi2) ... ok test_incomplete_gamma (test_Chi2.ModTest.test_incomplete_gamma) ... ok test_ln_gamma (test_Chi2.ModTest.test_ln_gamma) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.089 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ClustalOmega_tool.py test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.082 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.086 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Cluster.py test_Cluster ... ok test_clusterdistance (test_Cluster.TestCluster.test_clusterdistance) ... ok test_clusterdistance_arguments (test_Cluster.TestCluster.test_clusterdistance_arguments) ... ok test_distancematrix_arguments (test_Cluster.TestCluster.test_distancematrix_arguments) ... ok test_distancematrix_kmedoids (test_Cluster.TestCluster.test_distancematrix_kmedoids) ... ok test_kcluster (test_Cluster.TestCluster.test_kcluster) ... ok test_kcluster_arguments (test_Cluster.TestCluster.test_kcluster_arguments) ... ok test_kmedoids_arguments (test_Cluster.TestCluster.test_kmedoids_arguments) ... ok test_mask_parse (test_Cluster.TestCluster.test_mask_parse) ... ok test_matrix_parse (test_Cluster.TestCluster.test_matrix_parse) ... ok test_pca (test_Cluster.TestCluster.test_pca) ... ok test_pca_arguments (test_Cluster.TestCluster.test_pca_arguments) ... ok test_somcluster (test_Cluster.TestCluster.test_somcluster) ... ok test_somcluster_arguments (test_Cluster.TestCluster.test_somcluster_arguments) ... ok test_tree (test_Cluster.TestCluster.test_tree) ... ok test_tree_arguments (test_Cluster.TestCluster.test_tree_arguments) ... ok test_treecluster (test_Cluster.TestCluster.test_treecluster) ... ok test_treecluster_arguments (test_Cluster.TestCluster.test_treecluster_arguments) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.047 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_CodonTable.py test_CodonTable ... ok test_coding (test_CodonTable.AmbiguousCodonsTests.test_coding) Check a few ambiguous codons for correct coding. ... ok test_list_ambiguous_codons (test_CodonTable.AmbiguousCodonsTests.test_list_ambiguous_codons) Check if stop codons are properly extended. ... ok test_start_codons (test_CodonTable.AmbiguousCodonsTests.test_start_codons) Test various ambiguous codons as start codon. ... ok test_stop_codons (test_CodonTable.AmbiguousCodonsTests.test_stop_codons) Test various ambiguous codons as stop codon. ... ok test_ambiguous_tables (test_CodonTable.BasicSanityTests.test_ambiguous_tables) Check if all IDs and all names are present in ambiguous tables. ... ok test_complete_tables (test_CodonTable.BasicSanityTests.test_complete_tables) Check if all unambiguous codon tables have all entries. ... ok test_number_of_tables (test_CodonTable.BasicSanityTests.test_number_of_tables) Check if we have the same number of tables for each type. ... ok test_ambiguous_forward_table (test_CodonTable.ErrorConditions.test_ambiguous_forward_table) Raise errors in AmbiguousForwardTable. ... ok test_list_possible_proteins (test_CodonTable.ErrorConditions.test_list_possible_proteins) Raise errors in list_possible proteins. ... ok test_print_table (test_CodonTable.PrintTable.test_print_table) Test output of __str__ function. ... ok test_table01 (test_CodonTable.SingleTableTests.test_table01) Check table 1: Standard. ... ok test_table02 (test_CodonTable.SingleTableTests.test_table02) Check table 2: Vertebrate Mitochondrial. ... ok test_table03 (test_CodonTable.SingleTableTests.test_table03) Check table 3: Yeast Mitochondrial. ... ok test_table04 (test_CodonTable.SingleTableTests.test_table04) Check table 4: Mold Mitochondrial and others. ... ok test_table05 (test_CodonTable.SingleTableTests.test_table05) Check table 5: Invertebrate Mitochondrial. ... ok test_table06 (test_CodonTable.SingleTableTests.test_table06) Check table 6: Ciliate and Other Nuclear. ... ok test_table09 (test_CodonTable.SingleTableTests.test_table09) Check table 9: Echinoderm and Flatworm Mitochondrial. ... ok test_table10 (test_CodonTable.SingleTableTests.test_table10) Check table 10: Euplotid Nuclear. ... ok test_table11 (test_CodonTable.SingleTableTests.test_table11) Check table 11: Bacterial, Archaeal and Plant Plastid. ... ok test_table12 (test_CodonTable.SingleTableTests.test_table12) Check table 12: Alternative Yeast Nuclear. ... ok test_table13 (test_CodonTable.SingleTableTests.test_table13) Check table 13: Ascidian Mitochondrial. ... ok test_table14 (test_CodonTable.SingleTableTests.test_table14) Check table 14: Alternative Flatworm Mitochondrial. ... ok test_table16 (test_CodonTable.SingleTableTests.test_table16) Check table 16: Chlorophycean Mitochondrial. ... ok test_table21 (test_CodonTable.SingleTableTests.test_table21) Check table 21: Trematode Mitochondrial. ... ok test_table22 (test_CodonTable.SingleTableTests.test_table22) Check table 22: Scenedesmus obliquus Mitochondrial. ... ok test_table23 (test_CodonTable.SingleTableTests.test_table23) Check table 9: Thraustochytrium Mitochondrial. ... ok test_table24 (test_CodonTable.SingleTableTests.test_table24) Check table 24: Pterobranchia Mitochondrial. ... ok test_table25 (test_CodonTable.SingleTableTests.test_table25) Check table 25: Candidate Division SR1 and Gracilibacteria. ... ok test_table26 (test_CodonTable.SingleTableTests.test_table26) Check table 26: Pachysolen tannophilus Nuclear. ... ok test_table27 (test_CodonTable.SingleTableTests.test_table27) Check table 27: Karyorelict Nuclear. ... ok test_table28 (test_CodonTable.SingleTableTests.test_table28) Check table 28: Condylostoma Nuclear. ... ok test_table29 (test_CodonTable.SingleTableTests.test_table29) Check table 29: Mesodinium Nuclear. ... ok test_table30 (test_CodonTable.SingleTableTests.test_table30) Check table 30: Peritrich Nuclear. ... ok test_table31 (test_CodonTable.SingleTableTests.test_table31) Check table 31: Blastocrithidia Nuclear. ... ok test_table32 (test_CodonTable.SingleTableTests.test_table32) Check table 32: Balanophoraceae Plastid. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.062 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ColorSpiral.py test_ColorSpiral ... ok test_dict (test_ColorSpiral.DictTest.test_dict) get_color_dict() for classes A-D, no jitter. ... ok test_colorlist (test_ColorSpiral.SpiralTest.test_colorlist) Get set of eight colours, no jitter, using ColorSpiral. ... ok test_colorspiral (test_ColorSpiral.SpiralTest.test_colorspiral) Get set of 16 colours, no jitter, using ColorSpiral. ... ok test_colorspiral (test_ColorSpiral.SquareTest.test_colorspiral) Set of 625 colours, with jitter, using get_colors(). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.052 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_Compass.py test_Compass ... ok testAlignmentParsingOne (test_Compass.CompassTest.testAlignmentParsingOne) ... ok testAlignmentParsingTwo (test_Compass.CompassTest.testAlignmentParsingTwo) ... ok testCompassIteratorEasy (test_Compass.CompassTest.testCompassIteratorEasy) ... ok testCompassIteratorHard (test_Compass.CompassTest.testCompassIteratorHard) ... ok testCompassParser (test_Compass.CompassTest.testCompassParser) ... ok testCompassScanAndConsume (test_Compass.CompassTest.testCompassScanAndConsume) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.013 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Consensus.py test_Consensus ... ok test_bitstring (test_Consensus.BitStringTest.test_bitstring) ... ok test_bootstrap (test_Consensus.BootstrapTest.test_bootstrap) ... ok test_bootstrap_consensus (test_Consensus.BootstrapTest.test_bootstrap_consensus) ... ok test_bootstrap_trees (test_Consensus.BootstrapTest.test_bootstrap_trees) ... ok test_adam_consensus (test_Consensus.ConsensusTest.test_adam_consensus) ... ok test_count_clades (test_Consensus.ConsensusTest.test_count_clades) ... ok test_get_support (test_Consensus.ConsensusTest.test_get_support) ... ok test_majority_consensus (test_Consensus.ConsensusTest.test_majority_consensus) ... ok test_strict_consensus (test_Consensus.ConsensusTest.test_strict_consensus) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.701 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Dialign_tool.py test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.060 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_EMBL_unittest.py test_EMBL_unittest ... ok test_embl_0_line (test_EMBL_unittest.EMBLTests.test_embl_0_line) Test SQ line with 0 length sequence. ... ok test_embl_content_after_co (test_EMBL_unittest.EMBLTests.test_embl_content_after_co) Test a ValueError is thrown by content after a CO line. ... ok test_embl_no_coords (test_EMBL_unittest.EMBLTests.test_embl_no_coords) Test sequence lines without coordinates. ... ok test_embl_wrong_dr_line (test_EMBL_unittest.EMBLTests.test_embl_wrong_dr_line) Test files with wrong DR lines. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.080 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Emboss.py C test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss. ---------------------------------------------------------------------- Ran 1 test in 0.096 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.072 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_EmbossPrimer.py test_EmbossPrimer ... ok test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest.test_in_depth_single_parse) Make sure we get info right from a single primer find. ... ok test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest.test_indepth_regular_parse) Make sure we get the data from normal primer3 files okay. ... ok test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest.test_internal_oligo_single_parse) Make sure we can parse an internal oligo file correctly. ... ok test_multi_record_full (test_EmbossPrimer.Primer3ParseTest.test_multi_record_full) Test parsing multiple primer sets (NirK full). ... ok test_multi_record_fwd (test_EmbossPrimer.Primer3ParseTest.test_multi_record_fwd) Test parsing multiple primer sets (NirK forward). ... ok test_simple_parse (test_EmbossPrimer.Primer3ParseTest.test_simple_parse) Make sure that we can use all single target primer3 files. ... ok test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest.test_primer_representation) Make sure we can output primer information correctly. ... ok test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest.test_in_depth_normal_parse) Make sure the output from a simple primersearch file is correct. ... ok test_simple_parse (test_EmbossPrimer.PrimersearchParseTest.test_simple_parse) Make sure that we can parse all primersearch files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.017 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez.py test_Entrez ... ok test_custom_directory (test_Entrez.CustomDirectoryTest.test_custom_directory) ... ok test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction.test_construct_cgi_ecitmatch) ... ok test_construct_cgi_efetch (test_Entrez.TestURLConstruction.test_construct_cgi_efetch) ... ok test_construct_cgi_einfo (test_Entrez.TestURLConstruction.test_construct_cgi_einfo) Test constructed url for request to Entrez. ... ok test_construct_cgi_elink1 (test_Entrez.TestURLConstruction.test_construct_cgi_elink1) ... ok test_construct_cgi_elink2 (test_Entrez.TestURLConstruction.test_construct_cgi_elink2) Commas: Link from protein to gene. ... ok test_construct_cgi_elink3 (test_Entrez.TestURLConstruction.test_construct_cgi_elink3) Multiple ID entries: Find one-to-one links from protein to gene. ... ok test_construct_cgi_epost1 (test_Entrez.TestURLConstruction.test_construct_cgi_epost1) ... ok test_construct_cgi_epost2 (test_Entrez.TestURLConstruction.test_construct_cgi_epost2) ... ok test_email_warning (test_Entrez.TestURLConstruction.test_email_warning) Test issuing warning when user does not specify email address. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.743 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez_online.py test_Entrez_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.085 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez_parser.py test_Entrez_parser ... ok test_efetch_schemas (test_Entrez_parser.EFetchTest.test_efetch_schemas) Test parsing XML using Schemas. ... ok test_fasta (test_Entrez_parser.EFetchTest.test_fasta) Test error handling when presented with Fasta non-XML data. ... ok test_genbank (test_Entrez_parser.EFetchTest.test_genbank) Test error handling when presented with GenBank non-XML data. ... ok test_nucleotide1 (test_Entrez_parser.EFetchTest.test_nucleotide1) Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok test_nucleotide2 (test_Entrez_parser.EFetchTest.test_nucleotide2) Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok test_omim (test_Entrez_parser.EFetchTest.test_omim) Test parsing XML returned by EFetch, OMIM database. ... ok test_protein (test_Entrez_parser.EFetchTest.test_protein) Test parsing XML returned by EFetch, Protein database. ... ok test_pubmed1 (test_Entrez_parser.EFetchTest.test_pubmed1) Test parsing XML returned by EFetch, PubMed database (first test). ... ok test_pubmed2 (test_Entrez_parser.EFetchTest.test_pubmed2) Test parsing XML returned by EFetch, PubMed database (second test). ... ok test_pubmed_html (test_Entrez_parser.EFetchTest.test_pubmed_html) Test error handling when presented with HTML (so XML-like) data. ... ok test_pubmed_html_escaping (test_Entrez_parser.EFetchTest.test_pubmed_html_escaping) Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_mathml_tags) Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok test_pubmed_html_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_tags) Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_mathml_tags) Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok test_taxonomy (test_Entrez_parser.EFetchTest.test_taxonomy) Test parsing XML returned by EFetch, Taxonomy database. ... ok test_truncated_xml (test_Entrez_parser.EFetchTest.test_truncated_xml) Test error handling for a truncated XML declaration. ... ok test_xml_without_declaration (test_Entrez_parser.EFetchTest.test_xml_without_declaration) Test error handling for a missing XML declaration. ... ok test_xml_without_definition (test_Entrez_parser.EFetchTest.test_xml_without_definition) Test error handling for a missing DTD or XML Schema. ... ok test_egquery1 (test_Entrez_parser.EGQueryTest.test_egquery1) Test parsing XML output returned by EGQuery (first test). ... ok test_egquery2 (test_Entrez_parser.EGQueryTest.test_egquery2) Test parsing XML output returned by EGQuery (second test). ... ok test_corrupted (test_Entrez_parser.EInfoTest.test_corrupted) Test if corrupted XML is handled correctly. ... ok test_list (test_Entrez_parser.EInfoTest.test_list) Test parsing database list returned by EInfo. ... ok test_pubmed1 (test_Entrez_parser.EInfoTest.test_pubmed1) Test parsing database info returned by EInfo. ... ok test_pubmed2 (test_Entrez_parser.EInfoTest.test_pubmed2) Test validating the XML against the DTD. ... ok test_pubmed3 (test_Entrez_parser.EInfoTest.test_pubmed3) Test non-validating parser on XML with an inconsistent DTD. ... ok test_medline (test_Entrez_parser.ELinkTest.test_medline) Test parsing medline indexed articles returned by ELink. ... ok test_nucleotide (test_Entrez_parser.ELinkTest.test_nucleotide) Test parsing Nucleotide to Protein links returned by ELink. ... ok test_pubmed1 (test_Entrez_parser.ELinkTest.test_pubmed1) Test parsing pubmed links returned by ELink (first test). ... ok test_pubmed2 (test_Entrez_parser.ELinkTest.test_pubmed2) Test parsing pubmed links returned by ELink (second test). ... ok test_pubmed3 (test_Entrez_parser.ELinkTest.test_pubmed3) Test parsing pubmed link returned by ELink (third test). ... ok test_pubmed4 (test_Entrez_parser.ELinkTest.test_pubmed4) Test parsing pubmed links returned by ELink (fourth test). ... ok test_pubmed5 (test_Entrez_parser.ELinkTest.test_pubmed5) Test parsing pubmed links returned by ELink (fifth test). ... ok test_pubmed6 (test_Entrez_parser.ELinkTest.test_pubmed6) Test parsing pubmed links returned by ELink (sixth test). ... ok test_epost (test_Entrez_parser.EPostTest.test_epost) Test parsing XML returned by EPost. ... ok test_invalid (test_Entrez_parser.EPostTest.test_invalid) Test parsing XML returned by EPost with invalid id (overflow tag). ... ok test_wrong (test_Entrez_parser.EPostTest.test_wrong) Test parsing XML returned by EPost with incorrect arguments. ... ok test_journals (test_Entrez_parser.ESearchTest.test_journals) Test parsing XML returned by ESearch from the Journals database. ... ok test_notfound (test_Entrez_parser.ESearchTest.test_notfound) Test parsing XML returned by ESearch when no items were found. ... ok test_nucleotide (test_Entrez_parser.ESearchTest.test_nucleotide) Test parsing XML returned by ESearch from the Nucleotide database. ... ok test_pmc (test_Entrez_parser.ESearchTest.test_pmc) Test parsing XML returned by ESearch from PubMed Central. ... ok test_protein (test_Entrez_parser.ESearchTest.test_protein) Test parsing XML returned by ESearch from the Protein database. ... ok test_pubmed1 (test_Entrez_parser.ESearchTest.test_pubmed1) Test parsing XML returned by ESearch from PubMed (first test). ... ok test_pubmed2 (test_Entrez_parser.ESearchTest.test_pubmed2) Test parsing XML returned by ESearch from PubMed (second test). ... ok test_pubmed3 (test_Entrez_parser.ESearchTest.test_pubmed3) Test parsing XML returned by ESearch from PubMed (third test). ... ok test_espell (test_Entrez_parser.ESpellTest.test_espell) Test parsing XML output returned by ESpell. ... ok test_integer_none (test_Entrez_parser.ESummaryTest.test_integer_none) Test parsing ESummary XML where an Integer is not defined. ... ok test_journals (test_Entrez_parser.ESummaryTest.test_journals) Test parsing XML returned by ESummary from the Journals database. ... ok test_nucleotide (test_Entrez_parser.ESummaryTest.test_nucleotide) Test parsing XML returned by ESummary from the Nucleotide database. ... ok test_protein (test_Entrez_parser.ESummaryTest.test_protein) Test parsing XML returned by ESummary from the Protein database. ... ok test_pubmed (test_Entrez_parser.ESummaryTest.test_pubmed) Test parsing XML returned by ESummary from PubMed. ... ok test_structure (test_Entrez_parser.ESummaryTest.test_structure) Test parsing XML returned by ESummary from the Structure database. ... ok test_taxonomy (test_Entrez_parser.ESummaryTest.test_taxonomy) Test parsing XML returned by ESummary from the Taxonomy database. ... ok test_unists (test_Entrez_parser.ESummaryTest.test_unists) Test parsing XML returned by ESummary from the UniSTS database. ... ok test_wrong (test_Entrez_parser.ESummaryTest.test_wrong) Test parsing XML returned by ESummary with incorrect arguments. ... ok test_BytesIO (test_Entrez_parser.GeneralTests.test_BytesIO) Test parsing a BytesIO handle (bytes not string). ... ok test_closed_handle (test_Entrez_parser.GeneralTests.test_closed_handle) Test parsing closed handle fails gracefully. ... ok test_parse_bytes_handle (test_Entrez_parser.GeneralTests.test_parse_bytes_handle) Test parsing a handle opened in binary mode. ... ok test_parse_text_handle (test_Entrez_parser.GeneralTests.test_parse_text_handle) Test parsing a handle opened in text mode. ... ok test_read_bytes_handle (test_Entrez_parser.GeneralTests.test_read_bytes_handle) Test reading a handle opened in binary mode. ... ok test_read_text_handle (test_Entrez_parser.GeneralTests.test_read_text_handle) Test reading a handle opened in text mode. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.225 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Enzyme.py C test_Enzyme ... ok test_lactate (test_Enzyme.TestEnzyme.test_lactate) Parsing ENZYME record for lactate racemase (5.1.2.1). ... ok test_lipoprotein (test_Enzyme.TestEnzyme.test_lipoprotein) Parsing ENZYME record for lipoprotein lipase (3.1.1.34). ... ok test_parse_many (test_Enzyme.TestEnzyme.test_parse_many) Check parse function with multiple records. ... ok test_parse_one (test_Enzyme.TestEnzyme.test_parse_one) Check parse function with one record. ... ok test_parse_zero (test_Enzyme.TestEnzyme.test_parse_zero) ... ok test_proline (test_Enzyme.TestEnzyme.test_proline) Parsing ENZYME record for proline racemase (5.1.1.4). ... ok test_valine (test_Enzyme.TestEnzyme.test_valine) Parsing ENZYME record for valine decarboxylase (4.1.1.14). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.013 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ExPASy.py C test_ExPASy ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.012 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Fasttree_tool.py test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.107 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_File.py test_File ... ok test_custom_path_like_object (test_File.AsHandleTestCase.test_custom_path_like_object) Test as_handle with a custom path-like object. ... ok test_handle (test_File.AsHandleTestCase.test_handle) Test as_handle with a file-like object argument. ... ok test_path_object (test_File.AsHandleTestCase.test_path_object) Test as_handle with a pathlib.Path object. ... ok test_string_path (test_File.AsHandleTestCase.test_string_path) Test as_handle with a string path argument. ... ok test_stringio (test_File.AsHandleTestCase.test_stringio) Testing passing StringIO handles. ... ok test_instance_exception (test_File.BaseClassTests.test_instance_exception) ... ok test_bgzf (test_File.RandomAccess.test_bgzf) Test BGZF compressed file. ... ok test_gzip (test_File.RandomAccess.test_gzip) Test gzip compressed file. ... ok test_plain (test_File.RandomAccess.test_plain) Test plain text file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.014 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GenBank.py C test_GenBank ... /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning) ok test_embl_cds_interaction (test_GenBank.GenBankScannerTests.test_embl_cds_interaction) Test EMBL CDS interaction, parse CDS features on embl files. ... ok test_embl_record_interaction (test_GenBank.GenBankScannerTests.test_embl_record_interaction) Test EMBL Record interaction on embl files. ... ok test_genbank_cds_interaction (test_GenBank.GenBankScannerTests.test_genbank_cds_interaction) Test CDS interaction, parse CDS features on gb(k) files. ... ok test_genbank_interaction (test_GenBank.GenBankScannerTests.test_genbank_interaction) Test GenBank records interaction on gbk files. ... ok test_000_genbank_bad_loc_wrap_warning (test_GenBank.GenBankTests.test_000_genbank_bad_loc_wrap_warning) Feature line wrapping warning. ... ok test_001_genbank_bad_origin_wrapping_location (test_GenBank.GenBankTests.test_001_genbank_bad_origin_wrapping_location) Bad origin wrapping. ... ok test_001_implicit_orign_wrap_fix (test_GenBank.GenBankTests.test_001_implicit_orign_wrap_fix) Attempt to fix implied origin wrapping. ... ok test_001_negative_location_warning (test_GenBank.GenBankTests.test_001_negative_location_warning) Un-parsable feature location warning. ... ok test_compound_complex_origin_wrap (test_GenBank.GenBankTests.test_compound_complex_origin_wrap) Test the attempts to fix compound complex origin wrapping. ... ok test_dbline_embl_gb (test_GenBank.GenBankTests.test_dbline_embl_gb) Parse GenBank/EMBL paired records with PR project entry: EMBL. ... ok test_dbline_gb_embl (test_GenBank.GenBankTests.test_dbline_gb_embl) Parse GenBank/EMBL paired records with PR project entry: GenBank. ... ok test_dblink (test_GenBank.GenBankTests.test_dblink) Parse GenBank record with old DBLINK project entry. ... ok test_dblink_two (test_GenBank.GenBankTests.test_dblink_two) Parse GenBank record with old and new DBLINK project entries. ... ok test_dot_lineage (test_GenBank.GenBankTests.test_dot_lineage) Missing taxonomy lineage. ... ok test_extremely_long_sequence (test_GenBank.GenBankTests.test_extremely_long_sequence) Tests if extremely long sequences can be read. ... ok test_fuzzy_origin_wrap (test_GenBank.GenBankTests.test_fuzzy_origin_wrap) Test features that wrap an origin, and have fuzzy location. ... ok test_genbank_bad_loc_wrap_parsing (test_GenBank.GenBankTests.test_genbank_bad_loc_wrap_parsing) Bad location wrapping. ... ok test_genbank_date_correct (test_GenBank.GenBankTests.test_genbank_date_correct) Check if user provided date is inserted correctly. ... ok test_genbank_date_datetime (test_GenBank.GenBankTests.test_genbank_date_datetime) Check if datetime objects are handled correctly. ... ok test_genbank_date_default (test_GenBank.GenBankTests.test_genbank_date_default) Check if default date is handled correctly. ... ok test_genbank_date_invalid (test_GenBank.GenBankTests.test_genbank_date_invalid) Check if invalid dates are treated as default. ... ok test_genbank_date_list (test_GenBank.GenBankTests.test_genbank_date_list) Check if date lists are handled correctly. ... ok test_genbank_read (test_GenBank.GenBankTests.test_genbank_read) GenBank.read(...) simple test. ... ok test_genbank_read_invalid (test_GenBank.GenBankTests.test_genbank_read_invalid) GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok test_genbank_read_multirecord (test_GenBank.GenBankTests.test_genbank_read_multirecord) GenBank.read(...) error on multiple record input. ... ok test_genbank_read_no_origin_no_end (test_GenBank.GenBankTests.test_genbank_read_no_origin_no_end) GenBank.read(...) error on malformed file. ... ok test_implicit_orign_wrap_extract_and_translate (test_GenBank.GenBankTests.test_implicit_orign_wrap_extract_and_translate) Test that features wrapped around origin give expected data. ... ok test_invalid_product_line_raises_value_error (test_GenBank.GenBankTests.test_invalid_product_line_raises_value_error) Parsing invalid product line. ... ok test_locus_line_topogoly (test_GenBank.GenBankTests.test_locus_line_topogoly) Test if chromosome topology is conserved. ... ok test_long_names (test_GenBank.GenBankTests.test_long_names) Various GenBank names which push the column based LOCUS line. ... ok test_longer_locus_line (test_GenBank.GenBankTests.test_longer_locus_line) Check that we can read and write files with longer locus lines. ... ok test_malformed_structured_comment_parsing (test_GenBank.GenBankTests.test_malformed_structured_comment_parsing) Test malformed structured comment gives warning. ... ok test_multiline_structured_comment_parsing (test_GenBank.GenBankTests.test_multiline_structured_comment_parsing) Multiline structured comment parsing. ... ok test_negative_location (test_GenBank.GenBankTests.test_negative_location) Negative feature locations. ... ok test_qualifier_escaping_read (test_GenBank.GenBankTests.test_qualifier_escaping_read) Check qualifier escaping is preserved when parsing. ... ok test_qualifier_escaping_write (test_GenBank.GenBankTests.test_qualifier_escaping_write) Check qualifier escaping is preserved when writing. ... ok test_qualifier_order (test_GenBank.GenBankTests.test_qualifier_order) Check the qualifier order is preserved. ... ok test_structured_comment_parsing (test_GenBank.GenBankTests.test_structured_comment_parsing) Structured comment parsing. ... ok test_tsa (test_GenBank.GenBankTests.test_tsa) Test TSA annotation parsing. ... ok test_first_line_imgt (test_GenBank.LineOneTests.test_first_line_imgt) Check IMGT ID line parsing. ... ok test_topology_embl (test_GenBank.LineOneTests.test_topology_embl) Check EMBL ID line parsing. ... ok test_topology_genbank (test_GenBank.LineOneTests.test_topology_genbank) Check GenBank LOCUS line parsing. ... ok test_000_write_invalid_but_parsed_locus_line (test_GenBank.OutputTests.test_000_write_invalid_but_parsed_locus_line) Make sure we survive writing slightly invalid LOCUS lines we could parse. ... ok test_mad_dots (test_GenBank.OutputTests.test_mad_dots) Writing and reading back accesssion.version variants. ... ok test_seqrecord_default_description (test_GenBank.OutputTests.test_seqrecord_default_description) Read in file using SeqRecord default description. ... ok test_write_tsa_data_division (test_GenBank.OutputTests.test_write_tsa_data_division) Make sure we don't kill the TSA data_file_division for TSA files. ... ok test_cleaning_features (test_GenBank.TestBasics.test_cleaning_features) Test the ability to clean up feature values. ... ok test_ensembl_locus (test_GenBank.TestBasics.test_ensembl_locus) Test the ENSEMBL locus line. ... ok test_write_format (test_GenBank.TestBasics.test_write_format) Test writing to the difference formats. ... ok test_feature_parser_01 (test_GenBank.TestFeatureParser.test_feature_parser_01) ... ok test_feature_parser_02 (test_GenBank.TestFeatureParser.test_feature_parser_02) ... ok test_feature_parser_03 (test_GenBank.TestFeatureParser.test_feature_parser_03) ... ok test_feature_parser_04 (test_GenBank.TestFeatureParser.test_feature_parser_04) ... ok test_feature_parser_05 (test_GenBank.TestFeatureParser.test_feature_parser_05) ... ok test_feature_parser_06 (test_GenBank.TestFeatureParser.test_feature_parser_06) ... ok test_feature_parser_07 (test_GenBank.TestFeatureParser.test_feature_parser_07) ... ok test_feature_parser_08 (test_GenBank.TestFeatureParser.test_feature_parser_08) ... ok test_feature_parser_09 (test_GenBank.TestFeatureParser.test_feature_parser_09) ... ok test_feature_parser_10 (test_GenBank.TestFeatureParser.test_feature_parser_10) ... ok test_feature_parser_11 (test_GenBank.TestFeatureParser.test_feature_parser_11) ... ok test_feature_parser_12 (test_GenBank.TestFeatureParser.test_feature_parser_12) ... ok test_feature_parser_13 (test_GenBank.TestFeatureParser.test_feature_parser_13) ... ok test_feature_parser_14 (test_GenBank.TestFeatureParser.test_feature_parser_14) ... ok test_feature_parser_15 (test_GenBank.TestFeatureParser.test_feature_parser_15) ... ok test_feature_parser_16 (test_GenBank.TestFeatureParser.test_feature_parser_16) ... ok test_feature_parser_17 (test_GenBank.TestFeatureParser.test_feature_parser_17) ... ok test_feature_parser_18 (test_GenBank.TestFeatureParser.test_feature_parser_18) ... ok test_feature_parser_19 (test_GenBank.TestFeatureParser.test_feature_parser_19) ... ok test_feature_parser_20 (test_GenBank.TestFeatureParser.test_feature_parser_20) ... ok test_record_parser_01 (test_GenBank.TestRecordParser.test_record_parser_01) ... ok test_record_parser_02 (test_GenBank.TestRecordParser.test_record_parser_02) ... ok test_record_parser_03 (test_GenBank.TestRecordParser.test_record_parser_03) ... ok test_record_parser_04 (test_GenBank.TestRecordParser.test_record_parser_04) ... ok test_record_parser_05 (test_GenBank.TestRecordParser.test_record_parser_05) ... ok test_record_parser_06 (test_GenBank.TestRecordParser.test_record_parser_06) ... ok test_record_parser_07 (test_GenBank.TestRecordParser.test_record_parser_07) ... ok test_record_parser_08 (test_GenBank.TestRecordParser.test_record_parser_08) ... ok test_record_parser_09 (test_GenBank.TestRecordParser.test_record_parser_09) ... ok test_record_parser_10 (test_GenBank.TestRecordParser.test_record_parser_10) ... ok test_record_parser_11 (test_GenBank.TestRecordParser.test_record_parser_11) ... ok test_record_parser_12 (test_GenBank.TestRecordParser.test_record_parser_12) ... ok test_record_parser_13 (test_GenBank.TestRecordParser.test_record_parser_13) ... ok test_record_parser_14 (test_GenBank.TestRecordParser.test_record_parser_14) ... ok test_record_parser_15 (test_GenBank.TestRecordParser.test_record_parser_15) ... ok test_record_parser_16 (test_GenBank.TestRecordParser.test_record_parser_16) ... ok test_record_parser_17 (test_GenBank.TestRecordParser.test_record_parser_17) ... ok test_record_parser_18 (test_GenBank.TestRecordParser.test_record_parser_18) ... ok test_record_parser_19 (test_GenBank.TestRecordParser.test_record_parser_19) ... ok test_record_parser_20 (test_GenBank.TestRecordParser.test_record_parser_20) ... ok test_record_parser_tls (test_GenBank.TestRecordParser.test_record_parser_tls) ... ok test_record_parser_tsa (test_GenBank.TestRecordParser.test_record_parser_tsa) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.300 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GenomeDiagram.py x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! test_GenomeDiagram ... ok test_color_conversions (test_GenomeDiagram.ColorsTest.test_color_conversions) Test color translations. ... ok test_add_track (test_GenomeDiagram.DiagramTest.test_add_track) Add track. ... ok test_add_track_error (test_GenomeDiagram.DiagramTest.test_add_track_error) Test adding unspecified track. ... ok test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest.test_add_track_to_occupied_level) Add track to occupied level. ... ok test_del_tracks (test_GenomeDiagram.DiagramTest.test_del_tracks) Delete track. ... ok test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_methods_pdf) Construct and draw PDF using method approach. ... ok test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_object_pdf) Construct and draw PDF using object approach. ... ok test_get_tracks (test_GenomeDiagram.DiagramTest.test_get_tracks) Get track. ... ok test_move_track (test_GenomeDiagram.DiagramTest.test_move_track) Move a track. ... ok test_partial_diagram (test_GenomeDiagram.DiagramTest.test_partial_diagram) Construct and draw SVG and PDF for just part of a SeqRecord. ... ok test_renumber (test_GenomeDiagram.DiagramTest.test_renumber) Test renumbering tracks. ... ok test_str (test_GenomeDiagram.DiagramTest.test_str) Test diagram's info as string. ... ok test_write_arguments (test_GenomeDiagram.DiagramTest.test_write_arguments) Check how the write methods respond to output format arguments. ... ok test_limits (test_GenomeDiagram.GraphTest.test_limits) Check line graphs. ... ok test_slicing (test_GenomeDiagram.GraphTest.test_slicing) Check GraphData slicing. ... ok test_label_default (test_GenomeDiagram.LabelTest.test_label_default) Feature labels - default. ... ok test_all_sigils (test_GenomeDiagram.SigilsTest.test_all_sigils) All sigils. ... ok test_arrow_heads (test_GenomeDiagram.SigilsTest.test_arrow_heads) Feature arrow sigils, varying heads. ... ok test_arrow_shafts (test_GenomeDiagram.SigilsTest.test_arrow_shafts) Feature arrow sigils, varying shafts. ... ok test_big_arrow_shafts (test_GenomeDiagram.SigilsTest.test_big_arrow_shafts) Feature big-arrow sigils, varying shafts. ... ok test_labels (test_GenomeDiagram.SigilsTest.test_labels) Feature labels. ... ok test_long_arrow_heads (test_GenomeDiagram.SigilsTest.test_long_arrow_heads) Feature ARROW sigil heads within bounding box. ... ok test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest.test_long_bigarrow_heads) Feature BIGARROW sigil heads within bounding box. ... ok test_long_jaggy (test_GenomeDiagram.SigilsTest.test_long_jaggy) Feature JAGGY sigil heads within bounding box. ... ok test_long_octo_heads (test_GenomeDiagram.SigilsTest.test_long_octo_heads) Feature OCTO sigil heads within bounding box. ... ok test_short_arrow (test_GenomeDiagram.SigilsTest.test_short_arrow) Feature arrow sigil heads within bounding box. ... ok test_short_bigarrow (test_GenomeDiagram.SigilsTest.test_short_bigarrow) Feature big-arrow sigil heads within bounding box. ... ok test_short_jaggy (test_GenomeDiagram.SigilsTest.test_short_jaggy) Feature arrow sigil heads within bounding box. ... ok test_short_octo (test_GenomeDiagram.SigilsTest.test_short_octo) Feature big-arrow sigil heads within bounding box. ... ok ---------------------------------------------------------------------- Ran 1 test in 2.169 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsBitmaps.py test_GraphicsBitmaps ... ok test_simple_scatter_plot (test_GraphicsBitmaps.ComparativeTest.test_simple_scatter_plot) Test creation of a simple PNG scatter plot. