Mock Version: 5.5 Mock Version: 5.5 Mock Version: 5.5 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target loongarch64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/dist-an23-epao-build-516948-75299/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=86400uid=982gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.rm9wb0oy:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=TrueprintOutput=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.rm9wb0oy:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', '69ac3c6d3c40448e951d45d615f101de', '-D', '/var/lib/mock/dist-an23-epao-build-516948-75299/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.rm9wb0oy:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 --noclean --target loongarch64 --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: loongarch64 Building for target loongarch64 setting SOURCE_DATE_EPOCH=1772409600 Wrote: /builddir/build/SRPMS/python-biopython-1.86-1.an23.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target loongarch64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/dist-an23-epao-build-516948-75299/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=86400uid=982gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.rm9wb0oy:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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=TrueprintOutput=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.rm9wb0oy:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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', 'ee9b8dea14744c8180173c306cb66e4b', '-D', '/var/lib/mock/dist-an23-epao-build-516948-75299/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.rm9wb0oy:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 --noclean --target loongarch64 --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: loongarch64 Building for target loongarch64 setting SOURCE_DATE_EPOCH=1772409600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.TvB9mF + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf biopython-1.86 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.86.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd biopython-1.86 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/0001-backport-fix-cve-2025-68463.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + rm -rf biopython.egg-info + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.KH4LqP + 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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd biopython-1.86 + 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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 ' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP' running build running build_py creating build creating build/lib.linux-loongarch64-cpython-311 creating build/lib.linux-loongarch64-cpython-311/Bio copying Bio/Seq.py -> build/lib.linux-loongarch64-cpython-311/Bio copying Bio/File.py -> build/lib.linux-loongarch64-cpython-311/Bio copying Bio/bgzf.py -> build/lib.linux-loongarch64-cpython-311/Bio copying Bio/pairwise2.py -> build/lib.linux-loongarch64-cpython-311/Bio copying Bio/SeqRecord.py -> build/lib.linux-loongarch64-cpython-311/Bio copying Bio/SeqFeature.py -> build/lib.linux-loongarch64-cpython-311/Bio copying Bio/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio copying Bio/_utils.py -> build/lib.linux-loongarch64-cpython-311/Bio creating build/lib.linux-loongarch64-cpython-311/Bio/Affy copying Bio/Affy/CelFile.py -> build/lib.linux-loongarch64-cpython-311/Bio/Affy copying Bio/Affy/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Affy creating build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/fasta.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/chain.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/analysis.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/stockholm.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/nexus.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/a2m.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/psl.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/interfaces.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/clustal.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/bigpsl.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/bed.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/phylip.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/tabular.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/bigmaf.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/msf.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/maf.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/sam.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/mauve.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/exonerate.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/bigbed.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/emboss.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/hhr.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align creating build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices creating build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/AlignIO creating build/lib.linux-loongarch64-cpython-311/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Alphabet creating build/lib.linux-loongarch64-cpython-311/Bio/Blast copying Bio/Blast/_parser.py -> build/lib.linux-loongarch64-cpython-311/Bio/Blast copying Bio/Blast/NCBIXML.py -> build/lib.linux-loongarch64-cpython-311/Bio/Blast copying Bio/Blast/_writers.py -> build/lib.linux-loongarch64-cpython-311/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-loongarch64-cpython-311/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Blast creating build/lib.linux-loongarch64-cpython-311/Bio/CAPS copying Bio/CAPS/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/CAPS creating build/lib.linux-loongarch64-cpython-311/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Cluster creating build/lib.linux-loongarch64-cpython-311/Bio/codonalign copying Bio/codonalign/codonseq.py -> build/lib.linux-loongarch64-cpython-311/Bio/codonalign copying Bio/codonalign/codonalignment.py -> build/lib.linux-loongarch64-cpython-311/Bio/codonalign copying Bio/codonalign/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/codonalign creating build/lib.linux-loongarch64-cpython-311/Bio/Compass copying Bio/Compass/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Compass creating build/lib.linux-loongarch64-cpython-311/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-loongarch64-cpython-311/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-loongarch64-cpython-311/Bio/Data copying Bio/Data/PDBData.py -> build/lib.linux-loongarch64-cpython-311/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Data creating build/lib.linux-loongarch64-cpython-311/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-loongarch64-cpython-311/Bio/Emboss copying Bio/Emboss/Primer3.py -> build/lib.linux-loongarch64-cpython-311/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Emboss creating build/lib.linux-loongarch64-cpython-311/Bio/Entrez copying Bio/Entrez/Parser.py -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez copying Bio/Entrez/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez creating build/lib.linux-loongarch64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> build/lib.linux-loongarch64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> build/lib.linux-loongarch64-cpython-311/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-loongarch64-cpython-311/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-loongarch64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> build/lib.linux-loongarch64-cpython-311/Bio/ExPASy copying Bio/ExPASy/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/ExPASy creating build/lib.linux-loongarch64-cpython-311/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-loongarch64-cpython-311/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-loongarch64-cpython-311/Bio/GenBank copying Bio/GenBank/Scanner.py -> build/lib.linux-loongarch64-cpython-311/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/GenBank creating build/lib.linux-loongarch64-cpython-311/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-loongarch64-cpython-311/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Geo creating build/lib.linux-loongarch64-cpython-311/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics creating build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram creating build/lib.linux-loongarch64-cpython-311/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/HMM creating build/lib.linux-loongarch64-cpython-311/Bio/KEGG copying Bio/KEGG/REST.py -> build/lib.linux-loongarch64-cpython-311/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/KEGG creating build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Compound creating build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Enzyme creating build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Gene creating build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Map creating build/lib.linux-loongarch64-cpython-311/Bio/PDB creating build/lib.linux-loongarch64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB/mmtf creating build/lib.linux-loongarch64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-loongarch64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-loongarch64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/KEGG/KGML creating build/lib.linux-loongarch64-cpython-311/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Medline creating build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/pfm.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/mast.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/alignace.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/minimal.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/transfac.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/matrix.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/meme.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/thresholds.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/xms.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/clusterbuster.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/motifs/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs creating build/lib.linux-loongarch64-cpython-311/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/motifs/jaspar creating build/lib.linux-loongarch64-cpython-311/Bio/Nexus copying Bio/Nexus/Nodes.py -> build/lib.linux-loongarch64-cpython-311/Bio/Nexus copying Bio/Nexus/Nexus.py -> build/lib.linux-loongarch64-cpython-311/Bio/Nexus copying Bio/Nexus/Trees.py -> build/lib.linux-loongarch64-cpython-311/Bio/Nexus copying Bio/Nexus/StandardData.py -> build/lib.linux-loongarch64-cpython-311/Bio/Nexus copying Bio/Nexus/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Nexus creating build/lib.linux-loongarch64-cpython-311/Bio/NMR copying Bio/NMR/NOEtools.py -> build/lib.linux-loongarch64-cpython-311/Bio/NMR copying Bio/NMR/xpktools.py -> build/lib.linux-loongarch64-cpython-311/Bio/NMR copying Bio/NMR/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/NMR creating build/lib.linux-loongarch64-cpython-311/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Pathway creating build/lib.linux-loongarch64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-loongarch64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-loongarch64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Pathway/Rep copying Bio/PDB/FragmentMapper.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/StructureAlignment.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/ic_rebuild.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/MMCIFParser.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/Dice.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/PDBMLParser.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/SCADIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/cealign.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/PSEA.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/HSExposure.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/ResidueDepth.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/Superimposer.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/ic_data.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/alphafold_db.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/binary_cif.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/mmcifio.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/internal_coords.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/DSSP.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/PDBList.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/NACCESS.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/PICIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/vectors.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/SASA.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/qcprot.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-loongarch64-cpython-311/Bio/PDB creating build/lib.linux-loongarch64-cpython-311/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> build/lib.linux-loongarch64-cpython-311/Bio/phenotype copying Bio/phenotype/phen_micro.py -> build/lib.linux-loongarch64-cpython-311/Bio/phenotype copying Bio/phenotype/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/phenotype creating build/lib.linux-loongarch64-cpython-311/Bio/PopGen copying Bio/PopGen/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/PopGen creating build/lib.linux-loongarch64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-loongarch64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-loongarch64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/PopGen/GenePop creating build/lib.linux-loongarch64-cpython-311/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-loongarch64-cpython-311/Bio/Restriction copying Bio/Restriction/Restriction.py -> build/lib.linux-loongarch64-cpython-311/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> build/lib.linux-loongarch64-cpython-311/Bio/Restriction copying Bio/Restriction/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Restriction creating build/lib.linux-loongarch64-cpython-311/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-loongarch64-cpython-311/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-loongarch64-cpython-311/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-loongarch64-cpython-311/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-loongarch64-cpython-311/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-loongarch64-cpython-311/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-loongarch64-cpython-311/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SCOP creating build/lib.linux-loongarch64-cpython-311/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO copying Bio/SearchIO/_index.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO copying Bio/SearchIO/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO copying Bio/SearchIO/_utils.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO creating build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model creating build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/BlastIO creating build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HHsuiteIO creating build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO creating build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InfernalIO copying Bio/SearchIO/InfernalIO/infernal_text.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InfernalIO copying Bio/SearchIO/InfernalIO/infernal_tab.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InfernalIO copying Bio/SearchIO/InfernalIO/_base.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InfernalIO copying Bio/SearchIO/InfernalIO/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InfernalIO creating build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO creating build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InterproscanIO creating build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/_index.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/GfaIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO creating build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils creating build/lib.linux-loongarch64-cpython-311/Bio/Sequencing copying Bio/Sequencing/Ace.py -> build/lib.linux-loongarch64-cpython-311/Bio/Sequencing copying Bio/Sequencing/Phd.py -> build/lib.linux-loongarch64-cpython-311/Bio/Sequencing copying Bio/Sequencing/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Sequencing creating build/lib.linux-loongarch64-cpython-311/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SVDSuperimposer creating build/lib.linux-loongarch64-cpython-311/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-loongarch64-cpython-311/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/SwissProt creating build/lib.linux-loongarch64-cpython-311/Bio/TogoWS copying Bio/TogoWS/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/TogoWS creating build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/NexusIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/_io.