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.288 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsChromosome.py test_GraphicsChromosome ... ok test_add_count (test_GraphicsChromosome.ChromosomeCountTest.test_add_count) Add counts to specific chromosome segments. ... ok test_add_label (test_GraphicsChromosome.ChromosomeCountTest.test_add_label) Add labels to chromosome segments. ... ok test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest.test_color_from_count) Retrieve a color from a count number with the default color scheme. ... ok test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest.test_fill_chromosome) Test filling out the information on a chromosome. ... ok test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest.test_get_segment_info) Test retrieval of segment information. ... ok test_set_scale (test_GraphicsChromosome.ChromosomeCountTest.test_set_scale) Set the scale for a chromosome segment. ... ok test_random_organism (test_GraphicsChromosome.OrganismGraphicTest.test_random_organism) Generate an organism with random chromosome info. ... ok test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism) Test the basic functionality of drawing an organism. ... ok test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_pdf) Output a simple organism to a PDF file. ... ok test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_ps) Output a simple organism to a postscript file. ... ok test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_svg) Output a simple organism to an SVG file. ... ok test_widget (test_GraphicsChromosome.OrganismGraphicTest.test_widget) Try widget derived functionality. ... ok test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_seqfeatures) Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis. ... ok test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_tuples) Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.634 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsDistribution.py test_GraphicsDistribution ... ok test_multi_page (test_GraphicsDistribution.BarChartTest.test_multi_page) Create a page with multiple distributions on it. ... ok test_simple_page (test_GraphicsDistribution.BarChartTest.test_simple_page) Test displaying a page with single distribution. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.163 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsGeneral.py test_GraphicsGeneral ... ok test_simple_scatter_plot_1 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_1) Test creation of a simple ScatterPlot with one list. ... ok test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_7) Test creation of a simple ScatterPlot with more lists. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.679 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_HMMCasino.py test_HMMCasino ... ok test_baum_welch_training_standard (test_HMMCasino.TestHMMCasino.test_baum_welch_training_standard) Standard Training with known states. ... ok test_baum_welch_training_without (test_HMMCasino.TestHMMCasino.test_baum_welch_training_without) Baum-Welch training without known state sequences. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.328 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_HMMGeneral.py test_HMMGeneral ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_log_likelihood (test_HMMGeneral.AbstractTrainerTest.test_log_likelihood) Calculate log likelihood. ... ok test_ml_estimator (test_HMMGeneral.AbstractTrainerTest.test_ml_estimator) Test the maximum likelihood estimator for simple cases. ... ok test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest.test_allow_transition) Testing allow_transition. ... ok test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest.test_non_ergodic) Non-ergodic model (meaning that some transitions are not allowed). ... ok test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest.test_simple_hmm) Test a simple model with 2 states and 2 symbols. ... ok test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_from) Testing the calculation of transitions_from. ... ok test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_to) Testing the calculation of transitions_to. ... ok test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest.test_allow_all_transitions) Testing allow_all_transitions. ... ok test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_equal_probabilities) ... ok test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_initial_probabilities) ... ok test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_random_probabilities) ... ok test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest.test_test_initialize) Making sure MarkovModelBuilder is initialized correctly. ... ok test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest.test_calculate_s_value) Testing the calculation of s values. ... ok test_empty_state_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_empty_state_training_sequence) ... ok test_invalid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_invalid_training_sequence) ... ok test_valid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_valid_training_sequence) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.058 seconds C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KEGG.py test_KEGG ... ok test_irregular (test_KEGG.CompoundTests.test_irregular) compound.irregular tests. ... ok test_sample (test_KEGG.CompoundTests.test_sample) compound.sample tests. ... ok test_4letter (test_KEGG.EnzymeTests.test_4letter) enzyme.4letter tests. ... ok test_exceptions (test_KEGG.EnzymeTests.test_exceptions) enzyme.exceptions tests. ... ok test_irregular (test_KEGG.EnzymeTests.test_irregular) enzyme.irregular tests. ... ok test_new (test_KEGG.EnzymeTests.test_new) enzyme.new tests. ... ok test_sample (test_KEGG.EnzymeTests.test_sample) enzyme.sample tests. ... ok test_map00950 (test_KEGG.MapTests.test_map00950) map00950.rea tests. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.098 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KEGG_online.py test_KEGG_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.077 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics.py test_KGML_graphics ... ok test_render_KGML_basic (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_basic) Basic rendering of KGML: write to PDF without modification. ... ok test_render_KGML_modify (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_modify) Rendering of KGML to PDF, with modification. ... ok test_render_KGML_transparency (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_transparency) Rendering of KGML to PDF, with color alpha channel. ... ok ---------------------------------------------------------------------- Ran 1 test in 5.082 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics_online.py test_KGML_graphics_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.060 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KGML_nographics.py test_KGML_nographics ... ok test_read_and_write_KGML_files (test_KGML_nographics.KGMLPathwayTest.test_read_and_write_KGML_files) Read KGML from, and write KGML to, local files. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.171 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KeyWList.py test_KeyWList ... ok test_parse (test_KeyWList.KeyWListTest.test_parse) Test parsing keywlist.txt works. ... ok test_parse2 (test_KeyWList.KeyWListTest.test_parse2) Parsing keywlist2.txt (without header and footer). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.063 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_LogisticRegression.py C test_LogisticRegression ... ok test_calculate_model (test_LogisticRegression.TestLogisticRegression.test_calculate_model) ... ok test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression.test_calculate_model_with_update_callback) ... ok test_calculate_probability (test_LogisticRegression.TestLogisticRegression.test_calculate_probability) ... ok test_classify (test_LogisticRegression.TestLogisticRegression.test_classify) ... ok test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression.test_dimensionality_of_input_xs) ... ok test_leave_one_out (test_LogisticRegression.TestLogisticRegression.test_leave_one_out) ... ok test_model_accuracy (test_LogisticRegression.TestLogisticRegression.test_model_accuracy) ... ok test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression.test_xs_and_ys_input_parameter_lengths) ... ok test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression.test_ys_input_class_assignments) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.057 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.086 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_MafIO_index.py test_MafIO_index ... ok test_bundle_without_target (test_MafIO_index.NewIndexTest.test_bundle_without_target) ... ok test_good_big (test_MafIO_index.NewIndexTest.test_good_big) ... ok test_good_small (test_MafIO_index.NewIndexTest.test_good_small) ... ok test_length_coords_mismatch (test_MafIO_index.NewIndexTest.test_length_coords_mismatch) ... ok test_old (test_MafIO_index.PreBuiltIndexTest.test_old) ... ok test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest.test_old_corrupt_index) ... ok test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest.test_old_file_not_found) ... ok test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest.test_old_invalid_sqlite) ... ok test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest.test_old_unfinished_index) ... ok test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_filename) ... ok test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_target_seqname) ... ok test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_version) ... ok test_region2bin (test_MafIO_index.StaticMethodTest.test_region2bin) ... ok test_ucscbin (test_MafIO_index.StaticMethodTest.test_ucscbin) ... ok test_records_begin (test_MafIO_index.TestGetRecord.test_records_begin) ... ok test_records_end (test_MafIO_index.TestGetRecord.test_records_end) ... ok test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF.test_incorrect_bundle_coords) ... ok test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF.test_correct_block_boundary) Following issues 504 and 1086. ... ok test_correct_block_length (test_MafIO_index.TestSearchGoodMAF.test_correct_block_length) Following issues 504 and 1086. ... ok test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_1) Correct retrieval of Cnksr3 in mouse. ... ok test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_2) ... ok test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_3) Following issue 1083. ... ok test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_1) Checking that spliced sequences are correct. ... ok test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_2) Checking that spliced sequences are correct. ... ok test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_count) ... ok test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_schema) ... ok test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_1) ... ok test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_2) ... ok test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF.test_bundle_without_target) ... ok test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF.test_inconsistent_strand) ... ok test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF.test_correct_retrieval_1) Correct retrieval of Cnksr3 in mouse. ... ok test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF.test_invalid_strand) ... ok test_no_alignment (test_MafIO_index.TestSpliceGoodMAF.test_no_alignment) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.707 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.060 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_MarkovModel.py test_MarkovModel ... ok test_argmaxes (test_MarkovModel.TestMarkovModel.test_argmaxes) ... ok test_backward (test_MarkovModel.TestMarkovModel.test_backward) ... ok test_baum_welch (test_MarkovModel.TestMarkovModel.test_baum_welch) ... ok test_forward (test_MarkovModel.TestMarkovModel.test_forward) ... ok test_logsum_and_exp_logsum (test_MarkovModel.TestMarkovModel.test_logsum_and_exp_logsum) ... ok test_logvecadd (test_MarkovModel.TestMarkovModel.test_logvecadd) ... ok test_mle (test_MarkovModel.TestMarkovModel.test_mle) ... ok test_normalize_and_copy_and_check (test_MarkovModel.TestMarkovModel.test_normalize_and_copy_and_check) ... ok test_random_norm (test_MarkovModel.TestMarkovModel.test_random_norm) ... ok test_readline_and_check_start (test_MarkovModel.TestMarkovModel.test_readline_and_check_start) ... ok test_save_and_load (test_MarkovModel.TestMarkovModel.test_save_and_load) ... ok test_topcoder1 (test_MarkovModel.TestMarkovModel.test_topcoder1) ... ok test_topcoder2 (test_MarkovModel.TestMarkovModel.test_topcoder2) ... ok test_topcoder3 (test_MarkovModel.TestMarkovModel.test_topcoder3) ... ok test_topcoder4 (test_MarkovModel.TestMarkovModel.test_topcoder4) ... ok test_topcoder5 (test_MarkovModel.TestMarkovModel.test_topcoder5) ... ok test_train_bw (test_MarkovModel.TestMarkovModel.test_train_bw) ... ok test_train_visible (test_MarkovModel.TestMarkovModel.test_train_visible) ... ok test_uniform_norm (test_MarkovModel.TestMarkovModel.test_uniform_norm) ... ok test_viterbi (test_MarkovModel.TestMarkovModel.test_viterbi) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.229 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` C + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Medline.py test_Medline ... ok test_multiline_mesh (test_Medline.TestMedline.test_multiline_mesh) ... ok test_parse (test_Medline.TestMedline.test_parse) ... ok test_read (test_Medline.TestMedline.test_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.014 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.083 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_NCBITextParser.py test_NCBITextParser ... ok test_conversion (test_NCBITextParser.TestBlastRecord.test_conversion) Converting a Blast record multiple alignment. ... ok test_text_2010L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_001) Parsing BLASTN 2.0.10 output (text_2010L_blastn_001). ... ok test_text_2010L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_002) Parsing BLASTN 2.0.10 output without alignments (text_2010L_blastn_002). ... ok test_text_2010L_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_003) Parsing BLASTN 2.0.10 output without descriptions (text_2010L_blastn_003). ... ok test_text_2010L_blastn_004 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_004) Parsing BLASTN 2.0.10 output (text_2010L_blastn_004). ... ok test_text_2010L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_001) Parsing BLASTP 2.0.10 output (text_2010L_blastp_001). ... ok test_text_2010L_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_002) Parsing BLASTP 2.0.10 output without hits (text_2010L_blastp_002). ... ok test_text_2010L_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_003) Parsing BLASTP 2.0.10 output (text_2010L_blastp_003). ... ok test_text_2010L_blastp_004 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_004) Parsing BLASTP 2.0.10 output without descriptions (text_2010L_blastp_004). ... ok test_text_2010L_blastp_005 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_005) Parsing BLASTP 2.0.10 output without alignments (text_2010L_blastp_005). ... ok test_text_2010L_blastp_006 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_006) Parsing BLASTP 2.0.10 output (text_2010L_blastp_006). ... ok test_text_2010L_blastp_007 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_007) Parsing BLASTP 2.0.10 output (text_2010L_blastp_007). ... ok test_text_2010L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastx_001) Parsing BLASTX 2.0.10 output (text_2010L_blastx_001). ... ok test_text_2010L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastx_002) Parsing BLASTX 2.0.10 output without hits (text_2010L_blastx_002). ... ok test_text_2010L_phiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_001) Parsing PHI-BLAST, BLASTP 2.0.10 output, one round (text_2010L_phiblast_001). ... ok test_text_2010L_phiblast_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_002) Parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (text_2010L_phiblast_002). ... ok test_text_2010L_phiblast_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_003) Parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (text_2010L_phiblast_003). ... ok test_text_2010L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastn_001) Parsing TBLASTN 2.0.10 output (text_2010L_tblastn_001). ... ok test_text_2010L_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastn_002) Parsing TBLASTN 2.0.10 output without hits (text_2010L_tblastn_002). ... ok test_text_2010L_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastx_001) Parsing TBLASTX 2.0.10 output (text_2010L_tblastx_001). ... ok test_text_2011L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_001) Parsing BLASTN 2.0.11 output (text_2011L_blastn_001). ... ok test_text_2011L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_002) Parsing BLASTN 2.0.11 output without alignments (text_2011L_blastn_002). ... ok test_text_2011L_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_003) Parsing BLASTN 2.0.11 output without descriptions (text_2011L_blastn_003). ... ok test_text_2011L_blastn_004 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_004) Parsing BLASTN 2.0.11 output (text_2011L_blastn_004). ... ok test_text_2011L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_001) Parsing BLASTP 2.0.11 output (text_2011L_blastp_001). ... ok test_text_2011L_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_002) Parsing BLASTP 2.0.11 output without hits (text_2011L_blastp_002). ... ok test_text_2011L_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_003) Parsing BLASTP 2.0.11 output (text_2011L_blastp_003). ... ok test_text_2011L_blastp_004 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_004) Parsing BLASTP 2.0.11 output without descriptions (text_2011L_blastp_004). ... ok test_text_2011L_blastp_005 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_005) Parsing BLASTP 2.0.11 output without alignments (text_2011L_blastp_005). ... ok test_text_2011L_blastp_006 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_006) Parsing BLASTP 2.0.11 output (text_2011L_blastp_006). ... ok test_text_2011L_blastp_007 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_007) Parsing BLASTP 2.0.11 output (text_2011L_blastp_007). ... ok test_text_2011L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastx_001) Parsing BLASTX 2.0.11 output (text_2011L_blastx_001). ... ok test_text_2011L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastx_002) Parsing BLASTX 2.0.11 output without hits (text_2011L_blastx_002). ... ok test_text_2011L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_001) Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_001). ... ok test_text_2011L_psiblast_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_002) Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_002). ... ok test_text_2011L_psiblast_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_003) Parsing BLASTP 2.0.11 output (text_2011L_psiblast_003). ... ok test_text_2011L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastn_001) Parsing TBLASTN 2.0.11 output (text_2011L_tblastn_001). ... ok test_text_2011L_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastn_002) Parsing TBLASTN 2.0.11 output without hits (text_2011L_tblastn_002). ... ok test_text_2011L_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastx_001) Parsing TBLASTX 2.0.11 output (text_2011L_tblastx_001). ... ok test_text_2012L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2012L_psiblast_001) Parsing BLASTP 2.0.12 output (text_2012L_psiblast_001). ... ok test_text_2014L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2014L_blastn_001) Parsing BLASTN 2.0.14 output (text_2014L_blastn_001). ... ok test_text_2014L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2014L_psiblast_001) Parsing BLASTP 2.0.14 output (text_2014L_psiblast_001). ... ok test_text_2201L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2201L_blastx_001) Parsing BLASTX 2.2.1 output (text_2201L_blastx_001). ... ok test_text_2202L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastn_001) Parsing BLASTN 2.2.2 output with error messages (text_2202L_blastn_001). ... ok test_text_2202L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastn_002) Parsing BLASTN 2.2.2 output with missing error messages (text_2202L_blastn_002). ... ok test_text_2202L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastp_001) Parsing BLASTP 2.2.2 output with multiple records (text_2202L_blastp_001). ... ok test_text_2208L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2208L_psiblast_001) Parsing BLASTP 2.2.8 output (text_2208L_psiblast_001). ... ok test_text_2215L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2215L_blastx_001) Parsing BLASTX 2.2.15 output with no hits (text_2215L_blastx_001). ... ok test_text_2216L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2216L_tblastn_001) Parsing TBLASTN 2.2.16 output (text_2216L_tblastn_001). ... ok test_text_2220L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2220L_blastx_001) Parsing BLASTX 2.2.20 output (text_2220L_blastx_001). ... ok test_text_2220L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2220L_blastx_002) Parsing BLASTX 2.2.20 output with multiple queries (text_2220L_blastx_002). ... ok test_text_2221L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2221L_blastp_001) Parsing BLASTP 2.2.21 output with multiple queries (text_2221L_blastp_001). ... ok test_text_2222L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2222L_blastx_001) Parsing BLASTX 2.2.22 output with multiple queries (text_2222L_blastx_001). ... ok test_text_2222_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2222_blastx_001) Parsing BLASTX 2.2.22+ output with multiple queries (text_2222_blastx_001). ... ok test_text_2226_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_001) Parsing BLASTN 2.2.26+ output with no results. ... ok test_text_2226_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_002) Parsing BLASTN 2.2.26+ output with single hsp results. ... ok test_text_2226_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_003) Parsing BLASTN 2.2.26+ output with multiple hsp results present. ... ok test_text_2226_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_001) Parsing BLASTP 2.2.26+ with no results. ... ok test_text_2226_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_002) Parsing BLASTP 2.2.26+ with single hsp results. ... ok test_text_2226_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_003) Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok test_text_2226_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_001) Parsing BLASTX 2.2.26+ with no results. ... ok test_text_2226_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_002) Parsing BLASTX 2.2.26+ with single hsp results. ... ok test_text_2226_blastx_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_003) Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok test_text_2226_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_001) Parsing TBLASTN 2.2.26+ output with no results. ... ok test_text_2226_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_002) Parsing TBLASTN 2.2.26+ output with single hsp results. ... ok test_text_2226_tblastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_003) Parsing TBLASTN 2.2.26+ output with multiple hsp results present. ... ok test_text_2226_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_001) Parsing TBLASTX 2.2.26+ output with no results. ... ok test_text_2226_tblastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_002) Parsing TBLASTX 2.2.26+ output with single hsp results. ... ok test_text_2226_tblastx_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_003) Parsing TBLASTX 2.2.26+ output with multiple hsp results present. ... ok test_text_2230_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2230_blastp_001) Parsing BLASTP 2.2.30+ output with line of dashes. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.418 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_NCBIXML.py test_NCBIXML ... ok test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastn_001) Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001). ... ok test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastp_001) Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001). ... ok test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastx_001) Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001). ... ok test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastn_001) Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001). ... ok test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastx_001) 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.test_xml_2218L_blastp_001) Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001). ... ok test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_rpsblast_001) 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.test_xml_2218_blastp_001) Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001). ... ok test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_002) Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002). ... ok test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastp_001) Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001). ... ok test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastx_001) Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001). ... ok test_xml_2900_blastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v1) ... ok test_xml_2900_blastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v2) ... ok test_xml_2900_blastp_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v1) ... ok test_xml_2900_blastp_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v2) ... ok test_xml_2900_blastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v1) ... ok test_xml_2900_blastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v2) ... ok test_xml_2900_tblastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v1) ... ok test_xml_2900_tblastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v2) ... ok test_xml_2900_tblastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v1) ... ok test_xml_2900_tblastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.553 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.015 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NCBI_qblast.py test_NCBI_qblast ... ok test_blastp_nr_actin (test_NCBI_qblast.TestQblast.test_blastp_nr_actin) ... ok test_discomegablast (test_NCBI_qblast.TestQblast.test_discomegablast) ... ok test_error_conditions (test_NCBI_qblast.TestQblast.test_error_conditions) Test if exceptions were properly handled. ... ok test_orchid_est (test_NCBI_qblast.TestQblast.test_orchid_est) ... ok test_parse_qblast_ref_page (test_NCBI_qblast.TestQblast.test_parse_qblast_ref_page) ... ok test_pcr_primers (test_NCBI_qblast.TestQblast.test_pcr_primers) ... ok test_short_query (test_NCBI_qblast.TestQblast.test_short_query) Test SHORT_QUERY_ADJUST parameter. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.076 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NMR.py test_NMR ... ok test_noetools (test_NMR.NmrTests.test_noetools) Self test for NMR.NOEtools. ... ok test_xpktools (test_NMR.NmrTests.test_xpktools) Self test for NMR.xpktools. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.016 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NaiveBayes.py test_NaiveBayes ... ok test_car_data (test_NaiveBayes.CarTest.test_car_data) Simple example using car data. ... ok test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest.test_calculate_function_with_scale) ... ok test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest.test_calculate_function_wrong_dimensionality) ... ok test_classify_function (test_NaiveBayes.NaiveBayesTest.test_classify_function) ... ok test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest.test_train_function_input_lengths) ... ok test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_no_training_set) ... ok test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_uneven_dimension_of_training_set) ... ok test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest.test_train_function_with_priors) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.014 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_baseml.py test_PAML_baseml ... ok testAlignmentExists (test_PAML_baseml.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_baseml.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_baseml.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_baseml.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_baseml.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_baseml.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_baseml.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_baseml.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_baseml.ModTest.testOutputFileSpecified) ... ok testPamlErrorsCaught (test_PAML_baseml.ModTest.testPamlErrorsCaught) ... ok testParseAllVersions (test_PAML_baseml.ModTest.testParseAllVersions) ... ok testParseAlpha1Rho1 (test_PAML_baseml.ModTest.testParseAlpha1Rho1) ... ok testParseModel (test_PAML_baseml.ModTest.testParseModel) ... ok testParseNhomo (test_PAML_baseml.ModTest.testParseNhomo) ... ok testParseSEs (test_PAML_baseml.ModTest.testParseSEs) ... ok testResultsExist (test_PAML_baseml.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_baseml.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_baseml.ModTest.testResultsValid) ... ok testTreeExists (test_PAML_baseml.ModTest.testTreeExists) ... ok testTreeFileValid (test_PAML_baseml.ModTest.testTreeFileValid) ... ok testTreeSpecified (test_PAML_baseml.ModTest.testTreeSpecified) ... ok testWorkingDirValid (test_PAML_baseml.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.155 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_codeml.py test_PAML_codeml ... ok testAlignmentExists (test_PAML_codeml.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_codeml.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_codeml.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_codeml.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_codeml.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_codeml.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_codeml.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_codeml.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_codeml.ModTest.testOutputFileSpecified) ... ok testPamlErrorsCaught (test_PAML_codeml.ModTest.testPamlErrorsCaught) ... ok testParseAA (test_PAML_codeml.ModTest.testParseAA) ... ok testParseAAPairwise (test_PAML_codeml.ModTest.testParseAAPairwise) ... ok testParseAllNSsites (test_PAML_codeml.ModTest.testParseAllNSsites) ... ok testParseBranchSiteA (test_PAML_codeml.ModTest.testParseBranchSiteA) ... ok testParseCladeModelC (test_PAML_codeml.ModTest.testParseCladeModelC) ... ok testParseFreeRatio (test_PAML_codeml.ModTest.testParseFreeRatio) ... ok testParseM2arel (test_PAML_codeml.ModTest.testParseM2arel) ... ok testParseNSsite3 (test_PAML_codeml.ModTest.testParseNSsite3) ... ok testParseNgene2Mgene02 (test_PAML_codeml.ModTest.testParseNgene2Mgene02) ... ok testParseNgene2Mgene1 (test_PAML_codeml.ModTest.testParseNgene2Mgene1) ... ok testParseNgene2Mgene34 (test_PAML_codeml.ModTest.testParseNgene2Mgene34) ... ok testParsePairwise (test_PAML_codeml.ModTest.testParsePairwise) ... ok testParseSEs (test_PAML_codeml.ModTest.testParseSEs) ... ok testParseSitesParamsForPairwise (test_PAML_codeml.ModTest.testParseSitesParamsForPairwise) Verify that pairwise site estimates are indeed parsed. Fixes #483. ... ok testResultsExist (test_PAML_codeml.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_codeml.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_codeml.ModTest.testResultsValid) ... ok testTreeExists (test_PAML_codeml.ModTest.testTreeExists) ... ok testTreeFileValid (test_PAML_codeml.ModTest.testTreeFileValid) ... ok testTreeParseVersatility (test_PAML_codeml.ModTest.testTreeParseVersatility) Test finding trees in the results. ... ok testTreeSpecified (test_PAML_codeml.ModTest.testTreeSpecified) ... ok testWorkingDirValid (test_PAML_codeml.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.821 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_tools.py test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.090 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_yn00.py test_PAML_yn00 ... ok testAlignmentExists (test_PAML_yn00.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_yn00.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_yn00.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_yn00.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_yn00.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_yn00.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_yn00.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_yn00.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_yn00.ModTest.testOutputFileSpecified) ... ok testParseAllVersions (test_PAML_yn00.ModTest.testParseAllVersions) ... ok testParseDottedNames (test_PAML_yn00.ModTest.testParseDottedNames) ... ok testParseDottedNumNames (test_PAML_yn00.ModTest.testParseDottedNumNames) ... ok testParseLongNames (test_PAML_yn00.ModTest.testParseLongNames) ... ok testResultsExist (test_PAML_yn00.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_yn00.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_yn00.ModTest.testResultsValid) ... ok testWorkingDirValid (test_PAML_yn00.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDBList.py test_PDBList ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.065 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_DSSP.py test_PDB_DSSP ... ok test_DSSP_RSA (test_PDB_DSSP.DSSP_test.test_DSSP_RSA) Tests the usage of different ASA tables. ... ok test_DSSP_file (test_PDB_DSSP.DSSP_test.test_DSSP_file) Test parsing of pregenerated DSSP. ... ok test_DSSP_hbonds (test_PDB_DSSP.DSSP_test.test_DSSP_hbonds) Test parsing of DSSP hydrogen bond information. ... ok test_DSSP_in_model_obj (test_PDB_DSSP.DSSP_test.test_DSSP_in_model_obj) All elements correctly added to xtra attribute of input model object. ... ok test_DSSP_noheader_file (test_PDB_DSSP.DSSP_test.test_DSSP_noheader_file) Test parsing of pregenerated DSSP missing header information. ... ok setUpClass (test_PDB_DSSP.DSSP_tool_test) ... skipped 'Install dssp if you want to use it from Biopython.' ---------------------------------------------------------------------- Ran 1 test in 0.185 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Dice.py test_PDB_Dice ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_dice (test_PDB_Dice.DiceTests.test_dice) Self test for PDB.Dice module. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.103 seconds C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Disordered.py test_PDB_Disordered ... ok test_copy_and_write_disordered (test_PDB_Disordered.TestDisordered.test_copy_and_write_disordered) Extract, save, and parse again disordered atoms. ... ok test_copy_disordered_atom (test_PDB_Disordered.TestDisordered.test_copy_disordered_atom) Copies disordered atoms and all their children. ... ok test_copy_entire_chain (test_PDB_Disordered.TestDisordered.test_copy_entire_chain) Copy propagates throughout SMCRA object. ... ok test_disordered_cog (test_PDB_Disordered.TestDisordered.test_disordered_cog) Calculate DisorderedAtom center of geometry. ... ok test_empty_disordered (test_PDB_Disordered.TestDisordered.test_empty_disordered) Raise ValueError on center of mass calculation of empty DisorderedAtom. ... ok test_remove_disordered_atom (test_PDB_Disordered.TestDisordered.test_remove_disordered_atom) Remove altlocs from DisorderedAtom entities. ... ok test_remove_disordered_residue (test_PDB_Disordered.TestDisordered.test_remove_disordered_residue) Remove residues from DisorderedResidue entities. ... ok test_structure_w_disordered_com (test_PDB_Disordered.TestDisordered.test_structure_w_disordered_com) Calculate center of mass of structure including DisorderedAtoms. ... ok test_transform_disordered (test_PDB_Disordered.TestDisordered.test_transform_disordered) Transform propagates through disordered atoms. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.110 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Exposure.py test_PDB_Exposure ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_ExposureCN (test_PDB_Exposure.Exposure.test_ExposureCN) HSExposureCN. ... ok test_HSExposureCA (test_PDB_Exposure.Exposure.test_HSExposureCA) HSExposureCA. ... ok test_HSExposureCB (test_PDB_Exposure.Exposure.test_HSExposureCB) HSExposureCB. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.364 seconds C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_FragmentMapper.py test_PDB_FragmentMapper ... ok test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests.test_fragment_mapper) Self test for FragmentMapper module. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.128 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_KDTree.py test_PDB_KDTree ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_KDTree_exceptions (test_PDB_KDTree.KDTreeTest.test_KDTree_exceptions) ... ok test_KDTree_neighbor_search_manual (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_manual) Test all fixed radius neighbor search. ... ok test_KDTree_neighbor_search_simple (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_simple) Test all fixed radius neighbor search. ... ok test_KDTree_point_search (test_PDB_KDTree.KDTreeTest.test_KDTree_point_search) Test searching all points within a certain radius of center. ... ok test_neighbor_search (test_PDB_KDTree.NeighborTest.test_neighbor_search) NeighborSearch: Find nearby randomly generated coordinates. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.929 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIF2Dict.py test_PDB_MMCIF2Dict ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_MMCIF2dict (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_MMCIF2dict) ... ok test_inline_comments (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_inline_comments) Comments may begin outside of column 1 if preceded by whitespace. ... ok test_loop_keyword_case_insensitive (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_loop_keyword_case_insensitive) Comments may begin outside of column 1. ... ok test_quotefix (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_quotefix) ... ok test_splitline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_splitline) ... ok test_token_after_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_token_after_multiline) Multi-line string followed by token on the same line. ... ok test_truncated_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_truncated_multiline) ... ok test_underscores (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_underscores) ... ok test_verbatim_block (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_verbatim_block) Verbatim blocks parsed correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.113 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFIO.py test_PDB_MMCIFIO ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_mmcifio_multimodel (test_PDB_MMCIFIO.WriteTest.test_mmcifio_multimodel) Write a multi-model, multi-chain mmCIF file. ... ok test_mmcifio_select (test_PDB_MMCIFIO.WriteTest.test_mmcifio_select) Write a selection of the structure using a Select subclass. ... ok test_mmcifio_write_custom_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_custom_residue) Write a chainless residue using PDBIO. ... ok test_mmcifio_write_dict (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_dict) Write an mmCIF dictionary out, read it in and compare them. ... ok test_mmcifio_write_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue) Write a single residue using MMCIFIO. ... ok test_mmcifio_write_residue_w_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_w_chain) Write a single residue (chain id == X) using MMCIFIO. ... ok test_mmcifio_write_residue_wout_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_wout_chain) Write a single orphan residue using MMCIFIO. ... ok test_mmcifio_write_structure (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_structure) Write a full structure using MMCIFIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.282 seconds C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFParser.py test_PDB_MMCIFParser ... ok test_conversion (test_PDB_MMCIFParser.CIFtoPDB.test_conversion) Parse 1LCD.cif, write 1LCD.pdb, parse again and compare. ... ok test_conversion_not_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_not_preserve_numbering) Convert mmCIF to PDB and renumber atom serials. ... ok test_conversion_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_preserve_numbering) Convert mmCIF to PDB and preserve original serial numbering. ... ok testModels (test_PDB_MMCIFParser.ParseReal.testModels) Test file with multiple models. ... ok test_filehandle (test_PDB_MMCIFParser.ParseReal.test_filehandle) Test if the parser can handle file handle as well as filename. ... ok test_header (test_PDB_MMCIFParser.ParseReal.test_header) Test if the parser populates header data. ... ok test_insertions (test_PDB_MMCIFParser.ParseReal.test_insertions) Test file with residue insertion codes. ... ok test_parsers (test_PDB_MMCIFParser.ParseReal.test_parsers) Extract polypeptides from 1A80. ... ok test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal.test_point_mutations_fast) Test if FastMMCIFParser can parse point mutations correctly. ... ok test_point_mutations_main (test_PDB_MMCIFParser.ParseReal.test_point_mutations_main) Test if MMCIFParser parse point mutations correctly. ... ok test_with_anisotrop (test_PDB_MMCIFParser.ParseReal.test_with_anisotrop) ... ok ---------------------------------------------------------------------- Ran 1 test in 1.293 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_NACCESS.py test_PDB_NACCESS ... ok test_NACCESS (test_PDB_NACCESS.NACCESS_test.test_NACCESS) Test calling NACCESS from Bio.PDB. ... skipped 'Install naccess if you want to use it from Biopython.' test_NACCESS_asa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_asa_file) Test parsing of pregenerated asa NACCESS file. ... ok test_NACCESS_rsa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_rsa_file) Test parsing of pregenerated rsa NACCESS file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.078 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBIO.py test_PDB_PDBIO ... ok test_model_numbering (test_PDB_PDBIO.WriteTest.test_model_numbering) Preserve model serial numbers during I/O. ... ok test_pdbio_missing_occupancy (test_PDB_PDBIO.WriteTest.test_pdbio_missing_occupancy) Write PDB file with missing occupancy. ... ok test_pdbio_select (test_PDB_PDBIO.WriteTest.test_pdbio_select) Write a selection of the structure using a Select subclass. ... ok test_pdbio_write_auto_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_auto_numbering) Test writing PDB and do not preserve atom numbering. ... ok test_pdbio_write_custom_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_custom_residue) Write a chainless residue using PDBIO. ... ok test_pdbio_write_preserve_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_preserve_numbering) Test writing PDB and preserve atom numbering. ... ok test_pdbio_write_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue) Write a single residue using PDBIO. ... ok test_pdbio_write_residue_w_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_w_chain) Write a single residue (chain id == X) using PDBIO. ... ok test_pdbio_write_residue_wout_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_wout_chain) Write a single orphan residue using PDBIO. ... ok test_pdbio_write_structure (test_PDB_PDBIO.WriteTest.test_pdbio_write_structure) Write a full structure using PDBIO. ... ok test_pdbio_write_truncated (test_PDB_PDBIO.WriteTest.test_pdbio_write_truncated) Test parsing of truncated lines. ... ok test_pdbio_write_unk_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_unk_element) PDBIO raises ValueError when writing unrecognised atomic elements. ... ok test_pdbio_write_x_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_x_element) Write a structure with atomic element X with PDBIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.240 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBParser.py test_PDB_PDBParser ... ok test_1_flawedpdb_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_1_flawedpdb_permissive) Parse a flawed PDB file in permissive mode: check warnings. ... ok test_2_flawedpdb_strict (test_PDB_PDBParser.FlawedPDB_tests.test_2_flawedpdb_strict) Parse a flawed PDB file in permissive mode: check errors. ... ok test_3_bad_xyz_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_3_bad_xyz_permissive) Parse an entry with bad x,y,z value with PERMISSIVE=True. ... ok test_4_bad_xyz_strict (test_PDB_PDBParser.FlawedPDB_tests.test_4_bad_xyz_strict) Parse an entry with bad x,y,z value with PERMISSIVE=False. ... ok test_5_missing_occupancy_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_5_missing_occupancy_permissive) Parse file with missing occupancy with PERMISSIVE=True. ... ok test_6_missing_occupancy_strict (test_PDB_PDBParser.FlawedPDB_tests.test_6_missing_occupancy_strict) Parse file with missing occupancy with PERMISSIVE=False. ... ok test_structure_details (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_details) Verify details of the parsed example PDB file. ... ok test_structure_integrity (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_integrity) Verify the structure of the parsed example PDB file. ... ok test_1A8O_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_1A8O_strict) Parse 1A8O.pdb file in strict mode. ... ok test_SMCRA (test_PDB_PDBParser.ParseRealPDB_tests.test_SMCRA) Walk down the structure hierarchy and test parser reliability. ... ok test_duplicated_residue_permissive (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_permissive) Catch exception on duplicated residue. ... ok test_duplicated_residue_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_strict) Throw exception on duplicated residue. ... ok test_empty (test_PDB_PDBParser.ParseRealPDB_tests.test_empty) Parse an empty file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.129 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Polypeptide.py test_PDB_Polypeptide ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_cappbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real) Test CaPPBuilder on real PDB file. ... ok test_cappbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real_nonstd) Test CaPPBuilder on real PDB file allowing non-standard amino acids. ... ok test_cappbuilder_tau (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_tau) Test tau angles calculated with CaPPBuilder. ... ok test_ppbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real) Test PPBuilder on real PDB file. ... ok test_ppbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real_nonstd) Test PPBuilder on real PDB file allowing non-standard amino acids. ... ok test_ppbuilder_torsion (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_torsion) Test phi/psi angles calculated with PPBuilder. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.103 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_ResidueDepth.py test_PDB_ResidueDepth ... ok setUpClass (test_PDB_ResidueDepth.MSMS_tests) ... skipped 'Install MSMS if you want to use it from Biopython.' test_pdb_to_xyzr (test_PDB_ResidueDepth.ResidueDepth_tests.test_pdb_to_xyzr) Test generation of xyzr (atomic radii) file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.091 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_SASA.py test_PDB_SASA ... ok test_custom_radii (test_PDB_SASA.TestShrakeRupley.test_custom_radii) Run Shrake-Rupley with custom radii. ... ok test_default_algorithm (test_PDB_SASA.TestShrakeRupley.test_default_algorithm) Run Shrake-Rupley with default parameters. ... ok test_fail_compute_entity_level (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_level) Raise exception on input Atom entity. ... ok test_fail_compute_entity_type (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_type) Raise exception on unsupported entity type. ... ok test_fail_compute_level_1 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_1) Raise exception on invalid level parameter: X. ... ok test_fail_compute_level_2 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_2) Raise exception on invalid level parameter: S > C. ... ok test_fail_empty_entity (test_PDB_SASA.TestShrakeRupley.test_fail_empty_entity) Raise exception on invalid level parameter: S > C. ... ok test_fail_n_points (test_PDB_SASA.TestShrakeRupley.test_fail_n_points) Raise exception on bad n_points parameter. ... ok test_fail_probe_radius (test_PDB_SASA.TestShrakeRupley.test_fail_probe_radius) Raise exception on bad probe_radius parameter. ... ok test_higher_resolution (test_PDB_SASA.TestShrakeRupley.test_higher_resolution) Run Shrake-Rupley with 960 points per sphere. ... ok test_level_C (test_PDB_SASA.TestShrakeRupley.test_level_C) Run Shrake-Rupley with level C. ... ok test_level_R (test_PDB_SASA.TestShrakeRupley.test_level_R) Run Shrake-Rupley with level R. ... ok ---------------------------------------------------------------------- Ran 1 test in 3.534 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_SMCRA.py test_PDB_SMCRA ... ok test_assign_unknown_element (test_PDB_SMCRA.Atom_Element.test_assign_unknown_element) Unknown element is assigned 'X'. ... ok test_atom_element_assignment (test_PDB_SMCRA.Atom_Element.test_atom_element_assignment) Atom Element. ... ok test_hydrogens (test_PDB_SMCRA.Atom_Element.test_hydrogens) ... ok test_ions (test_PDB_SMCRA.Atom_Element.test_ions) Element for magnesium is assigned correctly. ... ok test_chain_cog (test_PDB_SMCRA.CenterOfMassTests.test_chain_cog) Calculate center of geometry of individual chains. ... ok test_com_empty_structure (test_PDB_SMCRA.CenterOfMassTests.test_com_empty_structure) Center of mass of empty structure raises ValueError. ... ok test_structure_cog (test_PDB_SMCRA.CenterOfMassTests.test_structure_cog) Calculate Structure center of geometry. ... ok test_structure_com (test_PDB_SMCRA.CenterOfMassTests.test_structure_com) Calculate Structure center of mass. ... ok test_change_chain_id (test_PDB_SMCRA.ChangingIdTests.test_change_chain_id) Change the id of a model. ... ok test_change_id_to_self (test_PDB_SMCRA.ChangingIdTests.test_change_id_to_self) Changing the id to itself does nothing (does not raise). ... ok test_change_model_id (test_PDB_SMCRA.ChangingIdTests.test_change_model_id) Change the id of a model. ... ok test_change_model_id_raises (test_PDB_SMCRA.ChangingIdTests.test_change_model_id_raises) Cannot change id to a value already in use by another child. ... ok test_change_residue_id (test_PDB_SMCRA.ChangingIdTests.test_change_residue_id) Change the id of a residue. ... ok test_full_id_is_updated_chain (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_chain) Invalidate cached full_ids if an id is changed. ... ok test_full_id_is_updated_residue (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_residue) Invalidate cached full_ids if an id is changed. ... ok test_atom_copy (test_PDB_SMCRA.CopyTests.test_atom_copy) ... ok test_entity_copy (test_PDB_SMCRA.CopyTests.test_entity_copy) Make a copy of a residue. ... ok test_get_atoms (test_PDB_SMCRA.IterationTests.test_get_atoms) Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok test_get_chains (test_PDB_SMCRA.IterationTests.test_get_chains) Yields chains from different models separately. ... ok test_get_residues (test_PDB_SMCRA.IterationTests.test_get_residues) Yields all residues from all models. ... ok test_comparison_entities (test_PDB_SMCRA.SortingTests.test_comparison_entities) Test comparing and sorting the several SMCRA objects. ... ok test_residue_sort (test_PDB_SMCRA.SortingTests.test_residue_sort) Test atoms are sorted correctly in residues. ... ok test_transform (test_PDB_SMCRA.TransformTests.test_transform) Transform entities (rotation and translation). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.401 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_StructureAlignment.py test_PDB_StructureAlignment ... ok test_StructAlign (test_PDB_StructureAlignment.StructureAlignTests.test_StructAlign) Tests on module to align two proteins according to a FASTA alignment file. ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.213 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Superimposer.py test_PDB_Superimposer ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_Superimposer (test_PDB_Superimposer.SuperimposerTests.test_Superimposer) Test on module that superimpose two protein structures. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.093 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_internal_coords.py test_PDB_internal_coords ... ok test_model_change_internal_coords (test_PDB_internal_coords.Rebuild.test_model_change_internal_coords) Get model internal coords, modify psi and chi1 values and check. ... ok test_rebuild_disordered_atoms_residues (test_PDB_internal_coords.Rebuild.test_rebuild_disordered_atoms_residues) Convert disordered protein to internal coordinates and back. ... ok test_rebuild_multichain_missing (test_PDB_internal_coords.Rebuild.test_rebuild_multichain_missing) Convert multichain missing atom protein to internal coordinates and back. ... ok test_write_SCAD (test_PDB_internal_coords.Rebuild.test_write_SCAD) Check SCAD output plus MaxPeptideBond and Gly CB. ... ok ---------------------------------------------------------------------- Ran 1 test in 5.466 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_parse_pdb_header.py test_PDB_parse_pdb_header ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_1 (test_PDB_parse_pdb_header.ParseReal.test_1) Parse the header of a known PDB file (1A8O). ... ok test_2 (test_PDB_parse_pdb_header.ParseReal.test_2) Parse the header of another PDB file (2BEG). ... ok test_parse_header_line (test_PDB_parse_pdb_header.ParseReal.test_parse_header_line) Unit test for parsing and converting fields in HEADER record. ... ok test_parse_no_title (test_PDB_parse_pdb_header.ParseReal.test_parse_no_title) Unit test for sensible result with no TITLE line. ... ok test_parse_pdb_with_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_465) Tests that parse_pdb_header now can identify some REMARK 465 entries. ... ok test_parse_pdb_with_remark_99 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_99) Tests that parse_pdb_header can identify REMARK 99 ASTRAL entries. ... ok test_parse_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_remark_465) A UNIT-test for the private function _parse_remark_465. ... ok test_parse_title_line (test_PDB_parse_pdb_header.ParseReal.test_parse_title_line) Unit test for correct parsing of multiline title records. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.108 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` C + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_vectors.py test_PDB_vectors ... ok test_Vector (test_PDB_vectors.VectorTests.test_Vector) Test Vector object. ... ok test_Vector_angles (test_PDB_vectors.VectorTests.test_Vector_angles) Test Vector angles. ... ok test_coord_space (test_PDB_vectors.VectorTests.test_coord_space) ... ok test_division (test_PDB_vectors.VectorTests.test_division) Confirm division works. ... ok test_get_spherical_coordinates (test_PDB_vectors.VectorTests.test_get_spherical_coordinates) Test spherical coordinates. ... ok test_m2rotaxis_0 (test_PDB_vectors.VectorTests.test_m2rotaxis_0) Test 0 deg rotation. Axis must be [1, 0, 0] as per Vector documentation. ... ok test_m2rotaxis_180 (test_PDB_vectors.VectorTests.test_m2rotaxis_180) Test 180 deg rotation. ... ok test_m2rotaxis_90 (test_PDB_vectors.VectorTests.test_m2rotaxis_90) Test 90 deg rotation. ... ok test_normalization (test_PDB_vectors.VectorTests.test_normalization) Test Vector normalization. ... ok test_refmat (test_PDB_vectors.VectorTests.test_refmat) ... ok test_rotmat_0 (test_PDB_vectors.VectorTests.test_rotmat_0) Test rotmat when the rotation is 0 deg (singularity). ... ok test_rotmat_180 (test_PDB_vectors.VectorTests.test_rotmat_180) Test rotmat when the rotation is 180 deg (singularity). ... ok test_rotmat_90 (test_PDB_vectors.VectorTests.test_rotmat_90) Test regular 90 deg rotation. ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PQR.py test_PQR ... ok test_bad_charge (test_PQR.ParseSimplePQR.test_bad_charge) Test if missing or malformed charge case is handled correctly. ... ok test_bad_radius (test_PQR.ParseSimplePQR.test_bad_radius) Test if missing, malformed or negative radius case is handled correctly. ... ok test_bad_xyz (test_PQR.ParseSimplePQR.test_bad_xyz) Test if bad coordinates exception is raised. ... ok test_single_input (test_PQR.ParseSimplePQR.test_single_input) Test if a single ATOM entry correctly parsed. ... ok test_pdbio_write_pqr_structure (test_PQR.WriteTest.test_pdbio_write_pqr_structure) Write a full structure using PDBIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.122 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Pathway.py test_Pathway ... ok testAdditionalFunctions (test_Pathway.GraphTestCase.testAdditionalFunctions) ... ok test_Edges (test_Pathway.GraphTestCase.test_Edges) ... ok test_Equals (test_Pathway.GraphTestCase.test_Equals) ... ok test_Nodes (test_Pathway.GraphTestCase.test_Nodes) ... ok test_RemoveNode (test_Pathway.GraphTestCase.test_RemoveNode) ... ok testAdditionalFunctions (test_Pathway.MultiGraphTestCase.testAdditionalFunctions) ... ok test_Edges (test_Pathway.MultiGraphTestCase.test_Edges) ... ok test_Equals (test_Pathway.MultiGraphTestCase.test_Equals) ... ok test_Nodes (test_Pathway.MultiGraphTestCase.test_Nodes) ... ok test_RemoveNode (test_Pathway.MultiGraphTestCase.test_RemoveNode) ... ok test_eq (test_Pathway.ReactionTestCase.test_eq) ... ok test_rev (test_Pathway.ReactionTestCase.test_rev) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.021 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Phd.py test_Phd ... ok test_check_SeqIO (test_Phd.PhdTest454.test_check_SeqIO) Test phd_454 using parser via SeqIO. ... ok test_check_SeqIO (test_Phd.PhdTestOne.test_check_SeqIO) Test phd1 using parser via SeqIO. ... ok test_check_record_parser (test_Phd.PhdTestOne.test_check_record_parser) Test phd1 file in detail. ... ok test_check_SeqIO (test_Phd.PhdTestSolexa.test_check_SeqIO) Test phd2 using parser via SeqIO. ... ok test_check_SeqIO (test_Phd.PhdTestTwo.test_check_SeqIO) Test phd2 using parser via SeqIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.090 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.021 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.015 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_nodepend.py test_PopGen_GenePop_nodepend ... ok test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_file_record_parser) Basic operation of the File Record Parser. ... ok test_remove_features (test_PopGen_GenePop_nodepend.FileParserTest.test_remove_features) Testing the ability to remove population/loci via class methods. ... ok test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_wrong_file_parser) Testing the ability to deal with wrongly formatted files. ... ok test_record_parser (test_PopGen_GenePop_nodepend.ParserTest.test_record_parser) Basic operation of the Record Parser. ... ok test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest.test_wrong_file_parser) Testing the ability to deal with wrongly formatted files. ... ok test_record_basic (test_PopGen_GenePop_nodepend.RecordTest.test_record_basic) Basic test on Record. ... ok test_utils (test_PopGen_GenePop_nodepend.UtilsTest.test_utils) Basic operation of GenePop Utils. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.037 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.084 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.100 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ProtParam.py test_ProtParam ... ok test_aromaticity (test_ProtParam.ProtParamTest.test_aromaticity) Calculate protein aromaticity. ... ok test_charge_at_pH (test_ProtParam.ProtParamTest.test_charge_at_pH) Test charge_at_pH function. ... ok test_count_amino_acids (test_ProtParam.ProtParamTest.test_count_amino_acids) Calculate amino acid counts. ... ok test_flexibility (test_ProtParam.ProtParamTest.test_flexibility) Calculate protein flexibility. ... ok test_get_amino_acids_percent (test_ProtParam.ProtParamTest.test_get_amino_acids_percent) Calculate amino acid percentages. ... ok test_get_molecular_weight (test_ProtParam.ProtParamTest.test_get_molecular_weight) Calculate protein molecular weight. ... ok test_get_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_molecular_weight_identical) Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight) Calculate monoisotopic molecular weight. ... ok test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight_identical) Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok test_gravy (test_ProtParam.ProtParamTest.test_gravy) Calculate gravy. Tests all pre-defined scales. ... ok test_instability_index (test_ProtParam.ProtParamTest.test_instability_index) Calculate protein instability index. ... ok test_isoelectric_point (test_ProtParam.ProtParamTest.test_isoelectric_point) Calculate the isoelectric point. ... ok test_molar_extinction_coefficient (test_ProtParam.ProtParamTest.test_molar_extinction_coefficient) Molar extinction coefficient. ... ok test_protein_scale (test_ProtParam.ProtParamTest.test_protein_scale) Calculate the Kite Doolittle scale. ... ok test_secondary_structure_fraction (test_ProtParam.ProtParamTest.test_secondary_structure_fraction) Calculate secondary structure fractions. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.069 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_QCPSuperimposer.py test_QCPSuperimposer ... ok test_get_init_rms (test_QCPSuperimposer.QCPSuperimposerTest.test_get_init_rms) ... ok test_get_rms (test_QCPSuperimposer.QCPSuperimposerTest.test_get_rms) ... ok test_get_rotran (test_QCPSuperimposer.QCPSuperimposerTest.test_get_rotran) ... ok test_get_transformed (test_QCPSuperimposer.QCPSuperimposerTest.test_get_transformed) ... ok test_oldTest (test_QCPSuperimposer.QCPSuperimposerTest.test_oldTest) ... ok test_run (test_QCPSuperimposer.QCPSuperimposerTest.test_run) ... ok test_set (test_QCPSuperimposer.QCPSuperimposerTest.test_set) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.098 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_RCSBFormats.py test_RCSBFormats ... ok test_compare_chains (test_RCSBFormats.CompareStructures.test_compare_chains) Compare parsed chains. ... ok test_compare_models (test_RCSBFormats.CompareStructures.test_compare_models) Compared parsed models. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.540 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Restriction.py test_Restriction ... ok test_basic_isochizomers (test_Restriction.EnzymeComparison.test_basic_isochizomers) Test to be sure isochizomer and neoschizomers are as expected. ... ok test_comparisons (test_Restriction.EnzymeComparison.test_comparisons) Test comparison operators between different enzymes. ... ok test_change (test_Restriction.RestrictionBatchPrintTest.test_change) Test that change() changes something. ... ok test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map1) Test that print_as('map'); print_that() correctly wraps round. ... ok test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map2) Test that print_as('map'); print_that() correctly wraps round. ... ok test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map3) Test that print_as('map'); print_that() correctly wraps round. ... ok test_analysis_restrictions (test_Restriction.RestrictionBatches.test_analysis_restrictions) Test Fancier restriction analysis. ... ok test_batch_analysis (test_Restriction.RestrictionBatches.test_batch_analysis) Sequence analysis with a restriction batch. ... ok test_creating_batch (test_Restriction.RestrictionBatches.test_creating_batch) Creating and modifying a restriction batch. ... ok test_premade_batches (test_Restriction.RestrictionBatches.test_premade_batches) Test content of premade batches CommOnly, NoComm, AllEnzymes. ... ok test_search_premade_batches (test_Restriction.RestrictionBatches.test_search_premade_batches) Test search with pre-made batches CommOnly, NoComm, AllEnzymes. ... ok test_formatted_seq (test_Restriction.SequenceTesting.test_formatted_seq) Test several methods of FormattedSeq. ... ok test_non_iupac_letters (test_Restriction.SequenceTesting.test_non_iupac_letters) Test if non-IUPAC letters raise a TypeError. ... ok test_sequence_object (test_Restriction.SequenceTesting.test_sequence_object) Test if sequence must be a Seq or MutableSeq object. ... ok test_circular_sequences (test_Restriction.SimpleEnzyme.test_circular_sequences) Deal with cutting circular sequences. ... ok test_cutting_border_positions (test_Restriction.SimpleEnzyme.test_cutting_border_positions) Check if cutting after first and penultimate position works. ... ok test_ear_cutting (test_Restriction.SimpleEnzyme.test_ear_cutting) Test basic cutting with EarI (ambiguous overhang). ... ok test_eco_cutting (test_Restriction.SimpleEnzyme.test_eco_cutting) Test basic cutting with EcoRI (5'overhang). ... ok test_init (test_Restriction.SimpleEnzyme.test_init) Check for error during __init__. ... ok test_kpn_cutting (test_Restriction.SimpleEnzyme.test_kpn_cutting) Test basic cutting with KpnI (3'overhang). ... ok test_overlapping_cut_sites (test_Restriction.SimpleEnzyme.test_overlapping_cut_sites) Check if overlapping recognition sites are properly handled. ... ok test_recognition_site_on_both_strands (test_Restriction.SimpleEnzyme.test_recognition_site_on_both_strands) Check if recognition sites on both strands are properly handled. ... ok test_shortcuts (test_Restriction.SimpleEnzyme.test_shortcuts) Check if '/' and '//' work as '.search' and '.catalyse'. ... ok test_sma_cutting (test_Restriction.SimpleEnzyme.test_sma_cutting) Test basic cutting with SmaI (blunt cutter). ... ok test_sna_cutting (test_Restriction.SimpleEnzyme.test_sna_cutting) Test basic cutting with SnaI (unknown). ... ok test_print_that (test_Restriction.TestPrintOutputs.test_print_that) Test print_that function. ... ok test_str_method (test_Restriction.TestPrintOutputs.test_str_method) Test __str__ and __repr__ outputs. ... ok test_supplier (test_Restriction.TestPrintOutputs.test_supplier) Test output of supplier list for different enzyme types. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.194 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Astral.py test_SCOP_Astral ... ok testConstructWithCustomFile (test_SCOP_Astral.AstralTests.testConstructWithCustomFile) ... ok testGetDomainsClustered (test_SCOP_Astral.AstralTests.testGetDomainsClustered) ... ok testGetDomainsFromFile (test_SCOP_Astral.AstralTests.testGetDomainsFromFile) ... ok testGetSeq (test_SCOP_Astral.AstralTests.testGetSeq) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Cla.py test_SCOP_Cla ... ok testError (test_SCOP_Cla.ClaTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testIndex (test_SCOP_Cla.ClaTests.testIndex) Test CLA file indexing. ... ok testParse (test_SCOP_Cla.ClaTests.testParse) Test if all records in a CLA file are being read. ... ok testRecord (test_SCOP_Cla.ClaTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Cla.ClaTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.080 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Des.py test_SCOP_Des ... ok testError (test_SCOP_Des.DesTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Des.DesTests.testParse) Test if all records in a DES file are being read. ... ok testRecord (test_SCOP_Des.DesTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Des.DesTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.094 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Dom.py test_SCOP_Dom ... ok testError (test_SCOP_Dom.DomTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Dom.DomTests.testParse) Test if all records in a DOM file are being read. ... ok testRecord (test_SCOP_Dom.DomTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Dom.DomTests.testStr) Test if we can convert each record to a string correctly. ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.094 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Hie.py test_SCOP_Hie ... ok testError (test_SCOP_Hie.HieTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Hie.HieTests.testParse) Test if all records in a HIE file are being read. ... ok testStr (test_SCOP_Hie.HieTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.081 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Raf.py test_SCOP_Raf ... ok testParse (test_SCOP_Raf.RafTests.testParse) Parse a RAF record. ... ok testSeqMapAdd (test_SCOP_Raf.RafTests.testSeqMapAdd) ... ok testSeqMapIndex (test_SCOP_Raf.RafTests.testSeqMapIndex) ... ok testSeqMapSlice (test_SCOP_Raf.RafTests.testSeqMapSlice) ... ok test_SeqMap_getAtoms_err (test_SCOP_Raf.RafTests.test_SeqMap_getAtoms_err) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.081 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Residues.py test_SCOP_Residues ... ok testAstralParse (test_SCOP_Residues.ResiduesTests.testAstralParse) Test if we can parse residue subsets enclosed in brackets. ... ok testJustPdbId (test_SCOP_Residues.ResiduesTests.testJustPdbId) ... ok testParse (test_SCOP_Residues.ResiduesTests.testParse) ... ok testParseError (test_SCOP_Residues.ResiduesTests.testParseError) ... ok testPdbId (test_SCOP_Residues.ResiduesTests.testPdbId) ... ok testStr (test_SCOP_Residues.ResiduesTests.testStr) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Scop.py test_SCOP_Scop ... ok testConstructFromDirectory (test_SCOP_Scop.ScopTests.testConstructFromDirectory) ... ok testGetAscendent (test_SCOP_Scop.ScopTests.testGetAscendent) ... ok testParse (test_SCOP_Scop.ScopTests.testParse) ... ok testParseDomain (test_SCOP_Scop.ScopTests.testParseDomain) ... ok testSccsOrder (test_SCOP_Scop.ScopTests.testSccsOrder) ... ok test_get_descendents (test_SCOP_Scop.ScopTests.test_get_descendents) Test getDescendents method. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_online.py test_SCOP_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.075 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SVDSuperimposer.py test_SVDSuperimposer ... ok test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest.test_get_init_rms) ... ok test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest.test_oldTest) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.013 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl.py test_SearchIO_blat_psl ... ok test_psl_34_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_001) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_002) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_003) Test parsing blat output (psl_34_003.psl). ... ok test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_004) Test parsing blat output (psl_34_004.psl). ... ok test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_005) Test parsing blat output (psl_34_005.psl). ... ok test_psl_35_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_001) Test parsing blat output (psl_35_001.psl). ... ok test_psl_35_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_002) Test parsing blat output (psl_35_002.psl). ... ok test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_001) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_002) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_003) Test parsing blat output (psl_34_003.psl). ... ok test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_004) Test parsing blat output (psl_34_004.psl). ... ok test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_005) Test parsing blat output (psl_34_005.psl). ... ok test_psl_35_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_001) Test parsing blat output (psl_35_001.psl). ... ok test_psl_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_002) Test parsing blat output (psl_35_002.psl). ... ok test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_001) Test parsing blat output (pslx_34_001.pslx). ... ok test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_002) Test parsing blat output (pslx_34_002.pslx). ... ok test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_003) Test parsing blat output (pslx_34_003.pslx). ... ok test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_004) Test parsing blat output (pslx_34_004.pslx). ... ok test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_005) Test parsing blat output (pslx_34_005.pslx). ... ok test_pslx_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_35_002) Test parsing blat output (pslx_35_002.pslx). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl_index.py test_SearchIO_blat_psl_index ... ok test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_001) Test blat-psl indexing, multiple queries. ... ok test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_002) Test blat-psl indexing, single query, no hits. ... ok test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_003) Test blat-psl indexing, single query, single hit. ... ok test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_004) Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_005) Test blat-psl indexing, multiple queries, no header. ... ok test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_006) Test blat-pslx indexing, multiple queries. ... ok test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_007) Test blat-pslx indexing, single query, no hits. ... ok test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_008) Test blat-pslx indexing, single query, single hit. ... ok test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_009) Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_010) Test blat-pslx indexing, multiple queries, no header. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.130 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate.py test_SearchIO_exonerate ... ok test_exn_22_o_vulgar_cigar (test_SearchIO_exonerate.ExonerateCigarCases.test_exn_22_o_vulgar_cigar) Test parsing exonerate output (exn_22_o_vulgar_cigar.exn). ... ok test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_c2c) Compares vulgar-text coordinate parsing for the coding2coding model. ... ok test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_g2g) Compares vulgar-text coordinate parsing for the genome2genome model. ... ok test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_p2d) Compares vulgar-text coordinate parsing for the protein2dna model. ... ok test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_affine_local) Test parsing exonerate output (exn_22_m_affine_local.exn). ... ok test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_cdna2genome) Test parsing exonerate output (exn_22_m_cdna2genome.exn). ... ok test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding) Test parsing exonerate output (exn_22_m_coding2coding.exn). ... ok test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding_fshifts) Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn). ... ok test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2genome) Test parsing exonerate output (exn_22_m_coding2genome.exn). ... ok test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_dna2protein) Test parsing exonerate output (exn_22_m_dna2protein.exn). ... ok test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_est2genome) Test parsing exonerate output (exn_22_m_est2genome.exn). ... ok test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_genome2genome) Test parsing exonerate output (exn_22_m_genome2genome.exn). ... ok test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ner) Test parsing exonerate output (exn_22_m_ner.exn). ... ok test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2dna_fshifts) Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn). ... ok test_exn_22_m_protein2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2genome) Test parsing exonerate output (exn_22_m_protein2genome.exn). ... ok test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped) Test parsing exonerate output (exn_22_m_ungapped.exn). ... ok test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped_trans) Test parsing exonerate output (exn_22_m_ungapped_trans.exn). ... ok test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_multiple) Test parsing exonerate output (exn_22_q_multiple.exn). ... ok test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_none) Test parsing exonerate output (exn_22_q_none.exn). ... ok test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar) Test parsing exonerate output (exn_22_o_vulgar.exn). ... ok test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar_fshifts) Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.137 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_text_index ... ok test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_m_est2genome) Test exonerate-text indexing, single. ... ok test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_q_multiple) Test exonerate-text indexing, single. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.092 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_vulgar_index.py test_SearchIO_exonerate_vulgar_index ... ok test_exn_22_m_est2genome (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_m_est2genome) Test exonerate-vulgar indexing, single. ... ok test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_q_multiple) Test exonerate-vulgar indexing, single. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.071 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10 ... ok test_output002 (test_SearchIO_fasta_m10.Fasta34Cases.test_output002) Test parsing fasta34 output (output002.m10). ... ok test_output003 (test_SearchIO_fasta_m10.Fasta34Cases.test_output003) Test parsing fasta34 output (output003.m10). ... ok test_output001 (test_SearchIO_fasta_m10.Fasta35Cases.test_output001) Test parsing fasta35 output (output001.m10). ... ok test_output004 (test_SearchIO_fasta_m10.Fasta35Cases.test_output004) Test parsing fasta35 output (output004.m10). ... ok test_output005 (test_SearchIO_fasta_m10.Fasta35Cases.test_output005) Test parsing ssearch35 output (output005.m10). ... ok test_output006 (test_SearchIO_fasta_m10.Fasta35Cases.test_output006) Test parsing fasta35 output (output006.m10). ... ok test_output007 (test_SearchIO_fasta_m10.Fasta36Cases.test_output007) Test parsing fasta36 output (output007.m10). ... ok test_output008 (test_SearchIO_fasta_m10.Fasta36Cases.test_output008) Test parsing tfastx36 output (output008.m10). ... ok test_output009 (test_SearchIO_fasta_m10.Fasta36Cases.test_output009) Test parsing fasta36 output (output009.m10). ... ok test_output010 (test_SearchIO_fasta_m10.Fasta36Cases.test_output010) Test parsing fasta36 output (output010.m10). ... ok test_output011 (test_SearchIO_fasta_m10.Fasta36Cases.test_output011) Test parsing fasta36 output (output011.m10). ... ok test_output012 (test_SearchIO_fasta_m10.Fasta36Cases.test_output012) Test parsing fasta36 output (output012.m10). ... ok test_output013 (test_SearchIO_fasta_m10.Fasta36Cases.test_output013) Test parsing fasta36 output (output013.m10). ... ok test_output014 (test_SearchIO_fasta_m10.Fasta36Cases.test_output014) Test parsing fasta36 output (output014.m10). ... ok test_output015 (test_SearchIO_fasta_m10.Fasta36Cases.test_output015) Test parsing fasta36 output (output015.m10). ... ok test_output016 (test_SearchIO_fasta_m10.Fasta36Cases.test_output016) Test parsing fasta36 output (output016.m10). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.116 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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_output_001) Test fasta-m10 indexing, fasta35, multiple queries. ... ok test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_002) Test fasta-m10 indexing, fasta34, multiple queries. ... ok test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_005) Test fasta-m10 indexing, ssearch35, multiple queries. ... ok test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_008) Test fasta-m10 indexing, tfastx36, multiple queries. ... ok test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_009) Test fasta-m10 indexing, fasta36, multiple queries. ... ok test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_010) Test fasta-m10 indexing, fasta36, single query, no hits. ... ok test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_011) Test fasta-m10 indexing, fasta36, single query, hits with single hsp. ... ok test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_012) Test fasta-m10 indexing, fasta36, single query with multiple hsps. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.121 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hhsuite2_text.py test_SearchIO_hhsuite2_text ... ok test_2uvo (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo) Parsing 2uvo. ... ok test_2uvo_emptytable (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_emptytable) Parsing 4uvo with empty results table. ... ok test_2uvo_onlyheader (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_onlyheader) Parsing 4uvo with only header present. ... ok test_4p79 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4p79) Parsing 4p79_hhsearch_server_NOssm.hhr file. ... ok test_4y9h_nossm (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4y9h_nossm) Parsing 4y9h_hhsearch_server_NOssm.hhr file. ... ok test_9590198 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_9590198) Parsing hhpred_9590198.hhr file. ... ok test_allx (test_SearchIO_hhsuite2_text.HhsuiteCases.test_allx) Parsing allx.hhr file. ... ok test_q9bsu1 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_q9bsu1) Parsing hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.129 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text ... ok test_hmmpfam_21 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_21) Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out). ... ok test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_22) Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out). ... ok test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out). ... ok test_hmmpfam_23_break_in_end_of_seq (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_break_in_end_of_seq) Test parsing hmmpfam 2.3 file with a line break in the end of seq marker. ... ok test_hmmpfam_23_missing_consensus (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_missing_consensus) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out). ... ok test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_no_match) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out). ... ok test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_24) Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out). ... ok test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_20) Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out). ... ok test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_22) Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.181 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer2_text_index ... ok test_hmmertext_text_21_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_21_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.1. ... ok test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.2. ... ok test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmsearch_001) Test hmmer2-text indexing, HMMER 2.2. ... ok test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_23_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.3. ... ok test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_24_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.4. ... ok test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_first_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_last_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_middle_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmpfam) Test hmmer2-text raw string retrieval, single query, hmmpfam. ... ok test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmsearch) Test hmmer2-text raw string retrieval, single query, hmmsearch. ... ok ---------------------------------------------------------------------- Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux Ran 1 test in 0.136 seconds C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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_domtab_30_hmmsearch_001) Parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001). ... ok test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_31b1_hmmsearch_001) Parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001). ... ok test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_001) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001). ... ok test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_002) 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_domtab_30_hmmscan_003) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003). ... ok test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_004) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004). ... ok test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_31b1_hmmscan_001) Parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.090 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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_hmmerdomtab_30_hmmscan_001) Test hmmscan-domtab indexing, HMMER 3.0, multiple queries. ... ok test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_002) Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits. ... ok test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_003) Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_004) Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmsearch_001) Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_first) 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_hmmerdomtab_30_multiple_last) 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_hmmerdomtab_30_multiple_middle) 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_hmmerdomtab_30_single) Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.081 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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_30_hmmscan_001) Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001). ... ok test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_002) 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_30_hmmscan_003) 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_30_hmmscan_004) 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_31b1_hmmscan_001) Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases.test_31b1_hmmsearch_001) Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.066 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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_hmmer3tab_30_hmmscan_001) Test hmmer3-tab indexing, HMMER 3.0, multiple queries. ... ok test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_002) Test hmmer3-tab indexing, HMMER 3.0, single query, no hits. ... ok test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_003) Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_004) Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_first) 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_hmmer3tab_30_multiple_last) 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_hmmer3tab_30_multiple_middle) 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_hmmer3tab_30_single) Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.073 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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_30_hmmsearch_001) Parsing hmmersearch 3.0 (text_30_hmmsearch_001). ... ok test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_002) Parsing hmmersearch 3.0 (text_30_hmmsearch_002). ... ok test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_003) Parsing hmmersearch 3.0 (text_30_hmmsearch_003). ... ok test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_004) Parsing hmmersearch 3.0 (text_30_hmmsearch_004). ... ok test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_005) Parsing hmmersearch 3.0 (text_30_hmmsearch_005). ... ok test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b1_hmmsearch_001) Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001). ... ok test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmscan_001) Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001). ... ok test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_001) Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001). ... ok test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_002) Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002). ... ok test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_001) Parsing hmmscan 3.0 (text_30_hmmscan_001). ... ok test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_002) Parsing hmmscan 3.0 (text_30_hmmscan_002). ... ok test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_003) Parsing hmmscan 3.0 (text_30_hmmscan_003). ... ok test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_004) Parsing hmmscan 3.0 (text_30_hmmscan_004). ... ok test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_005) Parsing hmmscan 3.0 (text_30_hmmscan_005). ... ok test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_006) Parsing hmmscan 3.0 (text_30_hmmscan_006). ... ok test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_007) Parsing hmmscan 3.0 (text_30_hmmscan_007). ... ok test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_008) Parsing hmmscan 3.0 (text_30_hmmscan_008). ... ok test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_009) Parsing hmmscan 3.0 (text_30_hmmscan_009). ... ok test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_010) Parsing hmmscan 3.0 (text_30_hmmscan_010). ... ok test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_31b1_hmmscan_001) Parsing hmmscan 3.1b1 (text_31b1_hmmscan_001). ... ok test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases.test_31b2_phmmer_001) Parsing phmmer 3.1b2 (text_31b2_phmmer_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.147 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text_index.py test_SearchIO_hmmer3_text_index ... ok test_hmmertext_text_30_hmmscan_001 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_001) Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_002) 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_hmmertext_text_30_hmmscan_006) 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_hmmertext_text_30_hmmscan_007) 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_hmmertext_text_30_hmmscan_008) 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_hmmertext_text_30_hmmsearch_005) Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_first) 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_hmmer3text_30_multiple_last) 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_hmmer3text_30_multiple_middle) 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_hmmer3text_30_single) Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.103 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_interproscan_xml.py test_SearchIO_interproscan_xml ... ok test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases.test_xml_001) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.062 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_legacy.py test_SearchIO_legacy ... ok test_TaggingConsumer (test_SearchIO_legacy.TestParserSupport.test_TaggingConsumer) ... ok test_attempt_read_and_call (test_SearchIO_legacy.TestParserSupport.test_attempt_read_and_call) ... ok test_is_blank_line (test_SearchIO_legacy.TestParserSupport.test_is_blank_line) ... ok test_read_and_call (test_SearchIO_legacy.TestParserSupport.test_read_and_call) ... ok test_safe_peekline (test_SearchIO_legacy.TestParserSupport.test_safe_peekline) ... ok test_safe_readline (test_SearchIO_legacy.TestParserSupport.test_safe_readline) ... ok test_one (test_SearchIO_legacy.UndoHandleTests.test_one) First test. ... ok test_read (test_SearchIO_legacy.UndoHandleTests.test_read) Test read method. ... ok test_undohandle_read_block (test_SearchIO_legacy.UndoHandleTests.test_undohandle_read_block) Test reading in blocks. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.059 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_model.py test_SearchIO_model ... ok test_coords_setters_getters (test_SearchIO_model.HSPFragmentCases.test_coords_setters_getters) Test HSPFragment query and hit coordinate-related setters and getters. ... ok test_coords_setters_readonly (test_SearchIO_model.HSPFragmentCases.test_coords_setters_readonly) Test HSPFragment query and hit coordinate-related read-only getters. ... ok test_default_attrs (test_SearchIO_model.HSPFragmentCases.test_default_attrs) Test HSPFragment attributes' default values. ... ok test_frame_set_error (test_SearchIO_model.HSPFragmentCases.test_frame_set_error) Test HSPFragment query and hit frame setters, invalid values. ... ok test_frame_set_ok (test_SearchIO_model.HSPFragmentCases.test_frame_set_ok) Test HSPFragment query and hit frame setters. ... ok test_getitem (test_SearchIO_model.HSPFragmentCases.test_getitem) Test HSPFragment.__getitem__. ... ok test_getitem_alignment_annot (test_SearchIO_model.HSPFragmentCases.test_getitem_alignment_annot) Test HSPFragment.__getitem__, with alignment annotation. ... ok test_getitem_attrs (test_SearchIO_model.HSPFragmentCases.test_getitem_attrs) Test HSPFragment.__getitem__, with attributes. ... ok test_id_desc_set (test_SearchIO_model.HSPFragmentCases.test_id_desc_set) Test HSPFragment query and hit id and description setters. ... ok test_init_with_seqrecord (test_SearchIO_model.HSPFragmentCases.test_init_with_seqrecord) Test HSPFragment.__init__, with SeqRecord. ... ok test_init_wrong_seqtypes (test_SearchIO_model.HSPFragmentCases.test_init_wrong_seqtypes) Test HSPFragment.__init__, wrong sequence argument types. ... ok test_len (test_SearchIO_model.HSPFragmentCases.test_len) Test HSPFragment.__len__. ... ok test_molecule_type_no_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_no_seq) Test HSPFragment molecule_type property, query and hit sequences not present. ... ok test_molecule_type_with_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_with_seq) Test HSPFragment molecule_type property, query or hit sequences present. ... ok test_pickle (test_SearchIO_model.HSPFragmentCases.test_pickle) Test pickling and unpickling of HSPFragment. ... ok test_repr (test_SearchIO_model.HSPFragmentCases.test_repr) Test HSPFragment.__repr__. ... ok test_seq_unequal_hit_query_len (test_SearchIO_model.HSPFragmentCases.test_seq_unequal_hit_query_len) Test HSPFragment sequence setter with unequal hit and query lengths. ... ok test_seqmodel (test_SearchIO_model.HSPFragmentCases.test_seqmodel) Test HSPFragment sequence attribute types and default values. ... ok test_strand_set_error (test_SearchIO_model.HSPFragmentCases.test_strand_set_error) Test HSPFragment query and hit strand setters, invalid values. ... ok test_strand_set_from_minus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_minus_frame) Test HSPFragment query and hit strand getters, from minus frame. ... ok test_strand_set_from_plus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_plus_frame) Test HSPFragment query and hit strand getters, from plus frame. ... ok test_strand_set_from_zero_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_zero_frame) Test HSPFragment query and hit strand getters, from zero frame. ... ok test_strand_set_ok (test_SearchIO_model.HSPFragmentCases.test_strand_set_ok) Test HSPFragment query and hit strand setters. ... ok test_getitem (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem) Test HSPFragment.__getitem__, no alignments. ... ok test_getitem_only_hit (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_hit) Test HSPFragment.__getitem__, only hit. ... ok test_getitem_only_query (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_query) Test HSPFragment.__getitem__, only query. ... ok test_init (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_init) Test HSPFragment.__init__ attributes. ... ok test_iter (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_iter) Test HSP.__iter__, no alignments. ... ok test_len (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_len) Test HSPFragment.__len__, no alignments. ... ok test_repr (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_repr) Test HSPFragment.__repr__, no alignments. ... ok test_seqmodel (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_seqmodel) Test HSPFragment sequence attributes, no alignments. ... ok test_contains (test_SearchIO_model.HSPMultipleFragmentCases.test_contains) Test HSP.__contains__. ... ok test_delitem (test_SearchIO_model.HSPMultipleFragmentCases.test_delitem) Test HSP.__delitem__. ... ok test_fragments (test_SearchIO_model.HSPMultipleFragmentCases.test_fragments) Test HSP.fragments property. ... ok test_getitem (test_SearchIO_model.HSPMultipleFragmentCases.test_getitem) Test HSP.__getitem__. ... ok test_id_desc_set (test_SearchIO_model.HSPMultipleFragmentCases.test_id_desc_set) Test HSP query and hit id and description setters. ... ok test_is_fragmented (test_SearchIO_model.HSPMultipleFragmentCases.test_is_fragmented) Test HSP.is_fragmented property. ... ok test_len (test_SearchIO_model.HSPMultipleFragmentCases.test_len) Test HSP.__len__. ... ok test_molecule_type (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type) Test HSP.molecule_type getter. ... ok test_molecule_type_set (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type_set) Test HSP.molecule_type setter. ... ok test_pickle (test_SearchIO_model.HSPMultipleFragmentCases.test_pickle) Test pickling and unpickling of HSP. ... ok test_range (test_SearchIO_model.HSPMultipleFragmentCases.test_range) Test HSP range properties. ... ok test_ranges (test_SearchIO_model.HSPMultipleFragmentCases.test_ranges) Test HSP ranges properties. ... ok test_seqs (test_SearchIO_model.HSPMultipleFragmentCases.test_seqs) Test HSP sequence properties. ... ok test_setitem_multiple (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_multiple) Test HSP.__setitem__, multiple items. ... ok test_setitem_single (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_single) Test HSP.__setitem___, single item. ... ok test_setters_readonly (test_SearchIO_model.HSPMultipleFragmentCases.test_setters_readonly) Test HSP read-only properties. ... ok test_span (test_SearchIO_model.HSPMultipleFragmentCases.test_span) Test HSP span properties. ... ok test_alignment (test_SearchIO_model.HSPSingleFragmentCases.test_alignment) Test HSP.alignment property. ... ok test_aln_span (test_SearchIO_model.HSPSingleFragmentCases.test_aln_span) Test HSP.aln_span property. ... ok test_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_fragment) Test HSP.fragment property. ... ok test_init_no_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_init_no_fragment) Test HSP.__init__ without fragments. ... ok test_is_fragmented (test_SearchIO_model.HSPSingleFragmentCases.test_is_fragmented) Test HSP.is_fragmented property. ... ok test_len (test_SearchIO_model.HSPSingleFragmentCases.test_len) Test HSP.__len__. ... ok test_range (test_SearchIO_model.HSPSingleFragmentCases.test_range) Test HSP range properties. ... ok test_seq (test_SearchIO_model.HSPSingleFragmentCases.test_seq) Test HSP sequence properties. ... ok test_setters_readonly (test_SearchIO_model.HSPSingleFragmentCases.test_setters_readonly) Test HSP read-only properties. ... ok test_span (test_SearchIO_model.HSPSingleFragmentCases.test_span) Test HSP span properties. ... ok test_append (test_SearchIO_model.HitCases.test_append) Test Hit.append. ... ok test_bool (test_SearchIO_model.HitCases.test_bool) Test Hit.__bool__. ... ok test_delitem (test_SearchIO_model.HitCases.test_delitem) Test Hit.__delitem__. ... ok test_desc_set (test_SearchIO_model.HitCases.test_desc_set) Test Hit.description setter. ... ok test_desc_set_no_seqrecord (test_SearchIO_model.HitCases.test_desc_set_no_seqrecord) Test Hit.description setter, without HSP SeqRecords. ... ok test_filter (test_SearchIO_model.HitCases.test_filter) Test Hit.filter. ... ok test_filter_no_filtered (test_SearchIO_model.HitCases.test_filter_no_filtered) Test Hit.hit_filter, all hits filtered out. ... ok test_filter_no_func (test_SearchIO_model.HitCases.test_filter_no_func) Test Hit.filter, without arguments. ... ok test_fragments (test_SearchIO_model.HitCases.test_fragments) Test Hit.fragments. ... ok test_getitem_multiple (test_SearchIO_model.HitCases.test_getitem_multiple) Test Hit.__getitem__, multiple items. ... ok test_getitem_single (test_SearchIO_model.HitCases.test_getitem_single) Test Hit.__getitem__, single item. ... ok test_hsp_map_no_func (test_SearchIO_model.HitCases.test_hsp_map_no_func) Test Hit.map, without arguments. ... ok test_hsps (test_SearchIO_model.HitCases.test_hsps) Test Hit.hsps. ... ok test_id_set (test_SearchIO_model.HitCases.test_id_set) Test Hit.id setter. ... ok test_index (test_SearchIO_model.HitCases.test_index) Test Hit.index. ... ok test_index_not_present (test_SearchIO_model.HitCases.test_index_not_present) Test Hit.index, when index is not present. ... ok test_init_hsps_only (test_SearchIO_model.HitCases.test_init_hsps_only) Test Hit.__init__, with hsps only. ... ok test_init_id_only (test_SearchIO_model.HitCases.test_init_id_only) Test Hit.__init__, with ID only. ... ok test_init_none (test_SearchIO_model.HitCases.test_init_none) Test Hit.__init__, no arguments. ... ok test_item_multiple (test_SearchIO_model.HitCases.test_item_multiple) Test Hit.__setitem__, multiple items. ... ok test_iter (test_SearchIO_model.HitCases.test_iter) Test Hit.__iter__. ... ok test_len (test_SearchIO_model.HitCases.test_len) Test Hit.__len__. ... ok test_map (test_SearchIO_model.HitCases.test_map) Test Hit.hsp_map. ... ok test_pickle (test_SearchIO_model.HitCases.test_pickle) Test pickling and unpickling of Hit. ... ok test_pop (test_SearchIO_model.HitCases.test_pop) Test Hit.pop. ... ok test_repr (test_SearchIO_model.HitCases.test_repr) Test Hit.__repr__. ... ok test_setitem_single (test_SearchIO_model.HitCases.test_setitem_single) Test Hit.__setitem__, single item. ... ok test_sort (test_SearchIO_model.HitCases.test_sort) Test Hit.sort. ... ok test_sort_not_in_place (test_SearchIO_model.HitCases.test_sort_not_in_place) Test Hit.sort, not in place. ... ok test_validate_hsp_ok (test_SearchIO_model.HitCases.test_validate_hsp_ok) Test Hit._validate_hsp. ... ok test_validate_hsp_wrong_hit_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_hit_id) Test Hit._validate_hsp, wrong hit ID. ... ok test_validate_hsp_wrong_query_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_query_id) Test Hit._validate_hsp, wrong query ID. ... ok test_validate_hsp_wrong_type (test_SearchIO_model.HitCases.test_validate_hsp_wrong_type) Test Hit._validate_hsp, wrong type. ... ok test_absorb_hit_does_not_exist (test_SearchIO_model.QueryResultCases.test_absorb_hit_does_not_exist) Test QueryResult.absorb, hit does not exist. ... ok test_absorb_hit_exists (test_SearchIO_model.QueryResultCases.test_absorb_hit_exists) Test QueryResult.absorb, hit with the same ID exists. ... ok test_append_alt_id_exists (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists) Test QueryResult.append, when alt ID exists. ... ok test_append_alt_id_exists_alt (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists_alt) Test QueryResult.append, when alt ID exists as primary. ... ok test_append_custom_hit_key_function_ok (test_SearchIO_model.QueryResultCases.test_append_custom_hit_key_function_ok) Test QueryResult.append, with custom hit key function. ... ok test_append_id_exists (test_SearchIO_model.QueryResultCases.test_append_id_exists) Test QueryResult.append, when ID exists. ... ok test_append_ok (test_SearchIO_model.QueryResultCases.test_append_ok) Test QueryResult.append. ... ok test_bool (test_SearchIO_model.QueryResultCases.test_bool) Test QueryResult.__bool__. ... ok test_contains (test_SearchIO_model.QueryResultCases.test_contains) Test QueryResult.__contains__. ... ok test_contains_alt (test_SearchIO_model.QueryResultCases.test_contains_alt) Test QueryResult.__contains__, with alternative IDs. ... ok test_delitem_alt_ok (test_SearchIO_model.QueryResultCases.test_delitem_alt_ok) Test QueryResult.__delitem__, with alt ID. ... ok test_delitem_int_ok (test_SearchIO_model.QueryResultCases.test_delitem_int_ok) Test QueryResult.__delitem__. ... ok test_delitem_slice_ok (test_SearchIO_model.QueryResultCases.test_delitem_slice_ok) Test QueryResult.__delitem__, with slice. ... ok test_delitem_string_ok (test_SearchIO_model.QueryResultCases.test_delitem_string_ok) Test QueryResult.__getitem__, with string. ... ok test_description_set (test_SearchIO_model.QueryResultCases.test_description_set) Test QueryResult.description setter. ... ok test_description_set_no_seqrecord (test_SearchIO_model.QueryResultCases.test_description_set_no_seqrecord) Test QueryResult.description setter, without HSP SeqRecords. ... ok test_fragments (test_SearchIO_model.QueryResultCases.test_fragments) Test QueryResult.fragments. ... ok test_getitem_alt_ok (test_SearchIO_model.QueryResultCases.test_getitem_alt_ok) Test QueryResult.__getitem__, single item with alternative ID. ... ok test_getitem_default_ok (test_SearchIO_model.QueryResultCases.test_getitem_default_ok) Test QueryResult.__getitem__. ... ok test_getitem_int_ok (test_SearchIO_model.QueryResultCases.test_getitem_int_ok) Test QueryResult.__getitem__, with integer. ... ok test_getitem_slice_ok (test_SearchIO_model.QueryResultCases.test_getitem_slice_ok) Test QueryResult.__getitem__, with slice. ... ok test_getitm_slice_alt_ok (test_SearchIO_model.QueryResultCases.test_getitm_slice_alt_ok) Test QueryResult.__getitem__, with slice and alt IDs. ... ok test_hit_filter (test_SearchIO_model.QueryResultCases.test_hit_filter) Test QueryResult.hit_filter. ... ok test_hit_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hit_filter_no_filtered) Test QueryResult.hit_filter, all hits filtered out. ... ok test_hit_filter_no_func (test_SearchIO_model.QueryResultCases.test_hit_filter_no_func) Test QueryResult.hit_filter, without arguments. ... ok test_hit_keys (test_SearchIO_model.QueryResultCases.test_hit_keys) Test QueryResult.hit_keys. ... ok test_hit_map (test_SearchIO_model.QueryResultCases.test_hit_map) Test QueryResult.hit_map. ... ok test_hit_map_no_func (test_SearchIO_model.QueryResultCases.test_hit_map_no_func) Test QueryResult.hit_map, without arguments. ... ok test_hits (test_SearchIO_model.QueryResultCases.test_hits) Test QueryResult.hits. ... ok test_hsp_filter (test_SearchIO_model.QueryResultCases.test_hsp_filter) Test QueryResult.hsp_filter. ... ok test_hsp_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_filtered) Test QueryResult.hsp_filter, all hits filtered out. ... ok test_hsp_filter_no_func (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_func) Test QueryResult.hsp_filter, no arguments. ... ok test_hsp_map (test_SearchIO_model.QueryResultCases.test_hsp_map) Test QueryResult.hsp_map. ... ok test_hsp_map_no_func (test_SearchIO_model.QueryResultCases.test_hsp_map_no_func) Test QueryResult.hsp_map, without arguments. ... ok test_hsps (test_SearchIO_model.QueryResultCases.test_hsps) Test QueryResult.hsps. ... ok test_id_set (test_SearchIO_model.QueryResultCases.test_id_set) Test QueryResult.id setter. ... ok test_index (test_SearchIO_model.QueryResultCases.test_index) Test QueryResult.index. ... ok test_index_alt (test_SearchIO_model.QueryResultCases.test_index_alt) Test QueryResult.index, with alt ID. ... ok test_index_not_present (test_SearchIO_model.QueryResultCases.test_index_not_present) Test QueryResult.index, when index is not present. ... ok test_init_hits_only (test_SearchIO_model.QueryResultCases.test_init_hits_only) Test QueryResult.__init__, with hits only. ... ok test_init_id_only (test_SearchIO_model.QueryResultCases.test_init_id_only) Test QueryResult.__init__, with ID only. ... ok test_init_none (test_SearchIO_model.QueryResultCases.test_init_none) Test QueryResult.__init__, no arguments. ... ok test_items (test_SearchIO_model.QueryResultCases.test_items) Test QueryResult.items. ... ok test_iter (test_SearchIO_model.QueryResultCases.test_iter) Test QueryResult.__iter__. ... ok test_len (test_SearchIO_model.QueryResultCases.test_len) Test QueryResult.__len__. ... ok test_order (test_SearchIO_model.QueryResultCases.test_order) ... ok test_pickle (test_SearchIO_model.QueryResultCases.test_pickle) Test pickling and unpickling of QueryResult. ... ok test_pop_int_index_ok (test_SearchIO_model.QueryResultCases.test_pop_int_index_ok) Test QueryResult.pop, with integer index. ... ok test_pop_ok (test_SearchIO_model.QueryResultCases.test_pop_ok) Test QueryResult.pop. ... ok test_pop_string_alt_ok (test_SearchIO_model.QueryResultCases.test_pop_string_alt_ok) Test QueryResult.pop, with alternative ID. ... ok test_pop_string_index_ok (test_SearchIO_model.QueryResultCases.test_pop_string_index_ok) Test QueryResult.pop, with string index. ... ok test_repr (test_SearchIO_model.QueryResultCases.test_repr) Test QueryResult.__repr__. ... ok test_setitem_from_empty (test_SearchIO_model.QueryResultCases.test_setitem_from_empty) Test QueryResult.__setitem__, from empty container. ... ok test_setitem_ok (test_SearchIO_model.QueryResultCases.test_setitem_ok) Test QueryResult.__setitem__. ... ok test_setitem_ok_alt (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt) Test QueryResult.__setitem__, checking alt hit IDs. ... ok test_setitem_ok_alt_existing (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_existing) Test QueryResult.__setitem__, existing key. ... ok test_setitem_ok_alt_ok_promote (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_ok_promote) Test QueryResult.__setitem__, previously alt ID. ... ok test_setitem_wrong_key_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_key_type) Test QueryResult.__setitem__, wrong key type. ... ok test_setitem_wrong_query_id (test_SearchIO_model.QueryResultCases.test_setitem_wrong_query_id) Test QueryResult.__setitem__, wrong query ID. ... ok test_setitem_wrong_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_type) Test QueryResult.__setitem__, wrong type. ... ok test_sort_key_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_key_not_in_place_ok) Test QueryResult.sort, with custom key, not in place. ... ok test_sort_key_ok (test_SearchIO_model.QueryResultCases.test_sort_key_ok) Test QueryResult.sort, with custom key. ... ok test_sort_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_not_in_place_ok) Test QueryResult.sort, not in place. ... ok test_sort_ok (test_SearchIO_model.QueryResultCases.test_sort_ok) Test QueryResult.sort. ... ok test_sort_reverse_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_not_in_place_ok) Test QueryResult.sort, reverse, not in place. ... ok test_sort_reverse_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_ok) Test QueryResult.sort, reverse. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.110 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_write.py test_SearchIO_write ... ok test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttab) 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_write_multiple_from_blasttabc) 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_write_multiple_from_blasttabc_allfields) 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_write_single_from_blasttab) 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_write_single_from_blasttabc) 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_write_multiple_from_blastxml) 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_write_single_from_blastxml) 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_write_multiple_from_blatpsl) Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl). ... ok test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpslx) Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx). ... ok test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl) Test blat-psl writing from blat-psl, single query (psl_34_004.psl). ... ok test_write_single_from_blatpsl_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl_protein_query) Test blat-psl writing from blat-psl, single query (psl_35_002.psl). ... ok test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx) Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx). ... ok test_write_single_from_blatpslx_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx_protein_query) Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx). ... ok test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_multiple_from_hmmscandomtab) 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_write_single_from_hmmscandomtab) 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_write_single_from_hmmsearchdomtab) 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_write_multiple_from_hmmertab) 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_write_single_from_hmmertab) Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.271 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqFeature.py test_SeqFeature ... ok test_eq_identical (test_SeqFeature.TestCompoundLocation.test_eq_identical) Test two identical locations are equal. ... ok test_eq_not_identical (test_SeqFeature.TestCompoundLocation.test_eq_not_identical) Test two different locations are not equal. ... ok test_reference_in_compound_location_record (test_SeqFeature.TestExtract.test_reference_in_compound_location_record) Test compound location with reference to another record. ... ok test_reference_in_compound_location_sequence (test_SeqFeature.TestExtract.test_reference_in_compound_location_sequence) Test compound location with reference to another sequence. ... ok test_reference_in_location_record (test_SeqFeature.TestExtract.test_reference_in_location_record) Test location with reference to another record. ... ok test_reference_in_location_sequence (test_SeqFeature.TestExtract.test_reference_in_location_sequence) Test location with reference to another sequence. ... ok test_eq_identical (test_SeqFeature.TestFeatureLocation.test_eq_identical) Test two identical locations are equal. ... ok test_eq_not_identical (test_SeqFeature.TestFeatureLocation.test_eq_not_identical) Test two different locations are not equal. ... ok test_start_before_end (test_SeqFeature.TestFeatureLocation.test_start_before_end) ... ok test_fuzzy (test_SeqFeature.TestLocations.test_fuzzy) Test fuzzy representations. ... ok test_pickle (test_SeqFeature.TestPositions.test_pickle) Test pickle behaviour of position instances. ... ok test_eq_identical (test_SeqFeature.TestReference.test_eq_identical) Test two identical references eq() to True. ... ok test_translation_checks_cds (test_SeqFeature.TestSeqFeature.test_translation_checks_cds) Test that a CDS feature is subject to respective checks. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.101 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO.py test_SeqIO ... ok test_abi1 (test_SeqIO.TestSeqIO.test_abi1) ... ok test_abi2 (test_SeqIO.TestSeqIO.test_abi2) ... ok test_abi3 (test_SeqIO.TestSeqIO.test_abi3) ... ok test_ace1 (test_SeqIO.TestSeqIO.test_ace1) ... ok test_ace2 (test_SeqIO.TestSeqIO.test_ace2) ... ok test_ace3 (test_SeqIO.TestSeqIO.test_ace3) ... ok test_cif_atom1 (test_SeqIO.TestSeqIO.test_cif_atom1) ... ok test_cif_atom2 (test_SeqIO.TestSeqIO.test_cif_atom2) ... ok test_cif_seqres1 (test_SeqIO.TestSeqIO.test_cif_seqres1) ... ok test_cif_seqres2 (test_SeqIO.TestSeqIO.test_cif_seqres2) ... ok test_clustal1 (test_SeqIO.TestSeqIO.test_clustal1) ... ok test_clustal2 (test_SeqIO.TestSeqIO.test_clustal2) ... ok test_clustal3 (test_SeqIO.TestSeqIO.test_clustal3) ... ok test_clustal4 (test_SeqIO.TestSeqIO.test_clustal4) ... ok test_clustal_to_nexus_with_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_with_mol_type) Convert Clustal to NEXUS with molecule type. ... ok test_clustal_to_nexus_without_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_without_mol_type) Convert Clustal to NEXUS without molecule type. ... ok test_embl1 (test_SeqIO.TestSeqIO.test_embl1) ... ok test_embl10 (test_SeqIO.TestSeqIO.test_embl10) ... ok test_embl11 (test_SeqIO.TestSeqIO.test_embl11) ... ok test_embl12 (test_SeqIO.TestSeqIO.test_embl12) ... ok test_embl13 (test_SeqIO.TestSeqIO.test_embl13) Test parsing embl file with wrapped locations and unspecified type. ... ok test_embl14 (test_SeqIO.TestSeqIO.test_embl14) Test parsing file with features over-indented for EMBL. ... ok test_embl2 (test_SeqIO.TestSeqIO.test_embl2) ... ok test_embl3 (test_SeqIO.TestSeqIO.test_embl3) ... ok test_embl4 (test_SeqIO.TestSeqIO.test_embl4) ... ok test_embl5 (test_SeqIO.TestSeqIO.test_embl5) ... ok test_embl6 (test_SeqIO.TestSeqIO.test_embl6) ... ok test_embl7 (test_SeqIO.TestSeqIO.test_embl7) ... ok test_embl8 (test_SeqIO.TestSeqIO.test_embl8) ... ok test_embl9 (test_SeqIO.TestSeqIO.test_embl9) ... ok test_emboss1 (test_SeqIO.TestSeqIO.test_emboss1) ... ok test_emboss2 (test_SeqIO.TestSeqIO.test_emboss2) ... ok test_emboss3 (test_SeqIO.TestSeqIO.test_emboss3) ... ok test_empty_file (test_SeqIO.TestSeqIO.test_empty_file) Check parsers can cope with an empty file. ... ok test_fasta1 (test_SeqIO.TestSeqIO.test_fasta1) ... ok test_fasta10 (test_SeqIO.TestSeqIO.test_fasta10) ... ok test_fasta11 (test_SeqIO.TestSeqIO.test_fasta11) ... ok test_fasta12 (test_SeqIO.TestSeqIO.test_fasta12) ... ok test_fasta13 (test_SeqIO.TestSeqIO.test_fasta13) ... ok test_fasta14 (test_SeqIO.TestSeqIO.test_fasta14) ... ok test_fasta15 (test_SeqIO.TestSeqIO.test_fasta15) ... ok test_fasta16 (test_SeqIO.TestSeqIO.test_fasta16) ... ok test_fasta17 (test_SeqIO.TestSeqIO.test_fasta17) ... ok test_fasta18 (test_SeqIO.TestSeqIO.test_fasta18) ... ok test_fasta19 (test_SeqIO.TestSeqIO.test_fasta19) ... ok test_fasta2 (test_SeqIO.TestSeqIO.test_fasta2) ... ok test_fasta20 (test_SeqIO.TestSeqIO.test_fasta20) ... ok test_fasta21 (test_SeqIO.TestSeqIO.test_fasta21) ... ok test_fasta22 (test_SeqIO.TestSeqIO.test_fasta22) ... ok test_fasta23 (test_SeqIO.TestSeqIO.test_fasta23) ... ok test_fasta24 (test_SeqIO.TestSeqIO.test_fasta24) ... ok test_fasta3 (test_SeqIO.TestSeqIO.test_fasta3) ... ok test_fasta4 (test_SeqIO.TestSeqIO.test_fasta4) ... ok test_fasta5 (test_SeqIO.TestSeqIO.test_fasta5) ... ok test_fasta6 (test_SeqIO.TestSeqIO.test_fasta6) ... ok test_fasta7 (test_SeqIO.TestSeqIO.test_fasta7) ... ok test_fasta8 (test_SeqIO.TestSeqIO.test_fasta8) ... ok test_fasta9 (test_SeqIO.TestSeqIO.test_fasta9) ... ok test_fasta_2line1 (test_SeqIO.TestSeqIO.test_fasta_2line1) ... ok test_fasta_to_seqxml_with_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_with_mol_type) Convert FASTA to SeqXML with molecule type. ... ok test_fasta_to_seqxml_without_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_without_mol_type) Convert FASTA to SeqXML without molecule type. ... ok test_fastq1 (test_SeqIO.TestSeqIO.test_fastq1) ... ok test_fastq2 (test_SeqIO.TestSeqIO.test_fastq2) ... ok test_fastq3 (test_SeqIO.TestSeqIO.test_fastq3) ... ok test_fastq4 (test_SeqIO.TestSeqIO.test_fastq4) ... ok test_fastq5 (test_SeqIO.TestSeqIO.test_fastq5) ... ok test_fastq_illumina1 (test_SeqIO.TestSeqIO.test_fastq_illumina1) ... ok test_fastq_solexa1 (test_SeqIO.TestSeqIO.test_fastq_solexa1) ... ok test_fastq_solexa2 (test_SeqIO.TestSeqIO.test_fastq_solexa2) ... ok test_genbank1 (test_SeqIO.TestSeqIO.test_genbank1) ... ok test_genbank10 (test_SeqIO.TestSeqIO.test_genbank10) ... ok test_genbank11 (test_SeqIO.TestSeqIO.test_genbank11) ... ok test_genbank12 (test_SeqIO.TestSeqIO.test_genbank12) ... ok test_genbank13 (test_SeqIO.TestSeqIO.test_genbank13) ... ok test_genbank14 (test_SeqIO.TestSeqIO.test_genbank14) ... ok test_genbank15 (test_SeqIO.TestSeqIO.test_genbank15) ... ok test_genbank16 (test_SeqIO.TestSeqIO.test_genbank16) Test parsing Genbank file from Vector NTI with an odd LOCUS line. ... ok test_genbank17 (test_SeqIO.TestSeqIO.test_genbank17) ... ok test_genbank18 (test_SeqIO.TestSeqIO.test_genbank18) ... ok test_genbank19 (test_SeqIO.TestSeqIO.test_genbank19) ... ok test_genbank2 (test_SeqIO.TestSeqIO.test_genbank2) ... ok test_genbank20 (test_SeqIO.TestSeqIO.test_genbank20) Test parsing GenPept file with nasty bond locations. ... ok test_genbank21 (test_SeqIO.TestSeqIO.test_genbank21) ... ok test_genbank22 (test_SeqIO.TestSeqIO.test_genbank22) Test that genbank format write doesn't destroy db_source in annotations. ... ok test_genbank3 (test_SeqIO.TestSeqIO.test_genbank3) ... ok test_genbank4 (test_SeqIO.TestSeqIO.test_genbank4) ... ok test_genbank5 (test_SeqIO.TestSeqIO.test_genbank5) ... ok test_genbank6 (test_SeqIO.TestSeqIO.test_genbank6) ... ok test_genbank7 (test_SeqIO.TestSeqIO.test_genbank7) ... ok test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8) ... ok test_genbank9 (test_SeqIO.TestSeqIO.test_genbank9) ... ok test_ig1 (test_SeqIO.TestSeqIO.test_ig1) ... ok test_ig2 (test_SeqIO.TestSeqIO.test_ig2) ... ok test_ig3 (test_SeqIO.TestSeqIO.test_ig3) Test parsing a MASE alignment with sequence O_ANT70 being shorter. ... ok test_imgt1 (test_SeqIO.TestSeqIO.test_imgt1) Test parsing file with features over-indented for EMBL. ... ok test_imgt2 (test_SeqIO.TestSeqIO.test_imgt2) ... ok test_nexus1 (test_SeqIO.TestSeqIO.test_nexus1) ... ok test_pdb_atom1 (test_SeqIO.TestSeqIO.test_pdb_atom1) ... ok test_pdb_atom2 (test_SeqIO.TestSeqIO.test_pdb_atom2) ... ok test_pdb_atom3 (test_SeqIO.TestSeqIO.test_pdb_atom3) ... ok test_pdb_seqres1 (test_SeqIO.TestSeqIO.test_pdb_seqres1) ... ok test_pdb_seqres2 (test_SeqIO.TestSeqIO.test_pdb_seqres2) ... ok test_phd1 (test_SeqIO.TestSeqIO.test_phd1) ... ok test_phd2 (test_SeqIO.TestSeqIO.test_phd2) ... ok test_phd3 (test_SeqIO.TestSeqIO.test_phd3) ... ok test_phd4 (test_SeqIO.TestSeqIO.test_phd4) ... ok test_phylip1 (test_SeqIO.TestSeqIO.test_phylip1) ... ok test_phylip2 (test_SeqIO.TestSeqIO.test_phylip2) ... ok test_phylip3 (test_SeqIO.TestSeqIO.test_phylip3) ... ok test_phylip4 (test_SeqIO.TestSeqIO.test_phylip4) ... ok test_phylip5 (test_SeqIO.TestSeqIO.test_phylip5) ... ok test_phylip6 (test_SeqIO.TestSeqIO.test_phylip6) ... ok test_phylip7 (test_SeqIO.TestSeqIO.test_phylip7) ... ok test_pir1 (test_SeqIO.TestSeqIO.test_pir1) ... ok test_pir2 (test_SeqIO.TestSeqIO.test_pir2) ... ok test_pir3 (test_SeqIO.TestSeqIO.test_pir3) ... ok test_pir4 (test_SeqIO.TestSeqIO.test_pir4) ... ok test_pir5 (test_SeqIO.TestSeqIO.test_pir5) ... ok test_qual1 (test_SeqIO.TestSeqIO.test_qual1) ... ok test_seqxml1 (test_SeqIO.TestSeqIO.test_seqxml1) ... ok test_seqxml2 (test_SeqIO.TestSeqIO.test_seqxml2) ... ok test_seqxml3 (test_SeqIO.TestSeqIO.test_seqxml3) ... ok test_sff1 (test_SeqIO.TestSeqIO.test_sff1) ... ok test_snapgene1 (test_SeqIO.TestSeqIO.test_snapgene1) ... ok test_stockholm1 (test_SeqIO.TestSeqIO.test_stockholm1) ... ok test_stockholm2 (test_SeqIO.TestSeqIO.test_stockholm2) ... ok test_swiss1 (test_SeqIO.TestSeqIO.test_swiss1) ... ok test_swiss10 (test_SeqIO.TestSeqIO.test_swiss10) ... ok test_swiss11 (test_SeqIO.TestSeqIO.test_swiss11) ... ok test_swiss12 (test_SeqIO.TestSeqIO.test_swiss12) ... ok test_swiss13 (test_SeqIO.TestSeqIO.test_swiss13) ... ok test_swiss14 (test_SeqIO.TestSeqIO.test_swiss14) ... ok test_swiss15 (test_SeqIO.TestSeqIO.test_swiss15) ... ok test_swiss16 (test_SeqIO.TestSeqIO.test_swiss16) ... ok test_swiss17 (test_SeqIO.TestSeqIO.test_swiss17) ... ok test_swiss18 (test_SeqIO.TestSeqIO.test_swiss18) ... ok test_swiss19 (test_SeqIO.TestSeqIO.test_swiss19) ... ok test_swiss2 (test_SeqIO.TestSeqIO.test_swiss2) ... ok test_swiss20 (test_SeqIO.TestSeqIO.test_swiss20) ... ok test_swiss3 (test_SeqIO.TestSeqIO.test_swiss3) ... ok test_swiss4 (test_SeqIO.TestSeqIO.test_swiss4) ... ok test_swiss5 (test_SeqIO.TestSeqIO.test_swiss5) ... ok test_swiss6 (test_SeqIO.TestSeqIO.test_swiss6) ... ok test_swiss7 (test_SeqIO.TestSeqIO.test_swiss7) ... ok test_swiss8 (test_SeqIO.TestSeqIO.test_swiss8) ... ok test_swiss9 (test_SeqIO.TestSeqIO.test_swiss9) ... ok test_tab1 (test_SeqIO.TestSeqIO.test_tab1) ... ok test_uniprot_xml1 (test_SeqIO.TestSeqIO.test_uniprot_xml1) ... ok test_uniprot_xml2 (test_SeqIO.TestSeqIO.test_uniprot_xml2) ... ok test_uniprot_xml3 (test_SeqIO.TestSeqIO.test_uniprot_xml3) ... ok test_uniprot_xml4 (test_SeqIO.TestSeqIO.test_uniprot_xml4) ... ok test_uniprot_xml5 (test_SeqIO.TestSeqIO.test_uniprot_xml5) ... ok test_xdna1 (test_SeqIO.TestSeqIO.test_xdna1) ... ok test_gzip_fasta (test_SeqIO.TestZipped.test_gzip_fasta) Testing FASTA with gzip. ... ok test_gzip_fastq (test_SeqIO.TestZipped.test_gzip_fastq) Testing FASTQ with gzip. ... ok test_gzip_genbank (test_SeqIO.TestZipped.test_gzip_genbank) Testing GenBank with gzip. ... ok ---------------------------------------------------------------------- Ran 1 test in 18.691 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_AbiIO.py test_SeqIO_AbiIO ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_file_type (test_SeqIO_AbiIO.TestAbi.test_file_type) Test if filetype is ABIF. ... ok test_no_smpl1 (test_SeqIO_AbiIO.TestAbi.test_no_smpl1) Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok test_raw (test_SeqIO_AbiIO.TestAbi.test_raw) Test access to raw ABIF tags. ... ok test_seqrecord (test_SeqIO_AbiIO.TestAbi.test_seqrecord) Test if the extracted seqrecords data are equal to expected values. ... ok test_trim (test_SeqIO_AbiIO.TestAbi.test_trim) Test if trim works. ... ok test_file_type (test_SeqIO_AbiIO.TestAbiFake.test_file_type) Test if error is raised if filetype is not ABIF. ... ok test_nonascii_tag (test_SeqIO_AbiIO.TestAbiNonAscii.test_nonascii_tag) Test that we can handle non-ascii tags. ... ok test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode.test_file_mode) Test if exception is raised if file is not opened in 'rb' mode. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.319 seconds C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_FastaIO.py test_SeqIO_FastaIO ... ok test_edgecases_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_FastaTwoLineParser) Test FastaTwoLineParser edge-cases. ... ok test_edgecases_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_SimpleFastaParser) Test SimpleFastaParser edge-cases. ... ok test_exceptions_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_exceptions_FastaTwoLineParser) Test FastaTwoLineParser exceptions. ... ok test_regular_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_FastaTwoLineParser) Test regular FastaTwoLineParser cases. ... ok test_regular_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_SimpleFastaParser) Test regular SimpleFastaParser cases. ... ok test_multi_dna_files (test_SeqIO_FastaIO.TitleFunctions.test_multi_dna_files) Test Fasta files containing multiple nucleotide sequences. ... ok test_multi_protein_files (test_SeqIO_FastaIO.TitleFunctions.test_multi_protein_files) Test Fasta files containing multiple protein sequences. ... ok test_no_name (test_SeqIO_FastaIO.TitleFunctions.test_no_name) Test FASTA record with no identifier. ... ok test_single_nucleic_files (test_SeqIO_FastaIO.TitleFunctions.test_single_nucleic_files) Test Fasta files containing a single nucleotide sequence. ... ok test_single_proteino_files (test_SeqIO_FastaIO.TitleFunctions.test_single_proteino_files) Test Fasta files containing a single protein sequence. ... ok test_fails (test_SeqIO_FastaIO.Wrapping.test_fails) Test case which should fail. ... ok test_passes (test_SeqIO_FastaIO.Wrapping.test_passes) Test case which should pass. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.104 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Gck.py test_SeqIO_Gck ... ok test_conflicting_lengths (test_SeqIO_Gck.TestGckWithArtificialData.test_conflicting_lengths) Read a file with incorrect length. ... ok test_read (test_SeqIO_Gck.TestGckWithArtificialData.test_read) Read an artificial sample file. ... ok test_read (test_SeqIO_Gck.TestGckWithDGVC.test_read) Read sample files. ... skipped 'Sample files missing and no Internet access' test_read (test_SeqIO_Gck.TestGckWithImproperHeader.test_read) Read a file with an incomplete header. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Insdc.py test_SeqIO_Insdc ... /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)? warnings.warn( /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: unassigned DNA warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning) ok test_conversion (test_SeqIO_Insdc.ConvertTestsInsdc.test_conversion) Test format conversion by SeqIO.write/SeqIO.parse and SeqIO.convert. ... ok test_annotation1 (test_SeqIO_Insdc.TestEmbl.test_annotation1) Check parsing of annotation from EMBL files (1). ... ok test_annotation2 (test_SeqIO_Insdc.TestEmbl.test_annotation2) Check parsing of annotation from EMBL files (2). ... ok test_annotation3 (test_SeqIO_Insdc.TestEmbl.test_annotation3) Check parsing of annotation from EMBL files (3). ... ok test_annotation4 (test_SeqIO_Insdc.TestEmbl.test_annotation4) Check parsing of annotation from EMBL files (4). ... ok test_writing_empty_qualifiers (test_SeqIO_Insdc.TestEmbl.test_writing_empty_qualifiers) ... ok test_annotation1 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation1) Check writing-and-parsing EMBL file (1). ... ok test_annotation2 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation2) Check writing-and-parsing EMBL file (2). ... ok test_annotation3 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation3) Check writing-and-parsing EMBL file (3). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.133 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_NibIO.py test_SeqIO_NibIO ... ok test_read_even (test_SeqIO_NibIO.TestNibReaderWriter.test_read_even) ... ok test_read_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_read_odd) ... ok test_write_even (test_SeqIO_NibIO.TestNibReaderWriter.test_write_even) ... ok test_write_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_write_odd) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.096 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_PdbIO.py test_SeqIO_PdbIO ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_atom_parse (test_SeqIO_PdbIO.TestCifAtom.test_atom_parse) Parse a multi-chain structure by ATOM entries. ... ok test_atom_read (test_SeqIO_PdbIO.TestCifAtom.test_atom_read) Read a single-chain structure by ATOM entries. ... ok test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom.test_atom_read_noheader) Read a single-chain CIF without a header by ATOM entries. ... ok test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_missing) Parse a PDB with no SEQRES entries. ... ok test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_parse) Parse a multi-chain PDB by SEQRES entries. ... ok test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_read) Read a single-chain structure by sequence entries. ... ok test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_noheader) Parse a PDB with no HEADER line. ... ok test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom.test_atom_parse) Parse a multi-chain structure by ATOM entries. ... ok test_atom_read (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read) Read a single-chain structure by ATOM entries. ... ok test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read_noheader) Read a single-chain PDB without a header by ATOM entries. ... ok test_atom_with_insertion (test_SeqIO_PdbIO.TestPdbAtom.test_atom_with_insertion) Read a PDB with residue insertion code. ... ok test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_missing) Parse a PDB with no SEQRES entries. ... ok test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_parse) Parse a multi-chain PDB by SEQRES entries. ... ok test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_read) Read a single-chain structure by sequence entries. ... ok ---------------------------------------------------------------------- Ran 1 test in 2.495 seconds C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_QualityIO.py test_SeqIO_QualityIO ... ok test_illumina_to_sanger (test_SeqIO_QualityIO.MappingTests.test_illumina_to_sanger) Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62). ... ok test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests.test_phred_quality_from_solexa) Mapping check for function phred_quality_from_solexa. ... ok test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests.test_sanger_to_illumina) Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62). ... ok test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests.test_sanger_to_solexa) Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62). ... ok test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests.test_solexa_quality_from_phred) Mapping check for function solexa_quality_from_phred. ... ok test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests.test_solexa_to_sanger) Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62). ... ok test_fasta_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_fasta_as_fastq) ... ok test_sff_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_sff_as_fastq) ... ok test_reject_high_and_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_and_low) ... ok test_reject_high_but_not_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_but_not_low) ... ok test_fasta (test_SeqIO_QualityIO.TestQual.test_fasta) Check FASTQ parsing matches FASTA parsing. ... ok test_fasta_out (test_SeqIO_QualityIO.TestQual.test_fasta_out) Check FASTQ to FASTA output. ... ok test_paired (test_SeqIO_QualityIO.TestQual.test_paired) Check FASTQ parsing matches FASTA+QUAL parsing. ... ok test_qual (test_SeqIO_QualityIO.TestQual.test_qual) Check FASTQ parsing matches QUAL parsing. ... ok test_qual_negative (test_SeqIO_QualityIO.TestQual.test_qual_negative) Check QUAL negative scores mapped to PHRED zero. ... ok test_qual_out (test_SeqIO_QualityIO.TestQual.test_qual_out) Check FASTQ to QUAL output. ... ok test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_1000) Read and write back simple example with mixed case 1000bp read. ... ok test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_2000) Read and write back simple example with upper case 2000bp read. ... ok test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_dna) Read and write back simple example with ambiguous DNA. ... ok test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_rna) Read and write back simple example with ambiguous RNA. ... ok test_reference_conversion (test_SeqIO_QualityIO.TestReferenceFastqConversions.test_reference_conversion) ... ok test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_end) Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL. ... ok test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_start) Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL. ... ok test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_in_middle) Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL. ... ok test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_end) Test converting E3MFGYR02_index_in_middle into FASTA+QUAL. ... ok test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_start) Test converting E3MFGYR02_index_at_start into FASTA+QUAL. ... ok test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions.test_no_manifest) Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL. ... ok test_original (test_SeqIO_QualityIO.TestReferenceSffConversions.test_original) Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL. ... ok test_negative_clip (test_SeqIO_QualityIO.TestSFF.test_negative_clip) ... ok test_overlapping_clip (test_SeqIO_QualityIO.TestSFF.test_overlapping_clip) ... ok test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02) Write and read back E3MFGYR02_random_10_reads.sff. ... ok test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_end) Write and read back E3MFGYR02_alt_index_at_end.sff. ... ok test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_start) Write and read back E3MFGYR02_alt_index_at_start.sff. ... ok test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_in_middle) Write and read back E3MFGYR02_alt_index_in_middle.sff. ... ok test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_at_start) Write and read back E3MFGYR02_index_at_start.sff. ... ok test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_in_middle) Write and read back E3MFGYR02_index_in_middle.sff. ... ok test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_no_manifest) Write and read back E3MFGYR02_no_manifest.sff. ... ok test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_trimmed) Write and read back E3MFGYR02_random_10_reads.sff (trimmed). ... ok test_example_fasta (test_SeqIO_QualityIO.TestWriteRead.test_example_fasta) Write and read back example.fasta. ... ok test_example_fastq (test_SeqIO_QualityIO.TestWriteRead.test_example_fastq) Write and read back example.fastq. ... ok test_example_qual (test_SeqIO_QualityIO.TestWriteRead.test_example_qual) Write and read back example.qual. ... ok test_generated (test_SeqIO_QualityIO.TestWriteRead.test_generated) Write and read back odd SeqRecord objects. ... ok test_greek_sff (test_SeqIO_QualityIO.TestWriteRead.test_greek_sff) Write and read back greek.sff. ... ok test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead.test_illumina_faked) Write and read back illumina_faked.fastq. ... ok test_paired_sff (test_SeqIO_QualityIO.TestWriteRead.test_paired_sff) Write and read back paired.sff. ... ok test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead.test_sanger_93) Write and read back sanger_93.fastq. ... ok test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead.test_sanger_faked) Write and read back sanger_faked.fastq. ... ok test_solexa_example (test_SeqIO_QualityIO.TestWriteRead.test_solexa_example) Write and read back solexa_example.fastq. ... ok test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead.test_solexa_faked) Write and read back solexa_faked.fastq. ... ok test_tricky (test_SeqIO_QualityIO.TestWriteRead.test_tricky) Write and read back tricky.fastq. ... ok test_conversion (test_SeqIO_QualityIO.TestsConverter.test_conversion) ... ok test_failure_detection (test_SeqIO_QualityIO.TestsConverter.test_failure_detection) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.449 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SeqXML.py test_SeqIO_SeqXML ... ok test_duplicated_dbxref (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_dbxref) Read multiple cross references to a single source. ... ok test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_property) Read property with multiple values. ... ok test_empty_description (test_SeqIO_SeqXML.TestDetailedRead.test_empty_description) Check empty description. ... ok test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead.test_full_characters_set_read) Read full characters set for each type. ... ok test_global_species (test_SeqIO_SeqXML.TestDetailedRead.test_global_species) Check global species. ... ok test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead.test_local_source_definition) Check local source. ... ok test_local_species (test_SeqIO_SeqXML.TestDetailedRead.test_local_species) Check local species. ... ok test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead.test_read_minimal_required) Check minimal record. ... ok test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_special_characters_desc) Read special XML characters in description. ... ok test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_unicode_characters_desc) Test special unicode characters in the description. ... ok test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_dna) Read and write DNA. ... ok test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_globalSpecies) Read and write global species. ... ok test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_protein) Read and write protein. ... ok test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_rna) Read and write RNA. ... ok test_write_species (test_SeqIO_SeqXML.TestReadAndWrite.test_write_species) Test writing species from annotation tags. ... ok test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles.test_for_errors) Handling of corrupt files. ... ok test_check_dna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_dna_header) Check if the header information is parsed. ... ok test_check_global_species_example_header (test_SeqIO_SeqXML.TestReadHeader.test_check_global_species_example_header) Check if the header information is parsed. ... ok test_check_protein_header (test_SeqIO_SeqXML.TestReadHeader.test_check_protein_header) Check if the header information is parsed. ... ok test_check_rna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_rna_header) Check if the header information is parsed. ... ok test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead.test_check_SeqIO) Files readable using parser via SeqIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.096 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SnapGene.py test_SeqIO_SnapGene ... ok test_extra_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_extra_dna) Read a file with supernumerary DNA packet. ... ok test_invalid_cookie (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_invalid_cookie) Read a file with missing or invalid cookie packet. ... ok test_missing_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_missing_dna) Read a file without a DNA packet. ... ok test_truncated_packet (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_truncated_packet) Read a file with incomplete packet. ... ok test_read (test_SeqIO_SnapGene.TestSnapGene.test_read) Read sample files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.103 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_TwoBitIO.py test_SeqIO_TwoBitIO ... ok test_bigendian (test_SeqIO_TwoBitIO.Parsing.test_bigendian) ... ok test_littleendian (test_SeqIO_TwoBitIO.Parsing.test_littleendian) ... ok test_sequence_long (test_SeqIO_TwoBitIO.Parsing.test_sequence_long) ... ok test_add (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_add) ... ok test_bytes (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_bytes) ... ok test_contains (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_contains) ... ok test_count (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_count) ... ok test_endswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_endswith) ... ok test_find (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_find) ... ok test_getitem (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_getitem) ... ok test_hash (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_hash) ... ok test_index (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_index) ... ok test_lower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lower) ... ok test_lstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lstrip) ... ok test_mul (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_mul) ... ok test_radd (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_radd) ... ok test_replace (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_replace) ... ok test_repr (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_repr) ... ok test_rfind (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rfind) ... ok test_rindex (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rindex) ... ok test_rsplit (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rsplit) ... ok test_rstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rstrip) ... ok test_split (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_split) ... ok test_startswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_startswith) ... ok test_str (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_str) ... ok test_strip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_strip) ... ok test_translate (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_translate) ... ok test_upper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_upper) ... ok test_eq (test_SeqIO_TwoBitIO.TestComparisons.test_eq) ... ok test_ge (test_SeqIO_TwoBitIO.TestComparisons.test_ge) ... ok test_gt (test_SeqIO_TwoBitIO.TestComparisons.test_gt) ... ok test_le (test_SeqIO_TwoBitIO.TestComparisons.test_le) ... ok test_lt (test_SeqIO_TwoBitIO.TestComparisons.test_lt) ... ok test_ne (test_SeqIO_TwoBitIO.TestComparisons.test_ne) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.736 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Xdna.py test_SeqIO_Xdna ... ok test_corrupted_length (test_SeqIO_Xdna.TestInvalidXdna.test_corrupted_length) Read a file with incorrect length. ... ok test_invalid_sequence_type (test_SeqIO_Xdna.TestInvalidXdna.test_invalid_sequence_type) Read a file with an unknown sequence type. ... ok test_missing_features (test_SeqIO_Xdna.TestInvalidXdna.test_missing_features) Read a file with an incorrect number of features. ... ok test_unsupported_version (test_SeqIO_Xdna.TestInvalidXdna.test_unsupported_version) Read a file with unexpected version number. ... ok test_read (test_SeqIO_Xdna.TestXdna.test_read) Read sample files. ... ok test_warnings_on_data_loss (test_SeqIO_Xdna.TestXdnaWriter.test_warnings_on_data_loss) Emit warnings when dropping data on write. ... ok test_write_sequence_type (test_SeqIO_Xdna.TestXdnaWriter.test_write_sequence_type) Write correct sequence type. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_features.py test_SeqIO_features ... /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: unassigned DNA warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1256: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn("Non-standard molecule type: %s" % mol_type, BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:548: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line warnings.warn( ok test_after (test_SeqIO_features.FeatureWriting.test_after) Features: write/read simple after locations. ... ok test_before (test_SeqIO_features.FeatureWriting.test_before) Features: write/read simple before locations. ... ok test_between (test_SeqIO_features.FeatureWriting.test_between) GenBank/EMBL write/read simple between locations. ... ok test_exact (test_SeqIO_features.FeatureWriting.test_exact) GenBank/EMBL write/read simple exact locations. ... ok test_fuzzy_join (test_SeqIO_features.FeatureWriting.test_fuzzy_join) Features: write/read fuzzy join locations. ... ok test_join (test_SeqIO_features.FeatureWriting.test_join) GenBank/EMBL write/read simple join locations. ... ok test_oneof (test_SeqIO_features.FeatureWriting.test_oneof) Features: write/read simple one-of locations. ... ok test_unknown (test_SeqIO_features.FeatureWriting.test_unknown) GenBank/EMBL write/read with unknown end points. ... ok test_within (test_SeqIO_features.FeatureWriting.test_within) Features: write/read simple within locations. ... ok test_mixed_strand (test_SeqIO_features.GenBankLocations.test_mixed_strand) ... ok test_rev_comp_styles (test_SeqIO_features.GenBankLocations.test_rev_comp_styles) ... ok test_CDS (test_SeqIO_features.NC_000932.test_CDS) Checking GenBank CDS translations vs FASTA faa file. ... ok test_CDS (test_SeqIO_features.NC_005816.test_CDS) Checking GenBank CDS translations vs FASTA faa file. ... ok test_Features (test_SeqIO_features.NC_005816.test_Features) Checking GenBank features sequences vs FASTA ffn file. ... ok test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816.test_GenBank_vs_EMBL) ... ok test_Genome (test_SeqIO_features.NC_005816.test_Genome) Checking GenBank sequence vs FASTA fna file. ... ok test_Translations (test_SeqIO_features.NC_005816.test_Translations) Checking translation of FASTA features (faa vs ffn). ... ok test_qualifiers (test_SeqIO_features.SeqFeatureCreation.test_qualifiers) Pass in qualifiers to SeqFeatures. ... ok test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_join) Feature on DNA (join, mixed strand). ... ok test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_multi_join) Feature on DNA (multi-join, mixed strand). ... ok test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_between) Feature on protein (between location, zero length). ... ok test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join) Feature on protein (join). ... ok test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join_fuzzy) Feature on protein (fuzzy join). ... ok test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_multi_join) Feature on protein (multi-join). ... ok test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_oneof) Feature on protein (one-of positions). ... ok test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_simple) Feature on protein (simple). ... ok test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna) Feature on DNA (simple, default strand). ... ok test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join) Feature on DNA (join, strand +1). ... ok test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_after) Feature on DNA (join, strand -1, after position). ... ok test_simple_dna_join_before (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_before) Feature on DNA (join, strand -1, before position). ... ok test_simple_dna_join_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_strand_minus) Feature on DNA (join, strand -1). ... ok test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand0) Feature on DNA (simple, strand 0). ... ok test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand1) Feature on DNA (simple, strand +1). ... ok test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_minus) Feature on DNA (simple, strand -1). ... ok test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_none) Feature on DNA (simple, strand None). ... ok test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_rna) Feature on RNA (simple, default strand). ... ok test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_single_letter_dna) Feature on DNA (single letter, default strand). ... ok test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna) Feature on DNA (between location, zero length, default strand). ... ok test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna_end) Feature on DNA (between location at end, zero length, default strand). ... ok test_AAA03323 (test_SeqIO_features.TestWriteRead.test_AAA03323) Write and read back AAA03323.embl. ... ok test_AE017046 (test_SeqIO_features.TestWriteRead.test_AE017046) Write and read back AE017046.embl. ... ok test_DD231055_edited (test_SeqIO_features.TestWriteRead.test_DD231055_edited) Write and read back DD231055_edited.embl. ... ok test_Human_contigs (test_SeqIO_features.TestWriteRead.test_Human_contigs) Write and read back Human_contigs.embl. ... ok test_NC_000932 (test_SeqIO_features.TestWriteRead.test_NC_000932) Write and read back NC_000932.gb. ... ok test_NC_005816 (test_SeqIO_features.TestWriteRead.test_NC_005816) Write and read back NC_005816.gb. ... ok test_NT_019265 (test_SeqIO_features.TestWriteRead.test_NT_019265) Write and read back NT_019265.gb. ... ok test_SC10H5 (test_SeqIO_features.TestWriteRead.test_SC10H5) Write and read back SC10H5.embl. ... ok test_TRBG361 (test_SeqIO_features.TestWriteRead.test_TRBG361) Write and read back TRBG361.embl. ... ok test_U87107 (test_SeqIO_features.TestWriteRead.test_U87107) Write and read back U87107.embl. ... ok test_arab1 (test_SeqIO_features.TestWriteRead.test_arab1) Write and read back arab1.gb. ... ok test_blank_seq (test_SeqIO_features.TestWriteRead.test_blank_seq) Write and read back blank_seq.gb. ... ok test_cor6 (test_SeqIO_features.TestWriteRead.test_cor6) Write and read back cor6_6.gb. ... ok test_dbsource_wrap (test_SeqIO_features.TestWriteRead.test_dbsource_wrap) Write and read back dbsource_wrap.gb. ... ok test_extra_keywords (test_SeqIO_features.TestWriteRead.test_extra_keywords) Write and read back extra_keywords.gb. ... ok test_gbvrl1_start (test_SeqIO_features.TestWriteRead.test_gbvrl1_start) Write and read back gbvrl1_start.seq. ... ok test_noref (test_SeqIO_features.TestWriteRead.test_noref) Write and read back noref.gb. ... ok test_one_of (test_SeqIO_features.TestWriteRead.test_one_of) Write and read back of_one.gb. ... ok test_origin_line (test_SeqIO_features.TestWriteRead.test_origin_line) Write and read back origin_line.gb. ... ok test_pri1 (test_SeqIO_features.TestWriteRead.test_pri1) Write and read back pri1.gb. ... ok test_protein_refseq (test_SeqIO_features.TestWriteRead.test_protein_refseq) Write and read back protein_refseq.gb. ... ok test_protein_refseq2 (test_SeqIO_features.TestWriteRead.test_protein_refseq2) Write and read back protein_refseq2.gb. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.562 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_index.py test_SeqIO_index ... ok test_alpha_fails (test_SeqIO_index.IndexDictTests.test_alpha_fails) Reject alphabet argument in Bio.SeqIO.index(). ... ok test_alpha_fails_db (test_SeqIO_index.IndexDictTests.test_alpha_fails_db) Reject alphabet argument in Bio.SeqIO.index_db(). ... ok test_duplicates_index (test_SeqIO_index.IndexDictTests.test_duplicates_index) Index file with duplicate identifiers with Bio.SeqIO.index(). ... ok test_duplicates_index_db (test_SeqIO_index.IndexDictTests.test_duplicates_index_db) Index file with duplicate identifiers with Bio.SeqIO.index_db(). ... ok test_duplicates_to_dict (test_SeqIO_index.IndexDictTests.test_duplicates_to_dict) Index file with duplicate identifiers with Bio.SeqIO.to_dict(). ... ok test_key_checks (test_SeqIO_index.IndexDictTests.test_key_checks) ... ok test_raw_checks (test_SeqIO_index.IndexDictTests.test_raw_checks) ... ok test_simple_checks (test_SeqIO_index.IndexDictTests.test_simple_checks) ... ok test_order_index_db (test_SeqIO_index.IndexOrderingManyFiles.test_order_index_db) Check index_db preserves order in multiple indexed files. ... ok test_order_index (test_SeqIO_index.IndexOrderingSingleFile.test_order_index) Check index preserves order in indexed file. ... ok test_order_index_db (test_SeqIO_index.IndexOrderingSingleFile.test_order_index_db) Check index_db preserves ordering indexed file. ... ok test_order_to_dict (test_SeqIO_index.IndexOrderingSingleFile.test_order_to_dict) Check to_dict preserves order in indexed file. ... ok test_child_folder_rel (test_SeqIO_index.NewIndexTest.test_child_folder_rel) Check relative links to child folder. ... ok test_same_folder (test_SeqIO_index.NewIndexTest.test_same_folder) Check relative links in same folder. ... ok test_some_abs (test_SeqIO_index.NewIndexTest.test_some_abs) Check absolute filenames in index. ... ok test_old (test_SeqIO_index.OldIndexTest.test_old) Load existing index with no options (from parent directory). ... ok test_old_check_same_thread (test_SeqIO_index.OldIndexTest.test_old_check_same_thread) Setting check_same_thread to False doesn't raise an exception. ... ok test_old_contents (test_SeqIO_index.OldIndexTest.test_old_contents) Check actual filenames in existing indexes. ... ok test_old_files (test_SeqIO_index.OldIndexTest.test_old_files) Load existing index with correct files (from parent directory). ... ok test_old_files_same_dir (test_SeqIO_index.OldIndexTest.test_old_files_same_dir) Load existing index with correct files (from same directory). ... ok test_old_files_wrong (test_SeqIO_index.OldIndexTest.test_old_files_wrong) Load existing index with wrong files. ... ok test_old_files_wrong2 (test_SeqIO_index.OldIndexTest.test_old_files_wrong2) Load existing index with wrong number of files. ... ok test_old_format (test_SeqIO_index.OldIndexTest.test_old_format) Load existing index with correct format. ... ok test_old_format_wrong (test_SeqIO_index.OldIndexTest.test_old_format_wrong) Load existing index with wrong format. ... ok test_old_rel (test_SeqIO_index.OldIndexTest.test_old_rel) Load existing index (with relative paths) with no options (from parent directory). ... ok test_old_same_dir (test_SeqIO_index.OldIndexTest.test_old_same_dir) Load existing index with no options (from same directory). ... ok test_old_same_dir_rel (test_SeqIO_index.OldIndexTest.test_old_same_dir_rel) Load existing index (with relative paths) with no options (from same directory). ... ok ---------------------------------------------------------------------- Ran 1 test in 7.526 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_online.py test_SeqIO_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.076 seconds C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_write.py test_SeqIO_write ... ok test_alignment_formats (test_SeqIO_write.WriterTests.test_alignment_formats) ... ok test_bad_handle (test_SeqIO_write.WriterTests.test_bad_handle) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.109 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqRecord.py test_SeqRecord ... ok test_annotations (test_SeqRecord.SeqRecordCreation.test_annotations) Pass in annotations to SeqRecords. ... ok test_letter_annotations (test_SeqRecord.SeqRecordCreation.test_letter_annotations) Pass in letter annotations to SeqRecords. ... ok test_replacing_seq (test_SeqRecord.SeqRecordCreation.test_replacing_seq) Replacing .seq if .letter_annotation present. ... ok test_valid_annotations (test_SeqRecord.SeqRecordCreation.test_valid_annotations) ... ok test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation.test_valid_dbxrefs) ... ok test_valid_description (test_SeqRecord.SeqRecordCreation.test_valid_description) ... ok test_valid_features (test_SeqRecord.SeqRecordCreation.test_valid_features) ... ok test_valid_id (test_SeqRecord.SeqRecordCreation.test_valid_id) ... ok test_valid_name (test_SeqRecord.SeqRecordCreation.test_valid_name) ... ok test_add_seq (test_SeqRecord.SeqRecordMethods.test_add_seq) Simple addition of Seq or string. ... ok test_add_seq_left (test_SeqRecord.SeqRecordMethods.test_add_seq_left) Simple left addition of Seq or string. ... ok test_add_seqrecord (test_SeqRecord.SeqRecordMethods.test_add_seqrecord) Simple left addition of SeqRecord from genbank file. ... ok test_add_simple (test_SeqRecord.SeqRecordMethods.test_add_simple) Simple addition. ... ok test_contains (test_SeqRecord.SeqRecordMethods.test_contains) ... ok test_format (test_SeqRecord.SeqRecordMethods.test_format) ... ok test_format_spaces (test_SeqRecord.SeqRecordMethods.test_format_spaces) ... ok test_format_str (test_SeqRecord.SeqRecordMethods.test_format_str) ... ok test_format_str_binary (test_SeqRecord.SeqRecordMethods.test_format_str_binary) ... ok test_iter (test_SeqRecord.SeqRecordMethods.test_iter) ... ok test_lower (test_SeqRecord.SeqRecordMethods.test_lower) ... ok test_repr (test_SeqRecord.SeqRecordMethods.test_repr) ... ok test_slice_add_shift (test_SeqRecord.SeqRecordMethods.test_slice_add_shift) Simple slice and add to shift. ... ok test_slice_add_simple (test_SeqRecord.SeqRecordMethods.test_slice_add_simple) Simple slice and add. ... ok test_slice_simple (test_SeqRecord.SeqRecordMethods.test_slice_simple) Simple slice. ... ok test_slice_variants (test_SeqRecord.SeqRecordMethods.test_slice_variants) Simple slices using different start/end values. ... ok test_slice_zero (test_SeqRecord.SeqRecordMethods.test_slice_zero) Zero slice. ... ok test_slicing (test_SeqRecord.SeqRecordMethods.test_slicing) ... ok test_str (test_SeqRecord.SeqRecordMethods.test_str) ... ok test_upper (test_SeqRecord.SeqRecordMethods.test_upper) ... ok test_eq_exception (test_SeqRecord.SeqRecordMethodsMore.test_eq_exception) ... ok test_ge_exception (test_SeqRecord.SeqRecordMethodsMore.test_ge_exception) ... ok test_gt_exception (test_SeqRecord.SeqRecordMethodsMore.test_gt_exception) ... ok test_hash_exception (test_SeqRecord.SeqRecordMethodsMore.test_hash_exception) ... ok test_le_exception (test_SeqRecord.SeqRecordMethodsMore.test_le_exception) ... ok test_lt_exception (test_SeqRecord.SeqRecordMethodsMore.test_lt_exception) ... ok test_ne_exception (test_SeqRecord.SeqRecordMethodsMore.test_ne_exception) ... ok test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_mutable_seq) ... ok test_reverse_complement_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_seq) ... ok test_translate (test_SeqRecord.SeqRecordMethodsMore.test_translate) ... ok test_defaults (test_SeqRecord.TestTranslation.test_defaults) ... ok test_new_annot (test_SeqRecord.TestTranslation.test_new_annot) ... ok test_preserve (test_SeqRecord.TestTranslation.test_preserve) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.143 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqUtils.py test_SeqUtils ... ok test_GC (test_SeqUtils.SeqUtilsTests.test_GC) ... ok test_GC_skew (test_SeqUtils.SeqUtilsTests.test_GC_skew) ... ok test_checksum1 (test_SeqUtils.SeqUtilsTests.test_checksum1) ... ok test_checksum2 (test_SeqUtils.SeqUtilsTests.test_checksum2) ... ok test_checksum3 (test_SeqUtils.SeqUtilsTests.test_checksum3) ... ok test_codon_adaptation_index (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index) ... ok test_codon_usage_custom (test_SeqUtils.SeqUtilsTests.test_codon_usage_custom) Test Codon Adaptation Index (CAI) using FASTA file for background. ... ok test_codon_usage_ecoli (test_SeqUtils.SeqUtilsTests.test_codon_usage_ecoli) Test Codon Adaptation Index (CAI) using default E. coli data. ... ok test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests.test_crc_checksum_collision) ... ok test_index (test_SeqUtils.SeqUtilsTests.test_index) ... ok test_seq1_seq3 (test_SeqUtils.SeqUtilsTests.test_seq1_seq3) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Seq_objs.py test_Seq_objs ... ok test_eq (test_Seq_objs.ComparisonTests.test_eq) ... ok test_ge (test_Seq_objs.ComparisonTests.test_ge) ... ok test_gt (test_Seq_objs.ComparisonTests.test_gt) ... ok test_le (test_Seq_objs.ComparisonTests.test_le) ... ok test_lt (test_Seq_objs.ComparisonTests.test_lt) ... ok test_ne (test_Seq_objs.ComparisonTests.test_ne) ... ok test_unknown_seq (test_Seq_objs.FileBasedTests.test_unknown_seq) Test if feature extraction works properly for unknown sequences. ... ok test_MutableSeq_init_typeerror (test_Seq_objs.StringMethodTests.test_MutableSeq_init_typeerror) Check MutableSeq __init__ gives TypeError exceptions. ... ok test_count_overlap (test_Seq_objs.StringMethodTests.test_count_overlap) Check count_overlap exception matches python string count method. ... ok test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_GG) Check our count_overlap method using GG with variable ends and starts. ... ok test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_NN) Check our count_overlap method using NN with variable ends and starts. ... ok test_equality (test_Seq_objs.StringMethodTests.test_equality) Test equality when mixing types. ... ok test_init_typeerror (test_Seq_objs.StringMethodTests.test_init_typeerror) Check Seq __init__ gives TypeError exceptions. ... ok test_join_MutableSeq (test_Seq_objs.StringMethodTests.test_join_MutableSeq) Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok test_join_MutableSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_MutableSeq_TypeError_iter) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_MutableSeq_mixed (test_Seq_objs.StringMethodTests.test_join_MutableSeq_mixed) Check MutableSeq objects can be joined. ... ok test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests.test_join_MutableSeq_with_file) Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok test_join_Seq (test_Seq_objs.StringMethodTests.test_join_Seq) Checks if Seq join correctly concatenates sequence with the spacer. ... ok test_join_Seq_TypeError (test_Seq_objs.StringMethodTests.test_join_Seq_TypeError) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_Seq_with_file (test_Seq_objs.StringMethodTests.test_join_Seq_with_file) Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok test_join_UnknownSeq (test_Seq_objs.StringMethodTests.test_join_UnknownSeq) Checks if UnknownSeq join correctly concatenates sequence with the spacer. ... ok test_join_UnknownSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_UnknownSeq_TypeError_iter) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_UnknownSeq_with_file (test_Seq_objs.StringMethodTests.test_join_UnknownSeq_with_file) Checks if UnknownSeq join correctly concatenates sequence from a file with the spacer. ... ok test_str_comparison (test_Seq_objs.StringMethodTests.test_str_comparison) ... ok test_str_count (test_Seq_objs.StringMethodTests.test_str_count) Check matches the python string count method. ... ok test_str_count_overlap_GG (test_Seq_objs.StringMethodTests.test_str_count_overlap_GG) Check our count_overlap method using GG. ... ok test_str_count_overlap_NN (test_Seq_objs.StringMethodTests.test_str_count_overlap_NN) Check our count_overlap method using NN. ... ok test_str_encode (test_Seq_objs.StringMethodTests.test_str_encode) Check matches the python string encode method. ... ok test_str_endswith (test_Seq_objs.StringMethodTests.test_str_endswith) Check matches the python string endswith method. ... ok test_str_find (test_Seq_objs.StringMethodTests.test_str_find) Check matches the python string find method. ... ok test_str_getitem (test_Seq_objs.StringMethodTests.test_str_getitem) Check slicing and indexing works like a string. ... ok test_str_hash (test_Seq_objs.StringMethodTests.test_str_hash) ... ok test_str_index (test_Seq_objs.StringMethodTests.test_str_index) Check matches the python string index method. ... ok test_str_length (test_Seq_objs.StringMethodTests.test_str_length) Check matches the python string __len__ method. ... ok test_str_lower (test_Seq_objs.StringMethodTests.test_str_lower) Check matches the python string lower method. ... ok test_str_lstrip (test_Seq_objs.StringMethodTests.test_str_lstrip) Check matches the python string lstrip method. ... ok test_str_replace (test_Seq_objs.StringMethodTests.test_str_replace) Check matches the python string replace method. ... ok test_str_rfind (test_Seq_objs.StringMethodTests.test_str_rfind) Check matches the python string rfind method. ... ok test_str_rindex (test_Seq_objs.StringMethodTests.test_str_rindex) Check matches the python string rindex method. ... ok test_str_rsplit (test_Seq_objs.StringMethodTests.test_str_rsplit) Check matches the python string rsplit method. ... ok test_str_rstrip (test_Seq_objs.StringMethodTests.test_str_rstrip) Check matches the python string rstrip method. ... ok test_str_split (test_Seq_objs.StringMethodTests.test_str_split) Check matches the python string split method. ... ok test_str_startswith (test_Seq_objs.StringMethodTests.test_str_startswith) Check matches the python string startswith method. ... ok test_str_strip (test_Seq_objs.StringMethodTests.test_str_strip) Check matches the python string strip method. ... ok test_str_upper (test_Seq_objs.StringMethodTests.test_str_upper) Check matches the python string upper method. ... ok test_the_back_transcription (test_Seq_objs.StringMethodTests.test_the_back_transcription) Check obj.back_transcribe() method. ... ok test_the_complement (test_Seq_objs.StringMethodTests.test_the_complement) Check obj.complement() method. ... ok test_the_reverse_complement (test_Seq_objs.StringMethodTests.test_the_reverse_complement) Check obj.reverse_complement() method. ... ok test_the_transcription (test_Seq_objs.StringMethodTests.test_the_transcription) Check obj.transcribe() method. ... ok test_the_translate (test_Seq_objs.StringMethodTests.test_the_translate) Check obj.translate() method. ... ok test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_ambig_codons) Check obj.translate() method with ambiguous codons. ... ok test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_invalid_codons) Check obj.translate() method with invalid codons. ... ok test_the_translation_of_stops (test_Seq_objs.StringMethodTests.test_the_translation_of_stops) Check obj.translate() method with stop codons. ... ok test_tomutable (test_Seq_objs.StringMethodTests.test_tomutable) Check creating a MutableSeq object. ... ok test_toseq (test_Seq_objs.StringMethodTests.test_toseq) Check creating a Seq object. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.833 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SffIO.py test_SffIO ... ok test_alt_index_at_end (test_SffIO.TestAlternativeIndexes.test_alt_index_at_end) ... ok test_alt_index_at_start (test_SffIO.TestAlternativeIndexes.test_alt_index_at_start) ... ok test_alt_index_in_middle (test_SffIO.TestAlternativeIndexes.test_alt_index_in_middle) ... ok test_index_at_start (test_SffIO.TestAlternativeIndexes.test_index_at_start) ... ok test_index_in_middle (test_SffIO.TestAlternativeIndexes.test_index_in_middle) ... ok test_trim (test_SffIO.TestAlternativeIndexes.test_trim) ... ok test_index1 (test_SffIO.TestConcatenated.test_index1) ... ok test_index2 (test_SffIO.TestConcatenated.test_index2) ... ok test_parse1 (test_SffIO.TestConcatenated.test_parse1) ... ok test_parse2 (test_SffIO.TestConcatenated.test_parse2) ... ok test_parses_gzipped_stream (test_SffIO.TestConcatenated.test_parses_gzipped_stream) ... ok test_30bytes (test_SffIO.TestErrors.test_30bytes) ... ok test_31bytes (test_SffIO.TestErrors.test_31bytes) ... ok test_31bytes_bad_flowgram (test_SffIO.TestErrors.test_31bytes_bad_flowgram) ... ok test_31bytes_bad_ver (test_SffIO.TestErrors.test_31bytes_bad_ver) ... ok test_31bytes_index_header (test_SffIO.TestErrors.test_31bytes_index_header) ... ok test_bad_index_eof (test_SffIO.TestErrors.test_bad_index_eof) ... ok test_bad_index_length (test_SffIO.TestErrors.test_bad_index_length) ... ok test_bad_index_offset (test_SffIO.TestErrors.test_bad_index_offset) ... ok test_empty (test_SffIO.TestErrors.test_empty) ... ok test_index_lengths (test_SffIO.TestErrors.test_index_lengths) ... ok test_index_mft_data_size (test_SffIO.TestErrors.test_index_mft_data_size) ... ok test_index_mft_version (test_SffIO.TestErrors.test_index_mft_version) ... ok test_index_name_no_null (test_SffIO.TestErrors.test_index_name_no_null) ... ok test_no_index (test_SffIO.TestErrors.test_no_index) ... ok test_no_manifest_xml (test_SffIO.TestErrors.test_no_manifest_xml) ... ok test_premature_end_of_index (test_SffIO.TestErrors.test_premature_end_of_index) ... ok test_unknown_index (test_SffIO.TestErrors.test_unknown_index) ... ok test_both_ways (test_SffIO.TestIndex.test_both_ways) ... ok test_manifest (test_SffIO.TestIndex.test_manifest) ... ok test_index (test_SffIO.TestSelf.test_index) ... ok test_read (test_SffIO.TestSelf.test_read) ... ok test_read_wrong (test_SffIO.TestSelf.test_read_wrong) ... ok test_write (test_SffIO.TestSelf.test_write) ... ok test_coords (test_SffIO.TestUAN.test_coords) ... ok test_region (test_SffIO.TestUAN.test_region) ... ok test_time (test_SffIO.TestUAN.test_time) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SwissProt.py test_SwissProt ... ok test_P0A186 (test_SwissProt.TestSwissProt.test_P0A186) Parsing SwissProt file P0A186.txt. ... ok test_P0CK95 (test_SwissProt.TestSwissProt.test_P0CK95) Parsing SwissProt file P0CK95.txt. ... ok test_P60137 (test_SwissProt.TestSwissProt.test_P60137) Parsing SwissProt file P60137.txt. ... ok test_Q13639 (test_SwissProt.TestSwissProt.test_Q13639) Parsing SwissProt file Q13639. ... ok test_ft_line (test_SwissProt.TestSwissProt.test_ft_line) Parsing SwissProt file O23729, which has a new-style FT line. ... ok test_sp001 (test_SwissProt.TestSwissProt.test_sp001) Parsing SwissProt file sp001. ... ok test_sp002 (test_SwissProt.TestSwissProt.test_sp002) Parsing SwissProt file sp002. ... ok test_sp003 (test_SwissProt.TestSwissProt.test_sp003) Parsing SwissProt file sp003. ... ok test_sp005 (test_SwissProt.TestSwissProt.test_sp005) Parsing SwissProt file sp005. ... ok test_sp006 (test_SwissProt.TestSwissProt.test_sp006) Parsing SwissProt file sp006. ... ok test_sp007 (test_SwissProt.TestSwissProt.test_sp007) Parsing SwissProt file sp007. ... ok test_sp008 (test_SwissProt.TestSwissProt.test_sp008) Parsing SwissProt file sp008. ... ok test_sp009 (test_SwissProt.TestSwissProt.test_sp009) Parsing SwissProt file sp009. ... ok test_sp010 (test_SwissProt.TestSwissProt.test_sp010) Parsing SwissProt file sp010. ... ok test_sp011 (test_SwissProt.TestSwissProt.test_sp011) Parsing SwissProt file sp011. ... ok test_sp012 (test_SwissProt.TestSwissProt.test_sp012) Parsing SwissProt file sp012. ... ok test_sp013 (test_SwissProt.TestSwissProt.test_sp013) Parsing SwissProt file sp013. ... ok test_sp015 (test_SwissProt.TestSwissProt.test_sp015) Parsing SwissProt file sp015. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.121 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.090 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_TogoWS.py test_TogoWS ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_TreeConstruction.py test_TreeConstruction ... ok test_known_matrices (test_TreeConstruction.DistanceCalculatorTest.test_known_matrices) ... ok test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest.test_nonmatching_seqs) ... ok test_bad_construction (test_TreeConstruction.DistanceMatrixTest.test_bad_construction) ... ok test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest.test_bad_manipulation) ... ok test_format_phylip (test_TreeConstruction.DistanceMatrixTest.test_format_phylip) ... ok test_good_construction (test_TreeConstruction.DistanceMatrixTest.test_good_construction) ... ok test_good_manipulation (test_TreeConstruction.DistanceMatrixTest.test_good_manipulation) ... ok test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest.test_built_tree) ... ok test_nj (test_TreeConstruction.DistanceTreeConstructorTest.test_nj) ... ok test_upgma (test_TreeConstruction.DistanceTreeConstructorTest.test_upgma) ... ok test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest.test_get_neighbors) ... ok test_get_score (test_TreeConstruction.ParsimonyScorerTest.test_get_score) ... ok test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest.test_build_tree) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.306 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_UniGene.py test_UniGene ... ok test_parse (test_UniGene.TestUniGene.test_parse) ... ok test_read (test_UniGene.TestUniGene.test_read) ... ok test_read_value_error (test_UniGene.TestUniGene.test_read_value_error) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.027 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_UniProt_GOA.py test_UniProt_GOA ... ok test_gaf_iterator (test_UniProt_GOA.GoaTests.test_gaf_iterator) Test GOA GAF file iterator. ... ok test_gpa_iterator (test_UniProt_GOA.GoaTests.test_gpa_iterator) Test GOA GPA file iterator. ... ok test_gpi_iterator (test_UniProt_GOA.GoaTests.test_gpi_iterator) Test GOA GPI file iterator, gpi-version: 1.1. ... ok test_gpi_iterator_one_two (test_UniProt_GOA.GoaTests.test_gpi_iterator_one_two) Test GOA GPI file iterator, gpi-version: 1.2. ... ok test_selection_writing (test_UniProt_GOA.GoaTests.test_selection_writing) Test record_has, and writerec. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.032 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Uniprot.py test_Uniprot ... ok test_F2CXE6 (test_Uniprot.TestUniprot.test_F2CXE6) Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok test_H2CNN8 (test_Uniprot.TestUniprot.test_H2CNN8) Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok test_P84001 (test_Uniprot.TestUniprot.test_P84001) Parse mass spec structured comment with unknown loc. ... ok test_Q13639 (test_Uniprot.TestUniprot.test_Q13639) Compare SwissProt text and uniprot XML versions of Q13639. ... ok test_multi_ex (test_Uniprot.TestUniprot.test_multi_ex) Compare SwissProt text and uniprot XML versions of several examples. ... ok test_multi_ex_index (test_Uniprot.TestUniprot.test_multi_ex_index) Index SwissProt text and uniprot XML versions of several examples. ... ok test_sp002 (test_Uniprot.TestUniprot.test_sp002) Parsing SwissProt file sp002. ... ok test_sp016 (test_Uniprot.TestUniprot.test_sp016) Parsing SwissProt file sp016. ... ok test_submittedName_allowed (test_Uniprot.TestUniprot.test_submittedName_allowed) Checks if parser supports new XML Element (submittedName). ... ok test_uni001 (test_Uniprot.TestUniprot.test_uni001) Parsing Uniprot file uni001. ... ok test_uni003 (test_Uniprot.TestUniprot.test_uni003) Parsing Uniprot file uni003. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.192 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` C + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Wise.py test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise. ---------------------------------------------------------------------- Ran 1 test in 0.085 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.100 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_align.py test_align ... ok test_basic_alignment (test_align.TestBasics.test_basic_alignment) Basic tests on a simple alignment of three sequences. ... ok test_empty_alignment (test_align.TestBasics.test_empty_alignment) Very simple tests on an empty alignment. ... ok test_format_conversion (test_align.TestReading.test_format_conversion) Parse the alignment file and get an alignment object. ... ok test_read_clustal1 (test_align.TestReading.test_read_clustal1) Parse an alignment file and get an alignment object. ... ok test_read_clustal2 (test_align.TestReading.test_read_clustal2) Parse an alignment file and get an alignment object. ... ok test_read_fasta (test_align.TestReading.test_read_fasta) ... ok test_read_write_clustal (test_align.TestReading.test_read_write_clustal) Test the base alignment stuff. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.109 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_align_substitution_matrices.py test_align_substitution_matrices ... ok test1_observed_frequencies (test_align_substitution_matrices.TestScoringMatrices.test1_observed_frequencies) ... ok test2_observed_probabilities (test_align_substitution_matrices.TestScoringMatrices.test2_observed_probabilities) ... ok test3_observed_symmetric_probabilities (test_align_substitution_matrices.TestScoringMatrices.test3_observed_symmetric_probabilities) ... ok test4_aminoacid_probabilities (test_align_substitution_matrices.TestScoringMatrices.test4_aminoacid_probabilities) ... ok test5_expected_probabilities (test_align_substitution_matrices.TestScoringMatrices.test5_expected_probabilities) ... ok test6_scores (test_align_substitution_matrices.TestScoringMatrices.test6_scores) ... ok test_ident (test_align_substitution_matrices.TestScoringMatrices.test_ident) ... ok test_basics_matrix (test_align_substitution_matrices.Test_basics.test_basics_matrix) ... ok test_basics_vector (test_align_substitution_matrices.Test_basics.test_basics_vector) ... ok test_nucleotide_freq (test_align_substitution_matrices.Test_basics.test_nucleotide_freq) ... ok test_pickling (test_align_substitution_matrices.Test_basics.test_pickling) ... ok test_protein_freq (test_align_substitution_matrices.Test_basics.test_protein_freq) ... ok test_read_write (test_align_substitution_matrices.Test_basics.test_read_write) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.404 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_cellosaurus.py test_cellosaurus ... ok test__str__ (test_cellosaurus.TestCellosaurus.test__str__) Test string function. ... ok test_parse (test_cellosaurus.TestCellosaurus.test_parse) Test parsing function. ... ok test_read (test_cellosaurus.TestCellosaurus.test_read) Test read function. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.021 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_codonalign.py test_codonalign ... /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython. warnings.warn( /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Seq.py:2954: BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be translated as amino acid. warnings.warn( /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA) warnings.warn( /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA) warnings.warn( ok test_TypeError (test_codonalign.TestAddition.test_TypeError) Check that TypeError is thrown for non CodonAlignment/MultipleSequenceAlignment objects. ... ok test_ValueError (test_codonalign.TestAddition.test_ValueError) Check that ValueError is thrown for Alignments of different lengths. ... ok test_addition_CodonAlignment (test_codonalign.TestAddition.test_addition_CodonAlignment) Check addition of CodonAlignment and CodonAlignment. ... ok test_addition_MultipleSeqAlignment (test_codonalign.TestAddition.test_addition_MultipleSeqAlignment) Check addition of CodonAlignment and MultipleSeqAlignment. ... ok test_IO (test_codonalign.TestBuildAndIO.test_IO) ... ok test_align (test_codonalign.TestCodonAlignment.test_align) ... ok test_seq (test_codonalign.TestCodonSeq.test_seq) ... ok test_mk (test_codonalign.Test_MK.test_mk) ... ok test_build (test_codonalign.Test_build.test_build) ... ok test_dn_ds (test_codonalign.Test_dn_ds.test_dn_ds) ... ok test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) ... ok ---------------------------------------------------------------------- Ran 1 test in 4.718 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_geo.py test_geo ... ok Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux test_GSE16 (test_geo.TestGeo.test_GSE16) ... ok test_GSM645 (test_geo.TestGeo.test_GSM645) ... ok test_GSM691 (test_geo.TestGeo.test_GSM691) ... ok test_GSM700 (test_geo.TestGeo.test_GSM700) ... ok test_GSM804 (test_geo.TestGeo.test_GSM804) ... ok test_record_str (test_geo.TestGeo.test_record_str) ... ok test_soft_ex_affy (test_geo.TestGeo.test_soft_ex_affy) ... ok test_soft_ex_affy_chp (test_geo.TestGeo.test_soft_ex_affy_chp) ... ok test_soft_ex_dual (test_geo.TestGeo.test_soft_ex_dual) ... ok test_soft_ex_family (test_geo.TestGeo.test_soft_ex_family) ... ok test_soft_ex_platform (test_geo.TestGeo.test_soft_ex_platform) ... ok test_soft_ex_series (test_geo.TestGeo.test_soft_ex_series) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.065 seconds C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_kNN.py test_kNN ... ok test_calculate_model (test_kNN.TestKNN.test_calculate_model) ... ok test_calculate_probability (test_kNN.TestKNN.test_calculate_probability) ... ok test_classify (test_kNN.TestKNN.test_classify) ... ok test_leave_one_out (test_kNN.TestKNN.test_leave_one_out) ... ok test_model_accuracy (test_kNN.TestKNN.test_model_accuracy) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.021 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_mmtf.py test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_mmtf_online.py test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) ---------------------------------------------------------------------- Ran 1 test in 0.077 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_motifs.py test_motifs ... ok test_calculate_pseudocounts (test_motifs.MotifTestPWM.test_calculate_pseudocounts) ... ok test_simple (test_motifs.MotifTestPWM.test_simple) Test if Bio.motifs PWM scoring works. ... ok test_with_bad_char (test_motifs.MotifTestPWM.test_with_bad_char) Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok test_with_mixed_case (test_motifs.MotifTestPWM.test_with_mixed_case) Test if Bio.motifs PWM scoring works with mixed case. ... ok test_TFoutput (test_motifs.MotifTestsBasic.test_TFoutput) Ensure that we can write proper TransFac output files. ... ok test_alignace_parsing (test_motifs.MotifTestsBasic.test_alignace_parsing) Test if Bio.motifs can parse AlignAce output files. ... ok test_clusterbuster_parsing_and_output (test_motifs.MotifTestsBasic.test_clusterbuster_parsing_and_output) Test if Bio.motifs can parse and output Cluster Buster PFM files. ... ok test_format (test_motifs.MotifTestsBasic.test_format) ... ok test_pfm_four_columns_parsing (test_motifs.MotifTestsBasic.test_pfm_four_columns_parsing) Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 columns). ... ok test_pfm_four_rows_parsing (test_motifs.MotifTestsBasic.test_pfm_four_rows_parsing) Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 rows). ... ok test_pfm_parsing (test_motifs.MotifTestsBasic.test_pfm_parsing) Test if Bio.motifs can parse JASPAR-style pfm files. ... ok test_reverse_complement (test_motifs.MotifTestsBasic.test_reverse_complement) Test if motifs can be reverse-complemented. ... ok test_sites_parsing (test_motifs.MotifTestsBasic.test_sites_parsing) Test if Bio.motifs can parse JASPAR-style sites files. ... ok test_xms_parsing (test_motifs.MotifTestsBasic.test_xms_parsing) Test if Bio.motifs can parse and output xms PFM files. ... ok test_mast_parser_1 (test_motifs.TestMAST.test_mast_parser_1) Parse motifs/mast.crp0.de.oops.txt.xml file. ... ok test_mast_parser_2 (test_motifs.TestMAST.test_mast_parser_2) Parse motifs/mast.adh.de.oops.html.xml file. ... ok test_mast_parser_3 (test_motifs.TestMAST.test_mast_parser_3) Parse motifs/mast.Klf1-200.cd.oops.xml.xml file. ... ok test_meme_parser_1 (test_motifs.TestMEME.test_meme_parser_1) Parse motifs/meme.INO_up800.classic.oops.xml file. ... ok test_meme_parser_2 (test_motifs.TestMEME.test_meme_parser_2) Parsing motifs/meme.adh.classic.oops.xml file. ... ok test_meme_parser_3 (test_motifs.TestMEME.test_meme_parser_3) Parse motifs/meme.farntrans5.classic.anr.xml file. ... ok test_meme_parser_rna (test_motifs.TestMEME.test_meme_parser_rna) Test if Bio.motifs can parse MEME output files using RNA. ... ok test_minimal_meme_parser (test_motifs.TestMEME.test_minimal_meme_parser) Parse motifs/minimal_test.meme file. ... ok test_permissive_transfac_parser (test_motifs.TestTransfac.test_permissive_transfac_parser) Parse the TRANSFAC-like file motifs/MA0056.1.transfac. ... ok test_transfac_parser (test_motifs.TestTransfac.test_transfac_parser) Parse motifs/transfac.dat file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.120 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_motifs_online.py test_motifs_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.058 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise2.py test_pairwise2 ... ok test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments) ``_clean_alignments`` removes redundant and wrong alignments. ... ok test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix) ``print_matrix`` prints nested lists as nice matrices. ... ok test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments) One possible start position in local alignment is not a match. ... ok test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name) Test for wrong function names. ... ok test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters) Test for number of parameters. ... ok test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names) Test for unknown parameter in parameter names. ... ok test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings) Test for warnings. ... ok test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1) Test 1. ... ok test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2) Test 2. ... ok test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple) Test globalxx. ... ok test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2) Do the same test with sequence order reversed. ... ok test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input) Do a global alignment with sequences supplied as lists. ... ok test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only) Test one_alignment_only parameter. ... ok test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords) Test equality of calls with and without keywords. ... ok test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62) Test localds with blosum62. ... ok test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result) Return no alignment. ... ok test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric) Test if alignment is independent on direction of sequence. ... ok test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms) Two different local alignments. ... ok test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1) Test localxx. ... ok test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2) Test localxx with ``full_sequences=True``. ... ok test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic) Test the generic method with local alignments. ... ok test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1) Test 1. ... ok test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2) Test 2. ... ok test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3) Test 3. ... ok test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1) Test sequence with only one match. ... ok test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2) Test sequences with two possible match positions. ... ok test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3) Like test 1, but global alignment. ... ok test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1) Test 1. ... ok test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2) Test 2. ... ok test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3) Test 3. ... ok test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4) Test 4. ... ok test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) Turn off end-gap penalties. ... ok test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2) Do the same, but use the generic method (with the same result). ... ok test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps) Test alignment where end-gaps are differently penalized. ... ok test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) Add gap-extend penalty to gap-opening penalty. ... ok test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) Test 1. ... ok test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) Test 2. ... ok test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) Test separate gap-extension penalties and list input. ... ok test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1) Open a gap in second sequence only. ... ok test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2) Force a bad alignment. ... ok test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global) Test ``score_only`` in a global alignment. ... ok test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local) Test ``score_only`` in a local alignment. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.121 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise2_no_C.py test_pairwise2_no_C ... ok test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments) ``_clean_alignments`` removes redundant and wrong alignments. ... ok test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix) ``print_matrix`` prints nested lists as nice matrices. ... ok test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments) One possible start position in local alignment is not a match. ... ok test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name) Test for wrong function names. ... ok test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters) Test for number of parameters. ... ok test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names) Test for unknown parameter in parameter names. ... ok test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings) Test for warnings. ... ok test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1) Test 1. ... ok test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2) Test 2. ... ok test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple) Test globalxx. ... ok test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2) Do the same test with sequence order reversed. ... ok test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input) Do a global alignment with sequences supplied as lists. ... ok test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only) Test one_alignment_only parameter. ... ok test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords) Test equality of calls with and without keywords. ... ok test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62) Test localds with blosum62. ... ok test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result) Return no alignment. ... ok test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric) Test if alignment is independent on direction of sequence. ... ok test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms) Two different local alignments. ... ok test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1) Test localxx. ... ok test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2) Test localxx with ``full_sequences=True``. ... ok test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic) Test the generic method with local alignments. ... ok test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1) Test 1. ... ok test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2) Test 2. ... ok test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3) Test 3. ... ok test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1) Test sequence with only one match. ... ok test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2) Test sequences with two possible match positions. ... ok test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3) Like test 1, but global alignment. ... ok test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1) Test 1. ... ok test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2) Test 2. ... ok test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3) Test 3. ... ok test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4) Test 4. ... ok test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) Turn off end-gap penalties. ... ok test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2) Do the same, but use the generic method (with the same result). ... ok test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps) Test alignment where end-gaps are differently penalized. ... ok test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) Add gap-extend penalty to gap-opening penalty. ... ok test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) Test 1. ... ok test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) Test 2. ... ok test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) Test separate gap-extension penalties and list input. ... ok test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1) Open a gap in second sequence only. ... ok test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2) Force a bad alignment. ... ok test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global) Test ``score_only`` in a global alignment. ... ok test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local) Test ``score_only`` in a local alignment. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.120 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` C + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise_alignment_map.py test_pairwise_alignment_map ... ok test1 (test_pairwise_alignment_map.TestComplex.test1) ... ok test2 (test_pairwise_alignment_map.TestComplex.test2) ... ok test_internal (test_pairwise_alignment_map.TestSimple.test_internal) ... ok test_left_overhang (test_pairwise_alignment_map.TestSimple.test_left_overhang) ... ok test_reverse_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_sequence) ... ok test_reverse_transcript (test_pairwise_alignment_map.TestSimple.test_reverse_transcript) ... ok test_reverse_transcript_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_transcript_sequence) ... ok test_right_overhang (test_pairwise_alignment_map.TestSimple.test_right_overhang) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.083 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_phenotype.py test_phenotype ... ok test_PlateRecord (test_phenotype.TestPhenoMicro.test_PlateRecord) Test basic functionalities of PlateRecord objects. ... ok test_PlateRecord_errors (test_phenotype.TestPhenoMicro.test_PlateRecord_errors) Test bad arguments with PlateRecord objects. ... ok test_WellRecord (test_phenotype.TestPhenoMicro.test_WellRecord) Test basic functionalities of WellRecord objects. ... ok test_bad_fit_args (test_phenotype.TestPhenoMicro.test_bad_fit_args) Test error handling of the fit method. ... ok test_phenotype_IO (test_phenotype.TestPhenoMicro.test_phenotype_IO) Test basic functionalities of phenotype IO methods. ... ok test_phenotype_IO_errors (test_phenotype.TestPhenoMicro.test_phenotype_IO_errors) Test bad arguments to phenotype IO methods. ... ok ---------------------------------------------------------------------- Ran 1 test in 9.178 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.018 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_phyml_tool.py test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.098 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_prodoc.py test_prodoc ... ok test_parse_pdoc (test_prodoc.TestProdocParse.test_parse_pdoc) Parsing an excerpt of prosite.doc. ... ok test_read_pdoc00100 (test_prodoc.TestProdocRead.test_read_pdoc00100) Reading Prodoc record PDOC00100. ... ok test_read_pdoc00113 (test_prodoc.TestProdocRead.test_read_pdoc00113) Reading Prodoc record PDOC00113. ... ok test_read_pdoc00144 (test_prodoc.TestProdocRead.test_read_pdoc00144) Reading Prodoc record PDOC00144. ... ok test_read_pdoc00149 (test_prodoc.TestProdocRead.test_read_pdoc00149) Reading Prodoc record PDOC00149. ... ok test_read_pdoc00340 (test_prodoc.TestProdocRead.test_read_pdoc00340) Reading Prodoc record PDOC00340. ... ok test_read_pdoc00424 (test_prodoc.TestProdocRead.test_read_pdoc00424) Reading Prodoc record PDOC00424. ... ok test_read_pdoc00472 (test_prodoc.TestProdocRead.test_read_pdoc00472) Reading Prodoc record PDOC00472. ... ok test_read_pdoc00640 (test_prodoc.TestProdocRead.test_read_pdoc00640) Reading Prodoc record PDOC00640. ... ok test_read_pdoc00787 (test_prodoc.TestProdocRead.test_read_pdoc00787) Reading Prodoc record PDOC00787. ... ok test_read_pdoc0933 (test_prodoc.TestProdocRead.test_read_pdoc0933) Reading Prodoc record PDOC00933. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.024 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_prosite.py test_prosite ... ok test_read1 (test_prosite.TestPrositeRead.test_read1) Parsing Prosite record ps00107.txt. ... ok test_read2 (test_prosite.TestPrositeRead.test_read2) Parsing Prosite record ps00159.txt. ... ok test_read3 (test_prosite.TestPrositeRead.test_read3) Parsing Prosite record ps00165.txt. ... ok test_read4 (test_prosite.TestPrositeRead.test_read4) Parsing Prosite record ps00432.txt. ... ok test_read5 (test_prosite.TestPrositeRead.test_read5) Parsing Prosite record ps00488.txt. ... ok test_read6 (test_prosite.TestPrositeRead.test_read6) Parsing Prosite record ps00546.txt. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.102 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_psw.py test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise. ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_raxml_tool.py test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.094 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 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 0.016 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_seq.py test_seq ... ok test_ambiguous_values (test_seq.TestAmbiguousComplements.test_ambiguous_values) Test that other tests do not introduce characters to our values. ... ok test_mutable_seq (test_seq.TestAttributes.test_mutable_seq) ... ok test_seq (test_seq.TestAttributes.test_seq) ... ok test_complement_ambiguous_dna_values (test_seq.TestComplement.test_complement_ambiguous_dna_values) ... ok test_complement_ambiguous_rna_values (test_seq.TestComplement.test_complement_ambiguous_rna_values) ... ok test_complement_incompatible_letters (test_seq.TestComplement.test_complement_incompatible_letters) ... ok test_complement_of_dna (test_seq.TestComplement.test_complement_of_dna) ... ok test_complement_of_mixed_dna_rna (test_seq.TestComplement.test_complement_of_mixed_dna_rna) ... ok test_complement_of_rna (test_seq.TestComplement.test_complement_of_rna) ... ok test_reverse_complements (test_seq.TestDoubleReverseComplement.test_reverse_complements) Test double reverse complement preserves the sequence. ... ok test_add_method (test_seq.TestMutableSeq.test_add_method) Test adding wrong type to MutableSeq. ... ok test_appending (test_seq.TestMutableSeq.test_appending) ... ok test_as_string (test_seq.TestMutableSeq.test_as_string) ... ok test_complement (test_seq.TestMutableSeq.test_complement) ... ok test_complement_dna_string (test_seq.TestMutableSeq.test_complement_dna_string) ... ok test_complement_mixed_aphabets (test_seq.TestMutableSeq.test_complement_mixed_aphabets) ... ok test_complement_rna (test_seq.TestMutableSeq.test_complement_rna) ... ok test_complement_rna_string (test_seq.TestMutableSeq.test_complement_rna_string) ... ok test_contains_method (test_seq.TestMutableSeq.test_contains_method) ... ok test_converting_to_immutable (test_seq.TestMutableSeq.test_converting_to_immutable) ... ok test_count (test_seq.TestMutableSeq.test_count) ... ok test_delete_stride_slice (test_seq.TestMutableSeq.test_delete_stride_slice) ... ok test_deleting_item (test_seq.TestMutableSeq.test_deleting_item) ... ok test_deleting_slice (test_seq.TestMutableSeq.test_deleting_slice) ... ok test_endswith (test_seq.TestMutableSeq.test_endswith) ... ok test_equal_comparison (test_seq.TestMutableSeq.test_equal_comparison) Test __eq__ comparison method. ... ok test_extend_method (test_seq.TestMutableSeq.test_extend_method) ... ok test_extend_with_mutable_seq (test_seq.TestMutableSeq.test_extend_with_mutable_seq) ... ok test_extract_third_nucleotide (test_seq.TestMutableSeq.test_extract_third_nucleotide) Test extracting every third nucleotide (slicing with stride 3). ... ok test_first_nucleotide (test_seq.TestMutableSeq.test_first_nucleotide) ... ok test_greater_than_comparison (test_seq.TestMutableSeq.test_greater_than_comparison) Test __gt__ comparison method. ... ok test_greater_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_comparison_of_incompatible_types) ... ok test_greater_than_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_comparison_with_str) ... ok test_greater_than_or_equal_comparison (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison) Test __ge__ comparison method. ... ok test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_of_incompatible_types) ... ok test_greater_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_with_str) ... ok test_index (test_seq.TestMutableSeq.test_index) ... ok test_inserting (test_seq.TestMutableSeq.test_inserting) ... ok test_length (test_seq.TestMutableSeq.test_length) ... ok test_less_than_comparison (test_seq.TestMutableSeq.test_less_than_comparison) Test __lt__ comparison method. ... ok test_less_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_comparison_of_incompatible_types) ... ok test_less_than_comparison_with_str (test_seq.TestMutableSeq.test_less_than_comparison_with_str) ... ok test_less_than_or_equal_comparison (test_seq.TestMutableSeq.test_less_than_or_equal_comparison) Test __le__ comparison method. ... ok test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_of_incompatible_types) ... ok test_less_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_with_str) ... ok test_mutableseq_construction (test_seq.TestMutableSeq.test_mutableseq_construction) Test MutableSeq object initialization. ... ok test_not_equal_comparison (test_seq.TestMutableSeq.test_not_equal_comparison) Test __ne__ comparison method. ... ok test_popping_last_item (test_seq.TestMutableSeq.test_popping_last_item) ... ok test_radd_method_wrong_type (test_seq.TestMutableSeq.test_radd_method_wrong_type) ... ok test_remove_items (test_seq.TestMutableSeq.test_remove_items) ... ok test_repr (test_seq.TestMutableSeq.test_repr) ... ok test_reverse (test_seq.TestMutableSeq.test_reverse) Test using reverse method. ... ok test_reverse_complement (test_seq.TestMutableSeq.test_reverse_complement) ... ok test_reverse_complement_rna (test_seq.TestMutableSeq.test_reverse_complement_rna) ... ok test_reverse_with_stride (test_seq.TestMutableSeq.test_reverse_with_stride) Test reverse using -1 stride. ... ok test_set_wobble_codon_to_n (test_seq.TestMutableSeq.test_set_wobble_codon_to_n) Test setting wobble codon to N (set slice with stride 3). ... ok test_setting_item (test_seq.TestMutableSeq.test_setting_item) ... ok test_setting_slices (test_seq.TestMutableSeq.test_setting_slices) ... ok test_startswith (test_seq.TestMutableSeq.test_startswith) ... ok test_transcribe (test_seq.TestMutableSeq.test_transcribe) ... ok test_truncated_repr (test_seq.TestMutableSeq.test_truncated_repr) ... ok test_reverse_complement (test_seq.TestReverseComplement.test_reverse_complement) ... ok test_reverse_complement_of_dna (test_seq.TestReverseComplement.test_reverse_complement_of_dna) ... ok test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement.test_reverse_complement_of_mixed_dna_rna) ... ok test_reverse_complement_of_rna (test_seq.TestReverseComplement.test_reverse_complement_of_rna) ... ok test_as_string (test_seq.TestSeq.test_as_string) Test converting Seq to string. ... ok test_concatenation_of_seq (test_seq.TestSeq.test_concatenation_of_seq) ... ok test_extract_third_nucleotide (test_seq.TestSeq.test_extract_third_nucleotide) Test extracting every third nucleotide (slicing with stride 3). ... ok test_first_nucleotide (test_seq.TestSeq.test_first_nucleotide) Test getting first nucleotide of Seq. ... ok test_last_nucleotide (test_seq.TestSeq.test_last_nucleotide) Test getting last nucleotide of Seq. ... ok test_length (test_seq.TestSeq.test_length) Test len method on Seq object. ... ok test_replace (test_seq.TestSeq.test_replace) ... ok test_repr (test_seq.TestSeq.test_repr) Test representation of Seq object. ... ok test_reverse (test_seq.TestSeq.test_reverse) Test reverse using -1 stride. ... ok test_seq_construction (test_seq.TestSeq.test_seq_construction) Test Seq object initialization. ... ok test_slicing (test_seq.TestSeq.test_slicing) Test slicing of Seq. ... ok test_truncated_repr (test_seq.TestSeq.test_truncated_repr) ... ok test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides) ... ok test_adding_generic_nucleotide_with_other_nucleotides_inplace (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides_inplace) ... ok test_adding_protein_with_nucleotides (test_seq.TestSeqAddition.test_adding_protein_with_nucleotides) ... ok test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides) ... ok test_addition_dna_rna_with_generic_nucleotides_inplace (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides_inplace) ... ok test_addition_dna_with_dna (test_seq.TestSeqAddition.test_addition_dna_with_dna) ... ok test_addition_dna_with_dna_inplace (test_seq.TestSeqAddition.test_addition_dna_with_dna_inplace) ... ok test_addition_dna_with_rna (test_seq.TestSeqAddition.test_addition_dna_with_rna) ... ok test_addition_proteins (test_seq.TestSeqAddition.test_addition_proteins) ... ok test_addition_proteins_inplace (test_seq.TestSeqAddition.test_addition_proteins_inplace) ... ok test_addition_rna_with_rna (test_seq.TestSeqAddition.test_addition_rna_with_rna) ... ok test_addition_rna_with_rna_inplace (test_seq.TestSeqAddition.test_addition_rna_with_rna_inplace) ... ok test_imul_method (test_seq.TestSeqMultiplication.test_imul_method) Test imul method; relies on addition and mull methods. ... ok test_imul_method_exceptions (test_seq.TestSeqMultiplication.test_imul_method_exceptions) Test imul method exceptions. ... ok test_mul_method (test_seq.TestSeqMultiplication.test_mul_method) Test mul method; relies on addition method. ... ok test_mul_method_exceptions (test_seq.TestSeqMultiplication.test_mul_method_exceptions) Test mul method exceptions. ... ok test_rmul_method (test_seq.TestSeqMultiplication.test_rmul_method) Test rmul method; relies on addition method. ... ok test_rmul_method_exceptions (test_seq.TestSeqMultiplication.test_rmul_method_exceptions) Test rmul method exceptions. ... ok test_add_method_using_wrong_object (test_seq.TestSeqStringMethods.test_add_method_using_wrong_object) ... ok test_append_nucleotides (test_seq.TestSeqStringMethods.test_append_nucleotides) ... ok test_append_proteins (test_seq.TestSeqStringMethods.test_append_proteins) ... ok test_contains_method (test_seq.TestSeqStringMethods.test_contains_method) ... ok test_counting_characters (test_seq.TestSeqStringMethods.test_counting_characters) ... ok test_endswith (test_seq.TestSeqStringMethods.test_endswith) ... ok test_finding_characters (test_seq.TestSeqStringMethods.test_finding_characters) ... ok test_greater_than_comparison (test_seq.TestSeqStringMethods.test_greater_than_comparison) Test __gt__ comparison method. ... ok test_greater_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_comparison_of_incompatible_types) Test incompatible types __gt__ comparison method. ... ok test_greater_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison) Test __ge__ comparison method. ... ok test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison_of_incompatible_types) Test incompatible types __ge__ comparison method. ... ok test_hash (test_seq.TestSeqStringMethods.test_hash) ... ok test_less_than_comparison (test_seq.TestSeqStringMethods.test_less_than_comparison) Test __lt__ comparison method. ... ok test_less_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_comparison_of_incompatible_types) Test incompatible types __lt__ comparison method. ... ok test_less_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison) Test __le__ comparison method. ... ok test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison_of_incompatible_types) Test incompatible types __le__ comparison method. ... ok test_mutableseq_upper_lower (test_seq.TestSeqStringMethods.test_mutableseq_upper_lower) ... ok test_not_equal_comparsion (test_seq.TestSeqStringMethods.test_not_equal_comparsion) Test __ne__ comparison method. ... ok test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods.test_radd_method_using_wrong_object) ... ok test_splits (test_seq.TestSeqStringMethods.test_splits) ... ok test_startswith (test_seq.TestSeqStringMethods.test_startswith) ... ok test_string_methods (test_seq.TestSeqStringMethods.test_string_methods) ... ok test_stripping_characters (test_seq.TestSeqStringMethods.test_stripping_characters) ... ok test_stops (test_seq.TestStopCodons.test_stops) ... ok test_translation_of_stops (test_seq.TestStopCodons.test_translation_of_stops) ... ok test_back_transcribe_rna_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_into_dna) ... ok test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_string_into_dna) ... ok test_seq_object_back_transcription_method (test_seq.TestTranscription.test_seq_object_back_transcription_method) ... ok test_seq_object_transcription_method (test_seq.TestTranscription.test_seq_object_transcription_method) ... ok test_transcription_dna_into_rna (test_seq.TestTranscription.test_transcription_dna_into_rna) ... ok test_transcription_dna_string_into_rna (test_seq.TestTranscription.test_transcription_dna_string_into_rna) ... ok test_gapped_seq_no_gap_char_given (test_seq.TestTranslating.test_gapped_seq_no_gap_char_given) ... ok test_gapped_seq_with_gap_char_given (test_seq.TestTranslating.test_gapped_seq_with_gap_char_given) ... ok test_translation (test_seq.TestTranslating.test_translation) ... ok test_translation_extra_stop_codon (test_seq.TestTranslating.test_translation_extra_stop_codon) ... ok test_translation_incomplete_codon (test_seq.TestTranslating.test_translation_incomplete_codon) ... ok test_translation_of_asparagine (test_seq.TestTranslating.test_translation_of_asparagine) ... ok test_translation_of_gapped_string_no_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_no_gap_char_given) ... ok test_translation_of_gapped_string_with_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_with_gap_char_given) ... ok test_translation_of_glutamine (test_seq.TestTranslating.test_translation_of_glutamine) ... ok test_translation_of_invalid_codon (test_seq.TestTranslating.test_translation_of_invalid_codon) ... ok test_translation_of_leucine (test_seq.TestTranslating.test_translation_of_leucine) ... ok test_translation_of_string (test_seq.TestTranslating.test_translation_of_string) ... ok test_translation_on_proteins (test_seq.TestTranslating.test_translation_on_proteins) Check translation fails on a protein. ... ok test_translation_to_stop (test_seq.TestTranslating.test_translation_to_stop) ... ok test_translation_using_cds (test_seq.TestTranslating.test_translation_using_cds) ... ok test_translation_using_tables_with_ambiguous_stop_codons (test_seq.TestTranslating.test_translation_using_tables_with_ambiguous_stop_codons) Check for error and warning messages. ... ok test_translation_with_bad_table_argument (test_seq.TestTranslating.test_translation_with_bad_table_argument) ... ok test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating.test_translation_with_codon_table_as_table_argument) ... ok test_translation_wrong_type (test_seq.TestTranslating.test_translation_wrong_type) Test translation table cannot be CodonTable. ... ok test_add_method (test_seq.TestUnknownSeq.test_add_method) ... ok test_back_transcribe (test_seq.TestUnknownSeq.test_back_transcribe) ... ok test_complement (test_seq.TestUnknownSeq.test_complement) ... ok test_count (test_seq.TestUnknownSeq.test_count) ... ok test_getitem_method (test_seq.TestUnknownSeq.test_getitem_method) ... ok test_length (test_seq.TestUnknownSeq.test_length) ... ok test_lower (test_seq.TestUnknownSeq.test_lower) ... ok test_repr (test_seq.TestUnknownSeq.test_repr) ... ok test_reverse_complement (test_seq.TestUnknownSeq.test_reverse_complement) ... ok test_transcribe (test_seq.TestUnknownSeq.test_transcribe) ... ok test_translation (test_seq.TestUnknownSeq.test_translation) ... ok test_ungap (test_seq.TestUnknownSeq.test_ungap) ... ok test_unknownseq_construction (test_seq.TestUnknownSeq.test_unknownseq_construction) ... ok test_upper (test_seq.TestUnknownSeq.test_upper) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_translate.py test_translate ... ok test_ambiguous (test_translate.TestTranscriptionTranslation.test_ambiguous) ... ok test_dna_rna_translation (test_translate.TestTranscriptionTranslation.test_dna_rna_translation) ... ok test_transcription (test_translate.TestTranscriptionTranslation.test_transcription) ... ok test_translation (test_translate.TestTranscriptionTranslation.test_translation) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.055 seconds Skipping any tests requiring internet access Python version: 3.11.0rc1 (main, Aug 8 2022, 00:00:00) [GCC 12.1.1 20220628 (Red Hat 12.1.1-3)] Operating system: posix linux ~/build/BUILD/python-biopython-1.79 + popd + RPM_EC=0 ++ jobs -p Processing files: python3-biopython-1.79-4.fc38.x86_64 + exit 0 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.kwz0Bj + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.79 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/doc/python3-biopython + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr python3/Scripts /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr python3/CONTRIB.rst /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr python3/DEPRECATED.rst /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr python3/NEWS.rst /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr python3/README.rst /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/doc/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.HvAlm1 + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.79 + LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/licenses/python3-biopython + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/licenses/python3-biopython + cp -pr python3/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/licenses/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-biopython = 1.79-4.fc38 python3-biopython = 1.79-4.fc38 python3-biopython(x86-64) = 1.79-4.fc38 python3.11-biopython = 1.79-4.fc38 python3.11dist(biopython) = 1.79 python3dist(biopython) = 1.79 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: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) python(abi) = 3.11 python3.11dist(numpy) rtld(GNU_HASH) Obsoletes: python-biopython < 1.79-4.fc38 Processing files: python-biopython-doc-1.79-4.fc38.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.zkgQOu + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.79 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/doc/python-biopython-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/doc/python-biopython-doc + cp -pr biopython-1.79/Doc /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/doc/python-biopython-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.3DlIDy + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.79 + LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/licenses/python-biopython-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/licenses/python-biopython-doc + cp -pr biopython-1.79/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64/usr/share/licenses/python-biopython-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-biopython-doc = 1.79-4.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-biopython-debugsource-1.79-4.fc38.x86_64 Provides: python-biopython-debugsource = 1.79-4.fc38 python-biopython-debugsource(x86-64) = 1.79-4.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-biopython-debuginfo-1.79-4.fc38.x86_64 Provides: debuginfo(build-id) = 212d694152e842e9367562d435e4b203a10b1e1e debuginfo(build-id) = 2a390a69a28cfa49a6da33de5d228b403786494b debuginfo(build-id) = 46b28c21678b3607ad6ca0d905552a42e15819e0 debuginfo(build-id) = 47b1f21c4784a3542f18f8be456a668d141dab2a debuginfo(build-id) = c90513527fa3566e70e77b040b81af665afd6451 debuginfo(build-id) = d7c708995e2302cca5f6d3983f14d6ad2b99b0ca debuginfo(build-id) = e363d6a70bd2b30ca4748e4724b7ec4056c4bf11 debuginfo(build-id) = f9a84783193a047a5a03800a1e2986b511d14d17 python-biopython-debuginfo = 1.79-4.fc38 python3-biopython-debuginfo = 1.79-4.fc38 python3-biopython-debuginfo(x86-64) = 1.79-4.fc38 python3.11-biopython-debuginfo = 1.79-4.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-biopython-debugsource(x86-64) = 1.79-4.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64 Wrote: /builddir/build/RPMS/python-biopython-doc-1.79-4.fc38.noarch.rpm Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.79-4.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.79-4.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/python3-biopython-1.79-4.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.nA0zee + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.79 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.79-4.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.4WVeyM + umask 022 + cd /builddir/build/BUILD + rm -rf python-biopython-1.79 python-biopython-1.79.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0