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/CDAO.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/NeXML.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/NewickIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/BaseTree.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/Consensus.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/Newick.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo copying Bio/Phylo/_utils.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo creating build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML creating build/lib.linux-loongarch64-cpython-311/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/UniGene creating build/lib.linux-loongarch64-cpython-311/Bio/UniProt copying Bio/UniProt/GOA.py -> build/lib.linux-loongarch64-cpython-311/Bio/UniProt copying Bio/UniProt/__init__.py -> build/lib.linux-loongarch64-cpython-311/Bio/UniProt creating build/lib.linux-loongarch64-cpython-311/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-loongarch64-cpython-311/BioSQL copying BioSQL/Loader.py -> build/lib.linux-loongarch64-cpython-311/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-loongarch64-cpython-311/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-loongarch64-cpython-311/BioSQL copying BioSQL/__init__.py -> build/lib.linux-loongarch64-cpython-311/BioSQL running egg_info creating biopython.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 writing manifest file 'biopython.egg-info/SOURCES.txt' reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Doc/_build/' 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' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Align.substitution_matrices' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Align.substitution_matrices' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Align.substitution_matrices' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Align.substitution_matrices' to be distributed and are already explicitly excluding 'Bio.Align.substitution_matrices' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying Bio/cpairwise2module.c -> build/lib.linux-loongarch64-cpython-311/Bio copying Bio/py.typed -> build/lib.linux-loongarch64-cpython-311/Bio copying Bio/Align/_aligncore.c -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/_alignmentcounts.c -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/_codonaligner.c -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/_pairwisealigner.c -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/_pairwisealigner.h -> build/lib.linux-loongarch64-cpython-311/Bio/Align copying Bio/Align/substitution_matrices/_arraycore.c -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/_arraycore.h -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices creating build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> build/lib.linux-loongarch64-cpython-311/Bio/Cluster copying Bio/Cluster/cluster.h -> build/lib.linux-loongarch64-cpython-311/Bio/Cluster copying Bio/Cluster/clustermodule.c -> build/lib.linux-loongarch64-cpython-311/Bio/Cluster creating build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/epost.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_clinvar.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_gene.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs creating build/lib.linux-loongarch64-cpython-311/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd -> build/lib.linux-loongarch64-cpython-311/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> build/lib.linux-loongarch64-cpython-311/Bio/motifs copying Bio/Nexus/cnexus.c -> build/lib.linux-loongarch64-cpython-311/Bio/Nexus copying Bio/PDB/bcifhelpermodule.c -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/ccealignmodule.c -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/PDB/kdtrees.c -> build/lib.linux-loongarch64-cpython-311/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-loongarch64-cpython-311/Bio/SeqIO copying BioSQL/py.typed -> build/lib.linux-loongarch64-cpython-311/BioSQL running build_ext building 'Bio.Align._aligncore' extension creating build/temp.linux-loongarch64-cpython-311 creating build/temp.linux-loongarch64-cpython-311/Bio creating build/temp.linux-loongarch64-cpython-311/Bio/Align gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Align/_aligncore.c -o build/temp.linux-loongarch64-cpython-311/Bio/Align/_aligncore.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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/Align/_aligncore.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/Align/_aligncore.cpython-311-loongarch64-linux-gnu.so building 'Bio.Align._alignmentcounts' extension gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Align/_alignmentcounts.c -o build/temp.linux-loongarch64-cpython-311/Bio/Align/_alignmentcounts.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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/Align/_alignmentcounts.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/Align/_alignmentcounts.cpython-311-loongarch64-linux-gnu.so building 'Bio.Align._codonaligner' extension gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Align/_codonaligner.c -o build/temp.linux-loongarch64-cpython-311/Bio/Align/_codonaligner.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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/Align/_codonaligner.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/Align/_codonaligner.cpython-311-loongarch64-linux-gnu.so building 'Bio.Align._pairwisealigner' extension gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Align/_pairwisealigner.c -o build/temp.linux-loongarch64-cpython-311/Bio/Align/_pairwisealigner.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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/Align/_pairwisealigner.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/Align/_pairwisealigner.cpython-311-loongarch64-linux-gnu.so building 'Bio.Align.substitution_matrices._arraycore' extension creating build/temp.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Align//substitution_matrices/_arraycore.c -o build/temp.linux-loongarch64-cpython-311/Bio/Align//substitution_matrices/_arraycore.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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/Align//substitution_matrices/_arraycore.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/_arraycore.cpython-311-loongarch64-linux-gnu.so building 'Bio.cpairwise2' extension gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/cpairwise2module.c -o build/temp.linux-loongarch64-cpython-311/Bio/cpairwise2module.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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/cpairwise2.cpython-311-loongarch64-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-loongarch64-cpython-311/Bio/Nexus gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Nexus/cnexus.c -o build/temp.linux-loongarch64-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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/Nexus/cnexus.cpython-311-loongarch64-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-loongarch64-cpython-311/Bio/motifs gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/motifs/_pwm.c -o build/temp.linux-loongarch64-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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/motifs/_pwm.cpython-311-loongarch64-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-loongarch64-cpython-311/Bio/Cluster gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Cluster/cluster.c -o build/temp.linux-loongarch64-cpython-311/Bio/Cluster/cluster.o -DCLUSTER_USE_PYTHON_MEMORY gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/Cluster/clustermodule.c -o build/temp.linux-loongarch64-cpython-311/Bio/Cluster/clustermodule.o -DCLUSTER_USE_PYTHON_MEMORY 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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/Cluster/cluster.o build/temp.linux-loongarch64-cpython-311/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/Cluster/_cluster.cpython-311-loongarch64-linux-gnu.so building 'Bio.PDB.ccealign' extension creating build/temp.linux-loongarch64-cpython-311/Bio/PDB gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-loongarch64-cpython-311/Bio/PDB/ccealignmodule.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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/PDB/ccealign.cpython-311-loongarch64-linux-gnu.so building 'Bio.PDB.kdtrees' extension gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/kdtrees.c -o build/temp.linux-loongarch64-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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/PDB/kdtrees.cpython-311-loongarch64-linux-gnu.so building 'Bio.PDB._bcif_helper' extension gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/bcifhelpermodule.c -o build/temp.linux-loongarch64-cpython-311/Bio/PDB/bcifhelpermodule.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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/PDB/bcifhelpermodule.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/PDB/_bcif_helper.cpython-311-loongarch64-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-loongarch64-cpython-311/Bio/SeqIO gcc -Wsign-compare -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.11 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-loongarch64-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/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 -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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-loongarch64-cpython-311/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-loongarch64-linux-gnu.so + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.L6wU5J + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64 ++ dirname /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64 + 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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd biopython-1.86 + 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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 ' + /usr/bin/python3 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64 --prefix /usr running install /usr/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running install_lib creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64 creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11 creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/GckIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/TwoBitIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/SnapGeneIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/_twoBitIO.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/XdnaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/GfaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/NibIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-loongarch64-cpython-311/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/NMR copying build/lib.linux-loongarch64-cpython-311/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/NMR copying build/lib.linux-loongarch64-cpython-311/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/NMR copying build/lib.linux-loongarch64-cpython-311/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/NMR creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Pathway creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-loongarch64-cpython-311/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-loongarch64-cpython-311/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-loongarch64-cpython-311/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-loongarch64-cpython-311/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Pathway copying build/lib.linux-loongarch64-cpython-311/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/_bcif_helper.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/ic_rebuild.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/PDBMLParser.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/SCADIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/cealign.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/bcifhelpermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/mmtf/mmtfio.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/ccealign.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/kdtrees.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/ccealignmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/ic_data.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/alphafold_db.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/binary_cif.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/internal_coords.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/PICIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/SASA.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/qcprot.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-loongarch64-cpython-311/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Medline copying build/lib.linux-loongarch64-cpython-311/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Medline creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InfernalIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InfernalIO/infernal_text.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InfernalIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InfernalIO/infernal_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InfernalIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InfernalIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InfernalIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/InfernalIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InfernalIO creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/HHsuiteIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO copying build/lib.linux-loongarch64-cpython-311/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/XSDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/XSDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/XSDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/XSDs creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/xhtml-table-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-list1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-references1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-display1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-funding1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/BITS-question-answer2.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-chars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-format1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-link1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-section1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-common1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-para1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/esummary_clinvar.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/elink.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-notat1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/epost.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/esummary_gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-math1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-loongarch64-cpython-311/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Compass copying build/lib.linux-loongarch64-cpython-311/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Compass copying build/lib.linux-loongarch64-cpython-311/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PopGen creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-loongarch64-cpython-311/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-loongarch64-cpython-311/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-loongarch64-cpython-311/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-loongarch64-cpython-311/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PopGen creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene copying build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme copying build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme copying build/lib.linux-loongarch64-cpython-311/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Map copying build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Map creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound copying build/lib.linux-loongarch64-cpython-311/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML copying build/lib.linux-loongarch64-cpython-311/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML copying build/lib.linux-loongarch64-cpython-311/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML copying build/lib.linux-loongarch64-cpython-311/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML copying build/lib.linux-loongarch64-cpython-311/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/UniGene copying build/lib.linux-loongarch64-cpython-311/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/UniGene copying build/lib.linux-loongarch64-cpython-311/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-loongarch64-cpython-311/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-loongarch64-cpython-311/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-loongarch64-cpython-311/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-loongarch64-cpython-311/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-loongarch64-cpython-311/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Emboss creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Affy copying build/lib.linux-loongarch64-cpython-311/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Affy copying build/lib.linux-loongarch64-cpython-311/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Affy creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-loongarch64-cpython-311/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-loongarch64-cpython-311/Bio/Nexus/cnexus.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-loongarch64-cpython-311/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-loongarch64-cpython-311/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-loongarch64-cpython-311/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-loongarch64-cpython-311/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-loongarch64-cpython-311/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-loongarch64-cpython-311/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/TogoWS copying build/lib.linux-loongarch64-cpython-311/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/TogoWS creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-loongarch64-cpython-311/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-loongarch64-cpython-311/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-loongarch64-cpython-311/Bio/Data/PDBData.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-loongarch64-cpython-311/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Data creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-loongarch64-cpython-311/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-loongarch64-cpython-311/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-loongarch64-cpython-311/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-loongarch64-cpython-311/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-loongarch64-cpython-311/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-loongarch64-cpython-311/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/phenotype copying build/lib.linux-loongarch64-cpython-311/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/phenotype copying build/lib.linux-loongarch64-cpython-311/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/phenotype copying build/lib.linux-loongarch64-cpython-311/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/phenotype creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-loongarch64-cpython-311/Bio/Blast/_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-loongarch64-cpython-311/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-loongarch64-cpython-311/Bio/Blast/_writers.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-loongarch64-cpython-311/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-loongarch64-cpython-311/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Geo copying build/lib.linux-loongarch64-cpython-311/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Geo copying build/lib.linux-loongarch64-cpython-311/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Geo creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/CAPS copying build/lib.linux-loongarch64-cpython-311/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/CAPS creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-loongarch64-cpython-311/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-loongarch64-cpython-311/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-loongarch64-cpython-311/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-loongarch64-cpython-311/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Restriction creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/codonalign copying build/lib.linux-loongarch64-cpython-311/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/codonalign copying build/lib.linux-loongarch64-cpython-311/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/codonalign copying build/lib.linux-loongarch64-cpython-311/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/codonalign creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/MsfIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-loongarch64-cpython-311/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-loongarch64-cpython-311/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-loongarch64-cpython-311/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-loongarch64-cpython-311/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-loongarch64-cpython-311/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/GenBank creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Alphabet copying build/lib.linux-loongarch64-cpython-311/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Alphabet creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-loongarch64-cpython-311/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-loongarch64-cpython-311/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-loongarch64-cpython-311/Bio/Cluster/_cluster.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-loongarch64-cpython-311/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-loongarch64-cpython-311/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Cluster creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Sequencing copying build/lib.linux-loongarch64-cpython-311/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Sequencing copying build/lib.linux-loongarch64-cpython-311/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Sequencing copying build/lib.linux-loongarch64-cpython-311/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Sequencing creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/_pwm.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/pfm.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/xms.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/clusterbuster.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-loongarch64-cpython-311/Bio/py.typed -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/UniProt copying build/lib.linux-loongarch64-cpython-311/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/UniProt copying build/lib.linux-loongarch64-cpython-311/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/UniProt creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer copying build/lib.linux-loongarch64-cpython-311/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-loongarch64-cpython-311/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-loongarch64-cpython-311/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-loongarch64-cpython-311/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-loongarch64-cpython-311/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-loongarch64-cpython-311/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-loongarch64-cpython-311/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-loongarch64-cpython-311/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-loongarch64-cpython-311/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-loongarch64-cpython-311/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-loongarch64-cpython-311/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SwissProt copying build/lib.linux-loongarch64-cpython-311/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SwissProt copying build/lib.linux-loongarch64-cpython-311/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SwissProt copying build/lib.linux-loongarch64-cpython-311/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-loongarch64-cpython-311/Bio/cpairwise2.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/fasta.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/chain.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/_aligncore.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/_pairwisealigner.h -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/analysis.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/stockholm.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/_alignmentcounts.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/a2m.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/psl.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/_aligncore.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/_codonaligner.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/_pairwisealigner.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/clustal.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/_arraycore.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/_arraycore.cpython-311-loongarch64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/_arraycore.h -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/JONES -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM45 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/MEGABLAST -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/BLASTN -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM62 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/LEVIN -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM50 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/NUC.4.4 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/PAM250 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/PAM30 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/JOHNSON -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/BENNER74 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/MDM78 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/BLASTP -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/SCHNEIDER -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM90 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/STR -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/BENNER22 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/GENETIC -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/TRANS -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM80 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/MCLACHLAN -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/PAM70 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/BENNER6 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/RISLER -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/HOXD70 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/DAYHOFF -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/GONNET1992 -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/RAO -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/data/FENG -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-loongarch64-cpython-311/Bio/Align/substitution_matrices/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices copying build/lib.linux-loongarch64-cpython-311/Bio/Align/bigpsl.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/bed.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/phylip.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/tabular.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/bigmaf.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/msf.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/_codonaligner.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/_pairwisealigner.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/maf.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/sam.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/_alignmentcounts.c -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/mauve.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/exonerate.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/bigbed.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/emboss.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/Align/hhr.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-loongarch64-cpython-311/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-loongarch64-cpython-311/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-loongarch64-cpython-311/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-loongarch64-cpython-311/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-loongarch64-cpython-311/BioSQL/py.typed -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-loongarch64-cpython-311/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-loongarch64-cpython-311/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-loongarch64-cpython-311/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/GckIO.py to GckIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/_index.py to _index.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/TwoBitIO.py to TwoBitIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SnapGeneIO.py to SnapGeneIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/XdnaIO.py to XdnaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/GfaIO.py to GfaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/NMR/NOEtools.py to NOEtools.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/NMR/xpktools.py to xpktools.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/NMR/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep/Graph.py to Graph.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep/MultiGraph.py to MultiGraph.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Pathway/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Seq.py to Seq.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/FragmentMapper.py to FragmentMapper.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/Atom.py to Atom.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/Structure.py to Structure.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/Model.py to Model.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/StructureAlignment.py to StructureAlignment.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBExceptions.py to PDBExceptions.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/ic_rebuild.py to ic_rebuild.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/StructureBuilder.py to StructureBuilder.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/MMCIFParser.py to MMCIFParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/NeighborSearch.py to NeighborSearch.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/Dice.py to Dice.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBMLParser.py to PDBMLParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/Entity.py to Entity.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/SCADIO.py to SCADIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/cealign.py to cealign.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/Residue.py to Residue.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/PSEA.py to PSEA.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/HSExposure.py to HSExposure.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf/mmtfio.py to mmtfio.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf/DefaultParser.py to DefaultParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/AbstractPropertyMap.py to AbstractPropertyMap.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/Chain.py to Chain.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBParser.py to PDBParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/MMCIF2Dict.py to MMCIF2Dict.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/ResidueDepth.py to ResidueDepth.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBIO.py to PDBIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/Superimposer.py to Superimposer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/ic_data.py to ic_data.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/Selection.py to Selection.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/alphafold_db.py to alphafold_db.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/binary_cif.py to binary_cif.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/mmcifio.py to mmcifio.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/internal_coords.py to internal_coords.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/DSSP.py to DSSP.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBList.py to PDBList.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/NACCESS.py to NACCESS.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/PICIO.py to PICIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/vectors.py to vectors.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/SASA.py to SASA.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/qcprot.py to qcprot.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PDB/Polypeptide.py to Polypeptide.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Medline/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/query.py to query.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/hit.py to hit.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/hsp.py to hsp.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/_base.py to _base.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_index.py to _index.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InfernalIO/infernal_text.py to infernal_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InfernalIO/infernal_tab.py to infernal_tab.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InfernalIO/_base.py to _base.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InfernalIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlatIO.py to BlatIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_utils.py to _utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/Parser.py to Parser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Entrez/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Compass/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/File.py to File.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/FileParser.py to FileParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/LargeFileParser.py to LargeFileParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/PopGen/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/REST.py to REST.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Map/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/KEGG/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/UniGene/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/HMM/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/bgzf.py to bgzf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Emboss/Primer3.py to Primer3.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Emboss/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Affy/CelFile.py to CelFile.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Affy/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/lcc.py to lcc.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus/Nodes.py to Nodes.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus/Nexus.py to Nexus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus/Trees.py to Trees.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus/StandardData.py to StandardData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Nexus/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/TogoWS/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Data/IUPACData.py to IUPACData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Data/CodonTable.py to CodonTable.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Data/PDBData.py to PDBData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Data/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy/Enzyme.py to Enzyme.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy/Prosite.py to Prosite.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy/cellosaurus.py to cellosaurus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy/Prodoc.py to Prodoc.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/ExPASy/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/phenotype/pm_fitting.py to pm_fitting.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/phenotype/phen_micro.py to phen_micro.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/phenotype/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast/_parser.py to _parser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast/NCBIXML.py to NCBIXML.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast/_writers.py to _writers.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast/NCBIWWW.py to NCBIWWW.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Blast/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Geo/Record.py to Record.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Geo/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/CAPS/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Restriction/Restriction_Dictionary.py to Restriction_Dictionary.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Restriction/Restriction.py to Restriction.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Restriction/PrintFormat.py to PrintFormat.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Restriction/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/codonalign/codonseq.py to codonseq.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/codonalign/codonalignment.py to codonalignment.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/codonalign/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/NexusIO.py to NexusIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/StockholmIO.py to StockholmIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/MauveIO.py to MauveIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/MsfIO.py to MsfIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/Interfaces.py to Interfaces.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/MafIO.py to MafIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/PhylipIO.py to PhylipIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/ClustalIO.py to ClustalIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/AlignIO/EmbossIO.py to EmbossIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/pairwise2.py to pairwise2.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/GenBank/utils.py to utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/GenBank/Record.py to Record.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/GenBank/Scanner.py to Scanner.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/GenBank/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Alphabet/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Cluster/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Ace.py to Ace.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Phd.py to Phd.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Sequencing/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/pfm.py to pfm.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/mast.py to mast.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/alignace.py to alignace.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/minimal.py to minimal.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar/db.py to db.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/transfac.py to transfac.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/matrix.py to matrix.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/meme.py to meme.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/thresholds.py to thresholds.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/xms.py to xms.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/clusterbuster.py to clusterbuster.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/motifs/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/UniProt/GOA.py to GOA.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/UniProt/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/Comparative.py to Comparative.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/Distribution.py to Distribution.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Graphics/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/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-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/_io.py to _io.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/CDAO.py to CDAO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/NeXML.py to NeXML.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/Consensus.py to Consensus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/Newick.py to Newick.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Phylo/_utils.py to _utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP/Raf.py to Raf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP/Hie.py to Hie.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP/Residues.py to Residues.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP/Cla.py to Cla.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP/Dom.py to Dom.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP/Des.py to Des.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SCOP/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqRecord.py to SeqRecord.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SwissProt/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/SeqFeature.py to SeqFeature.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/fasta.py to fasta.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/chain.py to chain.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/analysis.py to analysis.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/AlignInfo.py to AlignInfo.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/stockholm.py to stockholm.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/nexus.py to nexus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/a2m.py to a2m.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/psl.py to psl.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/interfaces.py to interfaces.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/clustal.py to clustal.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/bigpsl.py to bigpsl.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/bed.py to bed.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/phylip.py to phylip.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/tabular.py to tabular.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/bigmaf.py to bigmaf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/msf.py to msf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/maf.py to maf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/sam.py to sam.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/mauve.py to mauve.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/exonerate.py to exonerate.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/bigbed.py to bigbed.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/emboss.py to emboss.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/Align/hhr.py to hhr.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/Bio/_utils.py to _utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL/Loader.py to Loader.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL/DBUtils.py to DBUtils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL/BioSeq.py to BioSeq.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/BioSQL/__init__.py to __init__.cpython-311.pyc writing byte-compilation script '/tmp/tmpgf0qchlt.py' /usr/bin/python3 /tmp/tmpgf0qchlt.py removing /tmp/tmpgf0qchlt.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 'Doc/_build/' 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' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' Copying biopython.egg-info to /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11/site-packages/biopython-1.86-py3.11.egg-info running install_scripts + rm -rfv /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/bin/__pycache__ + /usr/bin/find-debuginfo -j32 --strict-build-id -m -i --build-id-seed 1.86-1.an23 --unique-debug-suffix -1.86-1.an23.loongarch64 --unique-debug-src-base python-biopython-1.86-1.an23.loongarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/biopython-1.86 find-debuginfo: starting Extracting debug info from 13 files DWARF-compressing 13 files sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/python-biopython-1.86-1.an23.loongarch64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/anolis/brp-ldconfig + COMPRESS='zstd -f --rm -19 -T0' + COMPRESS_EXT=.zst + /usr/lib/rpm/brp-compress + /usr/lib/rpm/anolis/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/anolis/clean_perl + /usr/lib/rpm/anolis/check_elf_files Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/cpairwise2.cpython-311-loongarch64-linux-gnu.so: PyExc_MemoryError PyExc_TypeError _Py_NoneStruct PyList_New PySequence_Check PyArg_ParseTupleAndKeywords PyObject_GetAttrString _Py_Dealloc PyErr_SetString PySequence_GetItem PyFloat_FromDouble PyLong_FromLong PySequence_Size PyErr_Clear Py_BuildValue PyErr_Occurred PyModule_Create2 PyObject_CallObject PyFloat_AsDouble PyArg_ParseTuple PyUnicode_AsASCIIString PyCallable_Check Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/SeqIO/_twoBitIO.cpython-311-loongarch64-linux-gnu.so: PyExc_RuntimeError PyMem_Free PyBuffer_Release PyBytes_FromStringAndSize _Py_Dealloc PyErr_SetString PyModule_Create2 _PyArg_ParseTupleAndKeywords_SizeT PyObject_GetBuffer PyErr_Format PyMem_Malloc Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/PDB/_bcif_helper.cpython-311-loongarch64-linux-gnu.so: PyExc_ValueError _Py_NoneStruct PyBuffer_Release PyErr_SetString PyModule_Create2 _PyArg_ParseTuple_SizeT PyObject_GetBuffer PyErr_Format Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/PDB/ccealign.cpython-311-loongarch64-linux-gnu.so: PyList_New PyMem_RawMalloc PyStructSequence_New _Py_Dealloc PyFloat_FromDouble PyLong_FromLong PyList_Append Py_BuildValue PyModule_Create2 PyMem_RawFree PyFloat_AsDouble PyArg_ParseTuple PyList_Size PyStructSequence_SetItem log10 sqrt PyStructSequence_NewType PyList_GetItem Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/PDB/kdtrees.cpython-311-loongarch64-linux-gnu.so: PyExc_RuntimeError PyExc_ValueError PyType_GenericNew PyUnicode_FromFormat PyList_New PyArg_ParseTupleAndKeywords PyMem_Free PyBuffer_Release _Py_Dealloc PyErr_NoMemory PyErr_SetString PyLong_FromSsize_t PyFloat_FromDouble PyType_Ready PyList_Append PyModule_Create2 PyArg_ParseTuple PyObject_GetBuffer PyModule_AddObject sqrt PyMem_Malloc Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/Nexus/cnexus.cpython-311-loongarch64-linux-gnu.so: PyMem_RawMalloc PyErr_NoMemory Py_BuildValue PyModule_Create2 PyMem_RawFree PyArg_ParseTuple Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/Cluster/_cluster.cpython-311-loongarch64-linux-gnu.so: PyExc_RuntimeError PyExc_ValueError PyExc_TypeError PyType_GenericNew PySlice_Type _Py_NoneStruct PyExc_IndexError PyList_Type PyList_New _PyUnicode_Ready PyArg_ParseTupleAndKeywords PyNumber_AsSsize_t PyMem_Free PyBuffer_Release _Py_Dealloc PyErr_NoMemory PyErr_SetString PyIndex_Check PyMem_Realloc PyFloat_FromDouble PyType_Ready PyLong_FromLong PySlice_AdjustIndices PyOS_double_to_string Py_BuildValue PyErr_Occurred PyModule_Create2 PyLong_AsLong exp PyFloat_AsDouble PyArg_ParseTuple PyObject_GetBuffer PyUnicode_FromString log PyModule_AddObject PySlice_Unpack sqrt PyType_IsSubtype PyErr_Format PyUnicode_Concat PyMem_Calloc PyMem_Malloc Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/motifs/_pwm.cpython-311-loongarch64-linux-gnu.so: PyExc_RuntimeError PyExc_ValueError _Py_NoneStruct PyBuffer_Release PyErr_SetString PyModule_Create2 _PyArg_ParseTupleAndKeywords_SizeT PyObject_GetBuffer PyErr_Format Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/Align/_alignmentcounts.cpython-311-loongarch64-linux-gnu.so: PyExc_RuntimeError PyExc_ValueError _Py_NoneStruct PyList_Type _PyUnicode_Ready PySequence_Check PyMem_Free PyBuffer_Release PyObject_GetAttrString _Py_Dealloc _PyObject_CallFunction_SizeT PyErr_SetString PyObject_IsInstance PySequence_GetSlice PyLong_FromSsize_t PyFloat_FromDouble PyType_Ready PyErr_Clear PyOS_double_to_string PyErr_Occurred PyModule_Create2 PyImport_ImportModule PyFloat_AsDouble PyType_GenericAlloc _PyArg_ParseTupleAndKeywords_SizeT PyObject_GetBuffer PyUnicode_FromString PyModule_AddObject PyType_IsSubtype PyErr_Format PyMem_Calloc Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/Align/_aligncore.cpython-311-loongarch64-linux-gnu.so: PyExc_RuntimeError PyExc_ValueError _Py_NoneStruct PyArg_ParseTupleAndKeywords PyMem_Free PyBuffer_Release PyBytes_FromStringAndSize _Py_Dealloc PyErr_SetString PyMem_Realloc PyType_Ready Py_BuildValue PyModule_Create2 PyArg_ParseTuple PyObject_GetBuffer PyModule_AddObject PyType_IsSubtype PyErr_Format PyMem_Calloc PyMem_Malloc Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/Align/_codonaligner.cpython-311-loongarch64-linux-gnu.so: PyExc_RuntimeError PyExc_ValueError PyExc_TypeError PyType_GenericNew PyExc_OverflowError _Py_NoneStruct PyObject_SelfIter PyUnicode_FromFormat _PyUnicode_Ready PyMem_Free PyBuffer_Release _Py_Dealloc PyErr_NoMemory PyErr_SetString PyFloat_FromDouble PyType_Ready PyLong_FromLong PyTuple_New PyErr_Occurred PyModule_Create2 PyFloat_AsDouble PyType_GenericAlloc _PyArg_ParseTupleAndKeywords_SizeT PyUnicode_FromString PyModule_AddObject PyErr_Format _Py_BuildValue_SizeT PyMem_Malloc Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/Align/_pairwisealigner.cpython-311-loongarch64-linux-gnu.so: PyExc_RuntimeError PyExc_MemoryError PyExc_UserWarning PyExc_ValueError PyExc_TypeError PyType_GenericNew PyExc_OverflowError _Py_NoneStruct PyObject_SelfIter PyUnicode_FromFormat _PyUnicode_Ready PyMem_Free PyBuffer_Release PyObject_GetAttrString PyErr_WarnEx _Py_Dealloc PyErr_NoMemory _PyObject_CallFunction_SizeT PyErr_SetString PyObject_IsInstance PyMem_Realloc PyErr_SetNone PyFloat_FromDouble PyType_Ready PyLong_FromLong PyOS_double_to_string PyTuple_New PyErr_Occurred PyModule_Create2 PyImport_ImportModule PyUnicode_CompareWithASCIIString PyFloat_AsDouble PyType_GenericAlloc _PyArg_ParseTupleAndKeywords_SizeT PyUnicode_FromKindAndData PyCallable_Check PyObject_GetBuffer PyUnicode_FromString PyModule_AddObject PyErr_Format _Py_BuildValue_SizeT PyMem_Calloc PyMem_Malloc PyErr_WriteUnraisable Warning: undefined symbols in /usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/_arraycore.cpython-311-loongarch64-linux-gnu.so: PyExc_RuntimeError PyExc_ValueError PyExc_TypeError _Py_NoneStruct PySequence_Check PyMem_Free PyBuffer_Release PyObject_GetAttrString _Py_Dealloc PyErr_SetString PyType_Ready PyBuffer_FillInfo PySequence_Size PyModule_AddObjectRef PyModule_Create2 PyImport_ImportModule PyUnicode_FromKindAndData PyObject_GetBuffer PyErr_Format PyMem_Malloc + /usr/lib/rpm/anolis/brp-mangle-shebangs + /usr/lib/rpm/anolis/remove-info-dir + /usr/lib/rpm/anolis/check-desktop-files + env -u SOURCE_DATE_EPOCH /usr/lib/rpm/anolis/brp-python-bytecompile '' 1 0 -j32 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib64/python3.11 using python3.11 Not clamping source mtimes, $SOURCE_DATE_EPOCH not set Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/lib/debug/usr/lib64/python3.11 using python3.11 Not clamping source mtimes, $SOURCE_DATE_EPOCH not set + /usr/lib/rpm/anolis/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.Hq04zr + 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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-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/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/anolis/anolis-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/anolis/anolis-hardened-ld -specs=/usr/lib/rpm/anolis/anolis-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd biopython-1.86 + /usr/bin/python3 setup.py test running test /builddir/build/BUILD/biopython-1.86/Bio/__init__.py:138: BiopythonWarning: You may be importing Biopython from inside the source tree. This is bad practice and might lead to downstream issues. In particular, you might encounter ImportErrors due to missing compiled C extensions. We recommend that you try running your code from outside the source tree. If you are outside the source tree then you have a setup.py file in an unexpected directory: /builddir/build/BUILD/biopython-1.86 warnings.warn( test_Ace ... ok test_Affy ... ok test_AlignIO ... loading tests failed: Failed to import test module: test_AlignIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_AlignIO.py", line 12, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_AlignIO_ClustalIO ... loading tests failed: Failed to import test module: test_AlignIO_ClustalIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_AlignIO_ClustalIO.py", line 9, in from Bio.AlignIO.ClustalIO import ClustalIterator File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_AlignIO_EmbossIO ... loading tests failed: Failed to import test module: test_AlignIO_EmbossIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_AlignIO_EmbossIO.py", line 10, in from Bio.AlignIO.EmbossIO import EmbossIterator File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_AlignIO_FastaIO ... loading tests failed: Failed to import test module: test_AlignIO_FastaIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_AlignIO_FastaIO.py", line 8, in from Bio.AlignIO import FastaIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_AlignIO_MauveIO ... loading tests failed: Failed to import test module: test_AlignIO_MauveIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_AlignIO_MauveIO.py", line 11, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_AlignIO_PhylipIO ... loading tests failed: Failed to import test module: test_AlignIO_PhylipIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_AlignIO_PhylipIO.py", line 10, in from Bio.AlignIO.PhylipIO import PhylipIterator File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_AlignIO_convert ... loading tests failed: Failed to import test module: test_AlignIO_convert Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_AlignIO_convert.py", line 9, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_Alignment ... loading tests failed: Failed to import test module: test_Align_Alignment Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_Alignment.py", line 21, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_a2m ... loading tests failed: Failed to import test module: test_Align_a2m Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_a2m.py", line 12, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_bed ... loading tests failed: Failed to import test module: test_Align_bed Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_bed.py", line 13, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_bigbed ... loading tests failed: Failed to import test module: test_Align_bigbed Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_bigbed.py", line 12, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_bigmaf ... loading tests failed: Failed to import test module: test_Align_bigmaf Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_bigmaf.py", line 12, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_bigpsl ... loading tests failed: Failed to import test module: test_Align_bigpsl Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_bigpsl.py", line 9, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_chain ... loading tests failed: Failed to import test module: test_Align_chain Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_chain.py", line 10, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_clustal ... loading tests failed: Failed to import test module: test_Align_clustal Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_clustal.py", line 12, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_codonalign ... loading tests failed: Failed to import test module: test_Align_codonalign Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_codonalign.py", line 20, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_emboss ... loading tests failed: Failed to import test module: test_Align_emboss Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_emboss.py", line 11, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_exonerate ... loading tests failed: Failed to import test module: test_Align_exonerate Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_exonerate.py", line 13, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_fasta ... loading tests failed: Failed to import test module: test_Align_fasta Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_fasta.py", line 12, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_format_matrix ... loading tests failed: Failed to import test module: test_Align_format_matrix Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_format_matrix.py", line 27, in from Bio.Align import PairwiseAligner File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_hhr ... loading tests failed: Failed to import test module: test_Align_hhr Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_hhr.py", line 12, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_maf ... loading tests failed: Failed to import test module: test_Align_maf Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_maf.py", line 10, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_mauve ... loading tests failed: Failed to import test module: test_Align_mauve Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_mauve.py", line 11, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_msf ... loading tests failed: Failed to import test module: test_Align_msf Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_msf.py", line 12, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_nexus ... loading tests failed: Failed to import test module: test_Align_nexus Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_nexus.py", line 11, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_phylip ... loading tests failed: Failed to import test module: test_Align_phylip Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_phylip.py", line 11, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_psl ... loading tests failed: Failed to import test module: test_Align_psl Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_psl.py", line 10, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_sam ... loading tests failed: Failed to import test module: test_Align_sam Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_sam.py", line 9, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_stockholm ... loading tests failed: Failed to import test module: test_Align_stockholm Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_stockholm.py", line 9, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Align_tabular ... loading tests failed: Failed to import test module: test_Align_tabular Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Align_tabular.py", line 11, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_BioSQL_MySQLdb ... loading tests failed: Failed to import test module: test_BioSQL_MySQLdb Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_BioSQL_MySQLdb.py", line 10, in from common_BioSQL import * # noqa: F403 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/common_BioSQL.py", line 18, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_BioSQL_MySQLdb_online ... loading tests failed: Failed to import test module: test_BioSQL_MySQLdb_online Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_BioSQL_MySQLdb_online.py", line 12, in from common_BioSQL import * # noqa: F403 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/common_BioSQL.py", line 18, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_BioSQL_mysql_connector ... loading tests failed: Failed to import test module: test_BioSQL_mysql_connector Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_BioSQL_mysql_connector.py", line 10, in from common_BioSQL import * # noqa: F403 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/common_BioSQL.py", line 18, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_BioSQL_mysql_connector_online ... loading tests failed: Failed to import test module: test_BioSQL_mysql_connector_online Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_BioSQL_mysql_connector_online.py", line 12, in from common_BioSQL import * # noqa: F403 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/common_BioSQL.py", line 18, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_BioSQL_psycopg2 ... loading tests failed: Failed to import test module: test_BioSQL_psycopg2 Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_BioSQL_psycopg2.py", line 10, in from common_BioSQL import * # noqa: F403 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/common_BioSQL.py", line 18, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_BioSQL_psycopg2_online ... loading tests failed: Failed to import test module: test_BioSQL_psycopg2_online Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_BioSQL_psycopg2_online.py", line 12, in from common_BioSQL import * # noqa: F403 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/common_BioSQL.py", line 18, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_BioSQL_sqlite3 ... loading tests failed: Failed to import test module: test_BioSQL_sqlite3 Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_BioSQL_sqlite3.py", line 11, in from common_BioSQL import * # noqa: F403 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/common_BioSQL.py", line 18, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_BioSQL_sqlite3_online ... loading tests failed: Failed to import test module: test_BioSQL_sqlite3_online Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_BioSQL_sqlite3_online.py", line 12, in from common_BioSQL import * # noqa: F403 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/common_BioSQL.py", line 18, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Blast_Record ... loading tests failed: Failed to import test module: test_Blast_Record Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Blast_Record.py", line 9, in from Bio.Blast.NCBIXML import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/Blast/__init__.py", line 44, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Blast_parser ... loading tests failed: Failed to import test module: test_Blast_parser Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Blast_parser.py", line 13, in from Bio import Blast File "/builddir/build/BUILD/biopython-1.86/Bio/Blast/__init__.py", line 44, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_CAPS ... loading tests failed: Failed to import test module: test_CAPS Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_CAPS.py", line 10, in from Bio import CAPS File "/builddir/build/BUILD/biopython-1.86/Bio/CAPS/__init__.py", line 16, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Chi2 ... /builddir/build/BUILD/biopython-1.86/Bio/Nexus/Nexus.py:2106: BiopythonWarning: Import of C module failed (cannot import name 'cnexus' from 'Bio.Nexus' (/builddir/build/BUILD/biopython-1.86/Bio/Nexus/__init__.py)). Falling back to slow Python implementation warnings.warn( loading tests failed: Failed to import test module: test_Chi2 Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Chi2.py", line 10, in from Bio.Phylo.PAML import chi2 File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Cluster ... FAIL test_CodonTable ... ok test_ColorSpiral ... skipping. Error: Install reportlab if you want to use Bio.Graphics. test_Compass ... ok test_Consensus ... loading tests failed: Failed to import test module: test_Consensus Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Consensus.py", line 13, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_EMBL_unittest ... loading tests failed: Failed to import test module: test_EMBL_unittest Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_EMBL_unittest.py", line 13, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_EmbossPrimer ... ok test_Entrez ... ok test_Entrez_online ... loading tests failed: Failed to import test module: test_Entrez_online Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_online.py", line 23, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Entrez_parser ... FAIL test_Enzyme ... ok test_ExPASy ... skipping. internet not available test_File ... ok test_GenBank ... loading tests failed: Failed to import test module: test_GenBank Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_GenBank.py", line 25, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_GenomeDiagram ... skipping. Error: Install reportlab if you want to use Bio.Graphics. test_GraphicsBitmaps ... skipping. Error: Install ReportLab if you want to use Bio.Graphics. test_GraphicsChromosome ... skipping. Error: Install reportlab if you want to use Bio.Graphics. test_GraphicsDistribution ... skipping. Install reportlab if you want to use Bio.Graphics. test_GraphicsGeneral ... skipping. Install reportlab if you want to use Bio.Graphics. test_KEGG ... ok test_KEGG_online ... loading tests failed: Failed to import test module: test_KEGG_online Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_KEGG_online.py", line 16, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_KGML_graphics ... skipping. Error: Please install ReportLab if you want to use Bio.Graphics. You can find ReportLab at http://www.reportlab.com/software/opensource/ test_KGML_graphics_online ... skipping. Install reportlab if you want to use Bio.Graphics. test_KGML_nographics ... ok test_KeyWList ... ok test_MafIO_index ... loading tests failed: Failed to import test module: test_MafIO_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_MafIO_index.py", line 20, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Medline ... ok test_NCBIXML ... loading tests failed: Failed to import test module: test_NCBIXML Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_NCBIXML.py", line 10, in from Bio.Blast import NCBIXML File "/builddir/build/BUILD/biopython-1.86/Bio/Blast/__init__.py", line 44, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_NCBI_qblast ... loading tests failed: Failed to import test module: test_NCBI_qblast Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_NCBI_qblast.py", line 38, in from Bio.Blast import NCBIWWW File "/builddir/build/BUILD/biopython-1.86/Bio/Blast/__init__.py", line 44, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_NMR ... ok test_Nexus ... loading tests failed: Failed to import test module: test_Nexus Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Nexus.py", line 20, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_PAML_baseml ... loading tests failed: Failed to import test module: test_PAML_baseml Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PAML_baseml.py", line 12, in from Bio.Phylo.PAML import baseml File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_PAML_codeml ... loading tests failed: Failed to import test module: test_PAML_codeml Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PAML_codeml.py", line 13, in from Bio.Phylo.PAML import codeml File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_PAML_tools ... loading tests failed: Failed to import test module: test_PAML_tools Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PAML_tools.py", line 13, in from Bio.Phylo.PAML import baseml File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_PAML_yn00 ... loading tests failed: Failed to import test module: test_PAML_yn00 Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PAML_yn00.py", line 13, in from Bio.Phylo.PAML import yn00 File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_PDB_CEAligner ... loading tests failed: Failed to import test module: test_PDB_CEAligner Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_CEAligner.py", line 20, in from Bio.PDB import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_DSSP ... loading tests failed: Failed to import test module: test_PDB_DSSP Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_DSSP.py", line 33, in from Bio.PDB import DSSP File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_Dice ... loading tests failed: Failed to import test module: test_PDB_Dice Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_Dice.py", line 12, in from Bio.PDB import Dice File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_Disordered ... loading tests failed: Failed to import test module: test_PDB_Disordered Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_Disordered.py", line 18, in from Bio.PDB import PDBIO File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_Exposure ... loading tests failed: Failed to import test module: test_PDB_Exposure Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_Exposure.py", line 29, in from Bio.PDB import ExposureCN File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_FragmentMapper ... loading tests failed: Failed to import test module: test_PDB_FragmentMapper Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_FragmentMapper.py", line 22, in from Bio.PDB import FragmentMapper File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_KDTree ... skipping. C module Bio.PDB.kdtrees not compiled test_PDB_MMCIF2Dict ... loading tests failed: Failed to import test module: test_PDB_MMCIF2Dict Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_MMCIF2Dict.py", line 27, in from Bio.PDB.MMCIF2Dict import MMCIF2Dict File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_MMCIFIO ... loading tests failed: Failed to import test module: test_PDB_MMCIFIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_MMCIFIO.py", line 21, in from Bio.PDB import Atom File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_MMCIFParser ... loading tests failed: Failed to import test module: test_PDB_MMCIFParser Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_MMCIFParser.py", line 32, in from Bio.PDB import CaPPBuilder File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_NACCESS ... loading tests failed: Failed to import test module: test_PDB_NACCESS Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_NACCESS.py", line 32, in from Bio.PDB import PDBParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_PDBIO ... loading tests failed: Failed to import test module: test_PDB_PDBIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_PDBIO.py", line 22, in from Bio.PDB import Atom File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_PDBList ... loading tests failed: Failed to import test module: test_PDB_PDBList Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_PDBList.py", line 18, in from Bio.PDB.PDBList import PDBList File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_PDBMLParser ... loading tests failed: Failed to import test module: test_PDB_PDBMLParser Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_PDBMLParser.py", line 11, in from Bio.PDB import MMCIFParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_PDBParser ... loading tests failed: Failed to import test module: test_PDB_PDBParser Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_PDBParser.py", line 29, in from Bio.PDB import PDBParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_PSEA ... loading tests failed: Failed to import test module: test_PDB_PSEA Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_PSEA.py", line 15, in from Bio.PDB import PDBParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_Polypeptide ... loading tests failed: Failed to import test module: test_PDB_Polypeptide Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_Polypeptide.py", line 16, in from Bio.PDB import CaPPBuilder File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_QCPSuperimposer ... loading tests failed: Failed to import test module: test_PDB_QCPSuperimposer Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_QCPSuperimposer.py", line 20, in from Bio.PDB import PDBParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_ResidueDepth ... loading tests failed: Failed to import test module: test_PDB_ResidueDepth Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_ResidueDepth.py", line 18, in from Bio.PDB import MMCIFParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_SASA ... loading tests failed: Failed to import test module: test_PDB_SASA Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_SASA.py", line 15, in from Bio.PDB import PDBParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_SMCRA ... loading tests failed: Failed to import test module: test_PDB_SMCRA Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_SMCRA.py", line 37, in from Bio.PDB import Atom File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_Selection ... loading tests failed: Failed to import test module: test_PDB_Selection Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_Selection.py", line 9, in from Bio.PDB import PDBParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_StructureAlignment ... loading tests failed: Failed to import test module: test_PDB_StructureAlignment Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_StructureAlignment.py", line 15, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_PDB_Superimposer ... loading tests failed: Failed to import test module: test_PDB_Superimposer Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_Superimposer.py", line 23, in from Bio.PDB import PDBParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_alphafold_db ... loading tests failed: Failed to import test module: test_PDB_alphafold_db Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_alphafold_db.py", line 7, in from Bio.PDB import alphafold_db File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_binary_cif ... loading tests failed: Failed to import test module: test_PDB_binary_cif Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_binary_cif.py", line 7, in from Bio.PDB import MMCIFParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_internal_coords ... loading tests failed: Failed to import test module: test_PDB_internal_coords Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_internal_coords.py", line 26, in from Bio.PDB.ic_rebuild import compare_residues File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_parse_pdb_header ... loading tests failed: Failed to import test module: test_PDB_parse_pdb_header Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_parse_pdb_header.py", line 22, in from Bio.PDB import PDBParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PDB_vectors ... loading tests failed: Failed to import test module: test_PDB_vectors Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PDB_vectors.py", line 21, in from Bio.PDB import calc_angle File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_PQR ... loading tests failed: Failed to import test module: test_PQR Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PQR.py", line 20, in from Bio.PDB.PDBIO import PDBIO File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_Pathway ... ok test_Phd ... loading tests failed: Failed to import test module: test_Phd Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Phd.py", line 9, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Phylo ... loading tests failed: Failed to import test module: test_Phylo Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Phylo.py", line 13, in from Bio import Phylo File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_PhyloXML ... loading tests failed: Failed to import test module: test_PhyloXML Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_PhyloXML.py", line 15, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Phylo_CDAO ... loading tests failed: Failed to import test module: test_Phylo_CDAO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Phylo_CDAO.py", line 13, in import Bio.Phylo as bp File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Phylo_NeXML ... loading tests failed: Failed to import test module: test_Phylo_NeXML Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Phylo_NeXML.py", line 14, in from Bio import Phylo File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Phylo_igraph ... loading tests failed: Failed to import test module: test_Phylo_igraph Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Phylo_igraph.py", line 13, in from Bio import Phylo File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Phylo_matplotlib ... loading tests failed: Failed to import test module: test_Phylo_matplotlib Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Phylo_matplotlib.py", line 13, in from Bio import Phylo File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Phylo_networkx ... loading tests failed: Failed to import test module: test_Phylo_networkx Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Phylo_networkx.py", line 12, in from Bio import Phylo File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_PopGen_GenePop_nodepend ... ok test_ProtParam ... ok test_RCSBFormats ... loading tests failed: Failed to import test module: test_RCSBFormats Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_RCSBFormats.py", line 28, in from Bio.PDB import PDBParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_Restriction ... ok test_SCOP_Astral ... loading tests failed: Failed to import test module: test_SCOP_Astral Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SCOP_Astral.py", line 10, in from Bio.SCOP import Astral File "/builddir/build/BUILD/biopython-1.86/Bio/SCOP/__init__.py", line 50, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SCOP_Cla ... loading tests failed: Failed to import test module: test_SCOP_Cla Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SCOP_Cla.py", line 12, in from Bio.SCOP import Cla File "/builddir/build/BUILD/biopython-1.86/Bio/SCOP/__init__.py", line 50, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SCOP_Des ... loading tests failed: Failed to import test module: test_SCOP_Des Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SCOP_Des.py", line 10, in from Bio.SCOP import Des File "/builddir/build/BUILD/biopython-1.86/Bio/SCOP/__init__.py", line 50, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SCOP_Dom ... loading tests failed: Failed to import test module: test_SCOP_Dom Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SCOP_Dom.py", line 13, in from Bio.SCOP import Dom File "/builddir/build/BUILD/biopython-1.86/Bio/SCOP/__init__.py", line 50, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SCOP_Hie ... loading tests failed: Failed to import test module: test_SCOP_Hie Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SCOP_Hie.py", line 10, in from Bio.SCOP import Hie File "/builddir/build/BUILD/biopython-1.86/Bio/SCOP/__init__.py", line 50, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SCOP_Raf ... loading tests failed: Failed to import test module: test_SCOP_Raf Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SCOP_Raf.py", line 11, in from Bio.SCOP import Raf File "/builddir/build/BUILD/biopython-1.86/Bio/SCOP/__init__.py", line 50, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SCOP_Residues ... loading tests failed: Failed to import test module: test_SCOP_Residues Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SCOP_Residues.py", line 10, in from Bio.SCOP.Residues import Residues File "/builddir/build/BUILD/biopython-1.86/Bio/SCOP/__init__.py", line 50, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SCOP_Scop ... loading tests failed: Failed to import test module: test_SCOP_Scop Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SCOP_Scop.py", line 13, in from Bio.SCOP import cmp_sccs File "/builddir/build/BUILD/biopython-1.86/Bio/SCOP/__init__.py", line 50, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SVDSuperimposer ... ok test_SearchIO_blast_tab ... loading tests failed: Failed to import test module: test_SearchIO_blast_tab Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_blast_tab.py", line 11, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_blast_tab_index ... loading tests failed: Failed to import test module: test_SearchIO_blast_tab_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_blast_tab_index.py", line 10, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_blast_xml ... loading tests failed: Failed to import test module: test_SearchIO_blast_xml Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_blast_xml.py", line 13, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_blast_xml_index ... loading tests failed: Failed to import test module: test_SearchIO_blast_xml_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_blast_xml_index.py", line 10, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_blat_psl ... loading tests failed: Failed to import test module: test_SearchIO_blat_psl Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_blat_psl.py", line 11, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_blat_psl_index ... loading tests failed: Failed to import test module: test_SearchIO_blat_psl_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_blat_psl_index.py", line 11, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_exonerate ... loading tests failed: Failed to import test module: test_SearchIO_exonerate Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_exonerate.py", line 11, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_exonerate_text_index ... loading tests failed: Failed to import test module: test_SearchIO_exonerate_text_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_exonerate_text_index.py", line 11, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_exonerate_vulgar_index ... loading tests failed: Failed to import test module: test_SearchIO_exonerate_vulgar_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_exonerate_vulgar_index.py", line 11, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_fasta_m10 ... loading tests failed: Failed to import test module: test_SearchIO_fasta_m10 Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_fasta_m10.py", line 11, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_fasta_m10_index ... loading tests failed: Failed to import test module: test_SearchIO_fasta_m10_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_fasta_m10_index.py", line 11, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_hhsuite2_text ... loading tests failed: Failed to import test module: test_SearchIO_hhsuite2_text Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_hhsuite2_text.py", line 11, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_hmmer2_text ... loading tests failed: Failed to import test module: test_SearchIO_hmmer2_text Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_hmmer2_text.py", line 12, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_hmmer2_text_index ... loading tests failed: Failed to import test module: test_SearchIO_hmmer2_text_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_hmmer2_text_index.py", line 11, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_hmmer3_domtab ... loading tests failed: Failed to import test module: test_SearchIO_hmmer3_domtab Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_hmmer3_domtab.py", line 11, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_hmmer3_domtab_index ... loading tests failed: Failed to import test module: test_SearchIO_hmmer3_domtab_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_hmmer3_domtab_index.py", line 11, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_hmmer3_tab ... loading tests failed: Failed to import test module: test_SearchIO_hmmer3_tab Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_hmmer3_tab.py", line 11, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_hmmer3_tab_index ... loading tests failed: Failed to import test module: test_SearchIO_hmmer3_tab_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_hmmer3_tab_index.py", line 11, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_hmmer3_text ... loading tests failed: Failed to import test module: test_SearchIO_hmmer3_text Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_hmmer3_text.py", line 11, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_hmmer3_text_index ... loading tests failed: Failed to import test module: test_SearchIO_hmmer3_text_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_hmmer3_text_index.py", line 10, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_infernal_tab ... loading tests failed: Failed to import test module: test_SearchIO_infernal_tab Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_infernal_tab.py", line 15, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_infernal_tab_index ... loading tests failed: Failed to import test module: test_SearchIO_infernal_tab_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_infernal_tab_index.py", line 14, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_infernal_text ... loading tests failed: Failed to import test module: test_SearchIO_infernal_text Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_infernal_text.py", line 14, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_infernal_text_index ... loading tests failed: Failed to import test module: test_SearchIO_infernal_text_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_infernal_text_index.py", line 15, in from search_tests_common import CheckIndex File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_interproscan_xml ... loading tests failed: Failed to import test module: test_SearchIO_interproscan_xml Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_interproscan_xml.py", line 10, in from Bio.SearchIO import parse File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_model ... loading tests failed: Failed to import test module: test_SearchIO_model Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_model.py", line 19, in from search_tests_common import SearchTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SearchIO_write ... loading tests failed: Failed to import test module: test_SearchIO_write Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SearchIO_write.py", line 11, in from search_tests_common import SearchTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/search_tests_common.py", line 18, in from Bio import SearchIO File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/__init__.py", line 200, in from Bio.SearchIO._model import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/__init__.py", line 47, in from .hit import Hit File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hit.py", line 15, in from .hsp import HSP File "/builddir/build/BUILD/biopython-1.86/Bio/SearchIO/_model/hsp.py", line 13, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqFeature ... loading tests failed: Failed to import test module: test_SeqFeature Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqFeature.py", line 16, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO ... loading tests failed: Failed to import test module: test_SeqIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_AbiIO ... loading tests failed: Failed to import test module: test_SeqIO_AbiIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_AbiIO.py", line 11, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_FastaIO ... loading tests failed: Failed to import test module: test_SeqIO_FastaIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_FastaIO.py", line 11, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_Gck ... loading tests failed: Failed to import test module: test_SeqIO_Gck Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_Gck.py", line 12, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_Gfa ... loading tests failed: Failed to import test module: test_SeqIO_Gfa Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_Gfa.py", line 6, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_Insdc ... loading tests failed: Failed to import test module: test_SeqIO_Insdc Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_Insdc.py", line 11, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_NibIO ... loading tests failed: Failed to import test module: test_SeqIO_NibIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_NibIO.py", line 6, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_PdbIO ... loading tests failed: Failed to import test module: test_SeqIO_PdbIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_PdbIO.py", line 26, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_QualityIO ... loading tests failed: Failed to import test module: test_SeqIO_QualityIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_QualityIO.py", line 13, in from test_SeqIO import SeqIOConverterTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_SeqXML ... loading tests failed: Failed to import test module: test_SeqIO_SeqXML Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_SeqXML.py", line 10, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_SffIO ... loading tests failed: Failed to import test module: test_SeqIO_SffIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_SffIO.py", line 13, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_SnapGene ... loading tests failed: Failed to import test module: test_SeqIO_SnapGene Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_SnapGene.py", line 13, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_TwoBitIO ... loading tests failed: Failed to import test module: test_SeqIO_TwoBitIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_TwoBitIO.py", line 5, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_UniprotIO ... loading tests failed: Failed to import test module: test_SeqIO_UniprotIO Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_UniprotIO.py", line 11, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_Xdna ... loading tests failed: Failed to import test module: test_SeqIO_Xdna Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_Xdna.py", line 13, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_features ... loading tests failed: Failed to import test module: test_SeqIO_features Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_features.py", line 17, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_index ... loading tests failed: Failed to import test module: test_SeqIO_index Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_index.py", line 23, in from seq_tests_common import SeqRecordTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/seq_tests_common.py", line 10, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_online ... loading tests failed: Failed to import test module: test_SeqIO_online Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_online.py", line 23, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqIO_write ... loading tests failed: Failed to import test module: test_SeqIO_write Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO_write.py", line 13, in from test_SeqIO import SeqIOTestBaseClass File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqIO.py", line 16, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqRecord ... loading tests failed: Failed to import test module: test_SeqRecord Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqRecord.py", line 18, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SeqUtils ... loading tests failed: Failed to import test module: test_SeqUtils Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SeqUtils.py", line 11, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Seq_objs ... loading tests failed: Failed to import test module: test_Seq_objs Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_Seq_objs.py", line 12, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_SwissProt ... loading tests failed: Failed to import test module: test_SwissProt Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_SwissProt.py", line 11, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_TogoWS ... loading tests failed: Failed to import test module: test_TogoWS Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_TogoWS.py", line 18, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_TreeConstruction ... loading tests failed: Failed to import test module: test_TreeConstruction Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_TreeConstruction.py", line 14, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_Tutorial ... skipping. Could not find ../Doc/Tutorial/index.rst file test_UniGene ... ok test_UniProt ... skipping. internet not available test_UniProt_GOA ... ok test_align ... loading tests failed: Failed to import test module: test_align Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_align.py", line 24, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_align_substitution_matrices ... loading tests failed: Failed to import test module: test_align_substitution_matrices Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_align_substitution_matrices.py", line 22, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_bgzf ... ok test_cellosaurus ... ok test_codonalign ... loading tests failed: Failed to import test module: test_codonalign Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_codonalign.py", line 12, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_geo ... ok test_mmtf ... skipping. Error: Install mmtf-python to use Bio.PDB.mmtf test_mmtf_online ... loading tests failed: Failed to import test module: test_mmtf_online Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_mmtf_online.py", line 14, in from Bio.PDB.mmtf import MMTFParser File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/__init__.py", line 40, in from .cealign import CEAligner File "/builddir/build/BUILD/biopython-1.86/Bio/PDB/cealign.py", line 23, in from Bio.PDB.ccealign import run_cealign ModuleNotFoundError: No module named 'Bio.PDB.ccealign' test_motifs ... loading tests failed: Failed to import test module: test_motifs Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_motifs.py", line 24, in from Bio import motifs File "/builddir/build/BUILD/biopython-1.86/Bio/motifs/__init__.py", line 32, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_motifs_online ... loading tests failed: Failed to import test module: test_motifs_online Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_motifs_online.py", line 16, in from Bio import motifs File "/builddir/build/BUILD/biopython-1.86/Bio/motifs/__init__.py", line 32, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_pairwise2 ... loading tests failed: Failed to import test module: test_pairwise2 Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_pairwise2.py", line 15, in from pairwise2_testCases import * # noqa: F401, F403 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/pairwise2_testCases.py", line 20, in from Bio import pairwise2 File "/builddir/build/BUILD/biopython-1.86/Bio/pairwise2.py", line 276, in from Bio.Align import substitution_matrices File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_pairwise2_no_C ... loading tests failed: Failed to import test module: test_pairwise2_no_C Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_pairwise2_no_C.py", line 15, in from pairwise2_testCases import * # noqa: F401, F403 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/pairwise2_testCases.py", line 20, in from Bio import pairwise2 File "/builddir/build/BUILD/biopython-1.86/Bio/pairwise2.py", line 276, in from Bio.Align import substitution_matrices File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_pairwise_aligner ... loading tests failed: Failed to import test module: test_pairwise_aligner Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_pairwise_aligner.py", line 24, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_pairwise_alignment_map ... loading tests failed: Failed to import test module: test_pairwise_alignment_map Traceback (most recent call last): File "/usr/lib64/python3.11/unittest/loader.py", line 162, in loadTestsFromName module = __import__(module_name) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Tests/test_pairwise_alignment_map.py", line 21, in from Bio import Align File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) test_phenotype ... ok test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. test_prodoc ... ok test_prosite ... ok test_seq ... ok test_translate ... ok Bio docstring test ... ok Bio.Affy docstring test ... ok Bio.Affy.CelFile docstring test ... ok Bio.Align docstring test ... FAIL, ImportError Bio.Align.AlignInfo docstring test ... FAIL, ImportError Bio.Align.a2m docstring test ... FAIL, ImportError Bio.Align.analysis docstring test ... FAIL, ImportError Bio.Align.bed docstring test ... FAIL, ImportError Bio.Align.bigbed docstring test ... FAIL, ImportError Bio.Align.bigmaf docstring test ... FAIL, ImportError Bio.Align.bigpsl docstring test ... FAIL, ImportError Bio.Align.chain docstring test ... FAIL, ImportError Bio.Align.clustal docstring test ... FAIL, ImportError Bio.Align.emboss docstring test ... FAIL, ImportError Bio.Align.exonerate docstring test ... FAIL, ImportError Bio.Align.fasta docstring test ... FAIL, ImportError Bio.Align.hhr docstring test ... FAIL, ImportError Bio.Align.interfaces docstring test ... FAIL, ImportError Bio.Align.maf docstring test ... FAIL, ImportError Bio.Align.mauve docstring test ... FAIL, ImportError Bio.Align.msf docstring test ... FAIL, ImportError Bio.Align.nexus docstring test ... FAIL, ImportError Bio.Align.phylip docstring test ... FAIL, ImportError Bio.Align.psl docstring test ... FAIL, ImportError Bio.Align.sam docstring test ... FAIL, ImportError Bio.Align.stockholm docstring test ... FAIL, ImportError Bio.Align.substitution_matrices docstring test ... FAIL, ImportError Bio.Align.tabular docstring test ... FAIL, ImportError Bio.AlignIO docstring test ... FAIL, ImportError Bio.AlignIO.ClustalIO docstring test ... FAIL, ImportError Bio.AlignIO.EmbossIO docstring test ... FAIL, ImportError Bio.AlignIO.FastaIO docstring test ... FAIL, ImportError Bio.AlignIO.Interfaces docstring test ... FAIL, ImportError Bio.AlignIO.MafIO docstring test ... FAIL, ImportError Bio.AlignIO.MauveIO docstring test ... FAIL, ImportError Bio.AlignIO.MsfIO docstring test ... FAIL, ImportError Bio.AlignIO.NexusIO docstring test ... FAIL, ImportError Bio.AlignIO.PhylipIO docstring test ... FAIL, ImportError Bio.AlignIO.StockholmIO docstring test ... FAIL, ImportError Bio.Blast docstring test ... FAIL, ImportError Bio.Blast.NCBIWWW docstring test ... FAIL, ImportError Bio.Blast.NCBIXML docstring test ... FAIL, ImportError Bio.Blast._parser docstring test ... FAIL, ImportError Bio.Blast._writers docstring test ... FAIL, ImportError Bio.CAPS docstring test ... FAIL, ImportError Bio.Cluster docstring test ... FAIL, ImportError Bio.Compass docstring test ... ok Bio.Data docstring test ... ok Bio.Data.CodonTable docstring test ... ok Bio.Data.IUPACData docstring test ... ok Bio.Data.PDBData docstring test ... ok Bio.Emboss docstring test ... ok Bio.Emboss.Primer3 docstring test ... ok Bio.Emboss.PrimerSearch docstring test ... ok Bio.Entrez docstring test ... FAIL Bio.Entrez.Parser docstring test ... ok Bio.ExPASy docstring test ... FAIL Bio.ExPASy.Enzyme docstring test ... ok Bio.ExPASy.Prodoc docstring test ... ok Bio.ExPASy.Prosite docstring test ... ok Bio.ExPASy.ScanProsite docstring test ... ok Bio.ExPASy.cellosaurus docstring test ... FAIL Bio.File docstring test ... ok Bio.GenBank docstring test ... ok Bio.GenBank.Record docstring test ... ok Bio.GenBank.Scanner docstring test ... ok Bio.GenBank.utils docstring test ... ok Bio.Geo docstring test ... ok Bio.Geo.Record docstring test ... ok Bio.Graphics docstring test ... skipped, missing Python dependency Bio.Graphics.BasicChromosome docstring test ... skipped, missing Python dependency Bio.Graphics.ColorSpiral docstring test ... skipped, missing Python dependency Bio.Graphics.Comparative docstring test ... skipped, missing Python dependency Bio.Graphics.DisplayRepresentation docstring test ... skipped, missing Python dependency Bio.Graphics.Distribution docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._AbstractDrawer docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._CircularDrawer docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._Colors docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._CrossLink docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._Diagram docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._Feature docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._FeatureSet docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._Graph docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._GraphSet docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._LinearDrawer docstring test ... skipped, missing Python dependency Bio.Graphics.GenomeDiagram._Track docstring test ... skipped, missing Python dependency Bio.Graphics.KGML_vis docstring test ... skipped, missing Python dependency Bio.HMM docstring test ... ok Bio.KEGG docstring test ... ok Bio.KEGG.Compound docstring test ... ok Bio.KEGG.Enzyme docstring test ... ok Bio.KEGG.Gene docstring test ... ok Bio.KEGG.KGML docstring test ... ok Bio.KEGG.KGML.KGML_parser docstring test ... ok Bio.KEGG.KGML.KGML_pathway docstring test ... ok Bio.KEGG.Map docstring test ... ok Bio.KEGG.REST docstring test ... ok Bio.Medline docstring test ... ok Bio.NMR docstring test ... ok Bio.NMR.NOEtools docstring test ... ok Bio.NMR.xpktools docstring test ... ok Bio.Nexus docstring test ... ok Bio.Nexus.Nexus docstring test ... ok Bio.Nexus.Nodes docstring test ... ok Bio.Nexus.StandardData docstring test ... ok Bio.Nexus.Trees docstring test ... ok Bio.PDB docstring test ... FAIL, ImportError Bio.PDB.AbstractPropertyMap docstring test ... FAIL, ImportError Bio.PDB.Atom docstring test ... ok Bio.PDB.Chain docstring test ... FAIL, ImportError Bio.PDB.DSSP docstring test ... FAIL, ImportError Bio.PDB.Dice docstring test ... FAIL, ImportError Bio.PDB.Entity docstring test ... ok Bio.PDB.FragmentMapper docstring test ... FAIL, ImportError Bio.PDB.HSExposure docstring test ... FAIL, ImportError Bio.PDB.MMCIF2Dict docstring test ... FAIL, ImportError Bio.PDB.MMCIFParser docstring test ... FAIL, ImportError Bio.PDB.Model docstring test ... FAIL, ImportError Bio.PDB.NACCESS docstring test ... FAIL, ImportError Bio.PDB.NeighborSearch docstring test ... FAIL, ImportError Bio.PDB.PDBExceptions docstring test ... ok Bio.PDB.PDBIO docstring test ... FAIL, ImportError Bio.PDB.PDBList docstring test ... FAIL, ImportError Bio.PDB.PDBMLParser docstring test ... FAIL, ImportError Bio.PDB.PDBParser docstring test ... FAIL, ImportError Bio.PDB.PICIO docstring test ... FAIL, ImportError Bio.PDB.PSEA docstring test ... FAIL, ImportError Bio.PDB.Polypeptide docstring test ... FAIL, ImportError Bio.PDB.Residue docstring test ... ok Bio.PDB.ResidueDepth docstring test ... FAIL, ImportError Bio.PDB.SASA docstring test ... FAIL, ImportError Bio.PDB.SCADIO docstring test ... FAIL, ImportError Bio.PDB.Selection docstring test ... ok Bio.PDB.Structure docstring test ... FAIL, ImportError Bio.PDB.StructureAlignment docstring test ... FAIL, ImportError Bio.PDB.StructureBuilder docstring test ... FAIL, ImportError Bio.PDB.Superimposer docstring test ... FAIL, ImportError Bio.PDB.alphafold_db docstring test ... FAIL, ImportError Bio.PDB.binary_cif docstring test ... FAIL, ImportError Bio.PDB.cealign docstring test ... FAIL, ImportError Bio.PDB.ic_data docstring test ... FAIL, ImportError Bio.PDB.ic_rebuild docstring test ... FAIL, ImportError Bio.PDB.internal_coords docstring test ... FAIL, ImportError Bio.PDB.mmcifio docstring test ... FAIL, ImportError Bio.PDB.mmtf docstring test ... FAIL, ImportError Bio.PDB.mmtf.DefaultParser docstring test ... FAIL, ImportError Bio.PDB.mmtf.mmtfio docstring test ... FAIL, ImportError Bio.PDB.parse_pdb_header docstring test ... FAIL, ImportError Bio.PDB.qcprot docstring test ... FAIL, ImportError Bio.PDB.vectors docstring test ... ok Bio.Pathway docstring test ... ok Bio.Pathway.Rep docstring test ... ok Bio.Pathway.Rep.Graph docstring test ... ok Bio.Pathway.Rep.MultiGraph docstring test ... ok Bio.Phylo docstring test ... FAIL, ImportError Bio.Phylo.BaseTree docstring test ... FAIL Bio.Phylo.CDAO docstring test ... FAIL, ImportError Bio.Phylo.CDAOIO docstring test ... FAIL, ImportError Bio.Phylo.Consensus docstring test ... FAIL, ImportError Bio.Phylo.NeXML docstring test ... ok Bio.Phylo.NeXMLIO docstring test ... ok Bio.Phylo.Newick docstring test ... ok Bio.Phylo.NewickIO docstring test ... ok Bio.Phylo.NexusIO docstring test ... ok Bio.Phylo.PAML docstring test ... FAIL, ImportError Bio.Phylo.PAML._paml docstring test ... FAIL, ImportError Bio.Phylo.PAML._parse_baseml docstring test ... FAIL, ImportError Bio.Phylo.PAML._parse_codeml docstring test ... FAIL, ImportError Bio.Phylo.PAML._parse_yn00 docstring test ... FAIL, ImportError Bio.Phylo.PAML.baseml docstring test ... FAIL, ImportError Bio.Phylo.PAML.chi2 docstring test ... FAIL, ImportError Bio.Phylo.PAML.codeml docstring test ... FAIL, ImportError Bio.Phylo.PAML.yn00 docstring test ... FAIL, ImportError Bio.Phylo.PhyloXML docstring test ... FAIL, ImportError Bio.Phylo.PhyloXMLIO docstring test ... FAIL, ImportError Bio.Phylo.TreeConstruction docstring test ... FAIL, ImportError Bio.Phylo._cdao_owl docstring test ... ok Bio.Phylo._io docstring test ... FAIL, ImportError Bio.Phylo._utils docstring test ... FAIL, ImportError Bio.PopGen docstring test ... ok Bio.PopGen.GenePop docstring test ... ok Bio.PopGen.GenePop.FileParser docstring test ... ok Bio.PopGen.GenePop.LargeFileParser docstring test ... ok Bio.Restriction docstring test ... ok Bio.Restriction.PrintFormat docstring test ... ok Bio.Restriction.Restriction docstring test ... ok Bio.Restriction.Restriction_Dictionary docstring test ... ok Bio.SCOP docstring test ... FAIL, ImportError Bio.SCOP.Cla docstring test ... FAIL, ImportError Bio.SCOP.Des docstring test ... FAIL, ImportError Bio.SCOP.Dom docstring test ... FAIL, ImportError Bio.SCOP.Hie docstring test ... FAIL, ImportError Bio.SCOP.Raf docstring test ... FAIL, ImportError Bio.SCOP.Residues docstring test ... FAIL, ImportError Bio.SVDSuperimposer docstring test ... ok Bio.SearchIO docstring test ... FAIL, ImportError Bio.SearchIO.BlastIO docstring test ... FAIL, ImportError Bio.SearchIO.BlastIO.blast_tab docstring test ... FAIL, ImportError Bio.SearchIO.BlastIO.blast_xml docstring test ... FAIL, ImportError Bio.SearchIO.BlatIO docstring test ... FAIL, ImportError Bio.SearchIO.ExonerateIO docstring test ... FAIL, ImportError Bio.SearchIO.ExonerateIO._base docstring test ... FAIL, ImportError Bio.SearchIO.ExonerateIO.exonerate_cigar docstring test ... FAIL, ImportError Bio.SearchIO.ExonerateIO.exonerate_text docstring test ... FAIL, ImportError Bio.SearchIO.ExonerateIO.exonerate_vulgar docstring test ... FAIL, ImportError Bio.SearchIO.FastaIO docstring test ... FAIL, ImportError Bio.SearchIO.HHsuiteIO docstring test ... FAIL, ImportError Bio.SearchIO.HHsuiteIO.hhsuite2_text docstring test ... FAIL, ImportError Bio.SearchIO.HmmerIO docstring test ... FAIL, ImportError Bio.SearchIO.HmmerIO._base docstring test ... FAIL, ImportError Bio.SearchIO.HmmerIO.hmmer2_text docstring test ... FAIL, ImportError Bio.SearchIO.HmmerIO.hmmer3_domtab docstring test ... FAIL, ImportError Bio.SearchIO.HmmerIO.hmmer3_tab docstring test ... FAIL, ImportError Bio.SearchIO.HmmerIO.hmmer3_text docstring test ... FAIL, ImportError Bio.SearchIO.InfernalIO docstring test ... FAIL, ImportError Bio.SearchIO.InfernalIO._base docstring test ... FAIL, ImportError Bio.SearchIO.InfernalIO.infernal_tab docstring test ... FAIL, ImportError Bio.SearchIO.InfernalIO.infernal_text docstring test ... FAIL, ImportError Bio.SearchIO.InterproscanIO docstring test ... FAIL, ImportError Bio.SearchIO.InterproscanIO.interproscan_xml docstring test ... FAIL, ImportError Bio.SearchIO._index docstring test ... FAIL, ImportError Bio.SearchIO._model docstring test ... FAIL, ImportError Bio.SearchIO._model._base docstring test ... ok Bio.SearchIO._model.hit docstring test ... FAIL, ImportError Bio.SearchIO._model.hsp docstring test ... FAIL, ImportError Bio.SearchIO._model.query docstring test ... FAIL, ImportError Bio.SearchIO._utils docstring test ... ok Bio.Seq docstring test ... ok Bio.SeqFeature docstring test ... FAIL Bio.SeqIO docstring test ... FAIL, ImportError Bio.SeqIO.AbiIO docstring test ... FAIL, ImportError Bio.SeqIO.AceIO docstring test ... FAIL, ImportError Bio.SeqIO.FastaIO docstring test ... FAIL, ImportError Bio.SeqIO.GckIO docstring test ... FAIL, ImportError Bio.SeqIO.GfaIO docstring test ... FAIL, ImportError Bio.SeqIO.IgIO docstring test ... FAIL, ImportError Bio.SeqIO.InsdcIO docstring test ... FAIL, ImportError Bio.SeqIO.Interfaces docstring test ... FAIL, ImportError Bio.SeqIO.NibIO docstring test ... FAIL, ImportError Bio.SeqIO.PdbIO docstring test ... FAIL, ImportError Bio.SeqIO.PhdIO docstring test ... FAIL, ImportError Bio.SeqIO.PirIO docstring test ... FAIL, ImportError Bio.SeqIO.QualityIO docstring test ... FAIL, ImportError Bio.SeqIO.SeqXmlIO docstring test ... FAIL, ImportError Bio.SeqIO.SffIO docstring test ... FAIL, ImportError Bio.SeqIO.SnapGeneIO docstring test ... FAIL, ImportError Bio.SeqIO.SwissIO docstring test ... FAIL, ImportError Bio.SeqIO.TabIO docstring test ... FAIL, ImportError Bio.SeqIO.TwoBitIO docstring test ... FAIL, ImportError Bio.SeqIO.UniprotIO docstring test ... FAIL, ImportError Bio.SeqIO.XdnaIO docstring test ... FAIL, ImportError Bio.SeqIO._index docstring test ... FAIL, ImportError Bio.SeqRecord docstring test ... FAIL Bio.SeqUtils docstring test ... ok Bio.SeqUtils.CheckSum docstring test ... ok Bio.SeqUtils.IsoelectricPoint docstring test ... ok Bio.SeqUtils.MeltingTemp docstring test ... ok Bio.SeqUtils.ProtParam docstring test ... ok Bio.SeqUtils.ProtParamData docstring test ... ok Bio.SeqUtils.lcc docstring test ... ok Bio.Sequencing docstring test ... ok Bio.Sequencing.Ace docstring test ... ok Bio.Sequencing.Phd docstring test ... ok Bio.SwissProt docstring test ... ok Bio.SwissProt.KeyWList docstring test ... ok Bio.TogoWS docstring test ... FAIL Bio.UniGene docstring test ... ok Bio.UniProt docstring test ... FAIL Bio.UniProt.GOA docstring test ... ok Bio._utils docstring test ... ok Bio.bgzf docstring test ... FAIL Bio.codonalign docstring test ... FAIL, ImportError Bio.codonalign.codonalignment docstring test ... FAIL, ImportError Bio.codonalign.codonseq docstring test ... FAIL, ImportError Bio.motifs docstring test ... FAIL, ImportError Bio.motifs.alignace docstring test ... FAIL, ImportError Bio.motifs.clusterbuster docstring test ... FAIL, ImportError Bio.motifs.jaspar docstring test ... FAIL, ImportError Bio.motifs.jaspar.db docstring test ... FAIL, ImportError Bio.motifs.mast docstring test ... FAIL, ImportError Bio.motifs.matrix docstring test ... FAIL, ImportError Bio.motifs.meme docstring test ... FAIL, ImportError Bio.motifs.minimal docstring test ... FAIL, ImportError Bio.motifs.pfm docstring test ... FAIL, ImportError Bio.motifs.thresholds docstring test ... FAIL, ImportError Bio.motifs.transfac docstring test ... FAIL, ImportError Bio.motifs.xms docstring test ... FAIL, ImportError Bio.pairwise2 docstring test ... FAIL, ImportError Bio.phenotype docstring test ... ok Bio.phenotype.phen_micro docstring test ... ok Bio.phenotype.pm_fitting docstring test ... skipped, missing Python dependency BioSQL docstring test ... ok BioSQL.BioSeq docstring test ... ok BioSQL.BioSeqDatabase docstring test ... ok BioSQL.DBUtils docstring test ... ok BioSQL.Loader docstring test ... ok ====================================================================== ERROR: test_clusterdistance (test_Cluster.TestCluster.test_clusterdistance) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 989, in test_clusterdistance from Bio.Cluster import clusterdistance File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_clusterdistance_arguments (test_Cluster.TestCluster.test_clusterdistance_arguments) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 727, in test_clusterdistance_arguments from Bio.Cluster._cluster import clusterdistance File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_distancematrix_arguments (test_Cluster.TestCluster.test_distancematrix_arguments) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 2666, in test_distancematrix_arguments from Bio.Cluster._cluster import distancematrix File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_distancematrix_kmedoids (test_Cluster.TestCluster.test_distancematrix_kmedoids) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 2753, in test_distancematrix_kmedoids from Bio.Cluster import distancematrix File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_kcluster (test_Cluster.TestCluster.test_kcluster) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 546, in test_kcluster from Bio.Cluster import clustercentroids File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_kcluster_arguments (test_Cluster.TestCluster.test_kcluster_arguments) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 371, in test_kcluster_arguments from Bio.Cluster._cluster import clustercentroids File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_kmedoids_arguments (test_Cluster.TestCluster.test_kmedoids_arguments) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 2731, in test_kmedoids_arguments from Bio.Cluster._cluster import distancematrix File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_mask_parse (test_Cluster.TestCluster.test_mask_parse) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 172, in test_mask_parse from Bio.Cluster import treecluster File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_matrix_parse (test_Cluster.TestCluster.test_matrix_parse) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 24, in test_matrix_parse from Bio.Cluster import treecluster File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_pca (test_Cluster.TestCluster.test_pca) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 3001, in test_pca from Bio.Cluster import pca File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_pca_arguments (test_Cluster.TestCluster.test_pca_arguments) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 2925, in test_pca_arguments from Bio.Cluster._cluster import pca File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_somcluster (test_Cluster.TestCluster.test_somcluster) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 2554, in test_somcluster from Bio.Cluster import somcluster File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_somcluster_arguments (test_Cluster.TestCluster.test_somcluster_arguments) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 2223, in test_somcluster_arguments from Bio.Cluster._cluster import somcluster File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_tree (test_Cluster.TestCluster.test_tree) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 1297, in test_tree from Bio.Cluster import Node File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_tree_arguments (test_Cluster.TestCluster.test_tree_arguments) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 1267, in test_tree_arguments from Bio.Cluster._cluster import Node File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_treecluster (test_Cluster.TestCluster.test_treecluster) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 1345, in test_treecluster from Bio.Cluster import treecluster File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_treecluster_arguments (test_Cluster.TestCluster.test_treecluster_arguments) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Cluster.py", line 1176, in test_treecluster_arguments from Bio.Cluster._cluster import Tree File "/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py", line 27, in from . import _cluster # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== ERROR: test_nucleotide1 (test_Entrez_parser.EFetchTest.test_nucleotide1) Test parsing XML returned by EFetch, Nucleotide database (first test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 11290, in test_nucleotide1 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd' ====================================================================== ERROR: test_nucleotide2 (test_Entrez_parser.EFetchTest.test_nucleotide2) Test parsing XML returned by EFetch, Nucleotide database (second test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 11786, in test_nucleotide2 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd' ====================================================================== ERROR: test_omim (test_Entrez_parser.EFetchTest.test_omim) Test parsing XML returned by EFetch, OMIM database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 10433, in test_omim record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/dtd/NCBI_Mim.dtd' ====================================================================== ERROR: test_protein (test_Entrez_parser.EFetchTest.test_protein) Test parsing XML returned by EFetch, Protein database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 11823, in test_protein record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd' ====================================================================== ERROR: test_pubmed1 (test_Entrez_parser.EFetchTest.test_pubmed1) Test parsing XML returned by EFetch, PubMed database (first test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 4644, in test_pubmed1 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_080101.dtd' ====================================================================== ERROR: test_pubmed2 (test_Entrez_parser.EFetchTest.test_pubmed2) Test parsing XML returned by EFetch, PubMed database (second test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 5323, in test_pubmed2 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_080101.dtd' ====================================================================== ERROR: test_taxonomy (test_Entrez_parser.EFetchTest.test_taxonomy) Test parsing XML returned by EFetch, Taxonomy database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 11172, in test_taxonomy record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd' ====================================================================== ERROR: test_truncated_xml (test_Entrez_parser.EFetchTest.test_truncated_xml) Test error handling for a truncated XML declaration. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 12349, in test_truncated_xml self.assertRaises(CorruptedXMLError, next, records) File "/usr/lib64/python3.11/unittest/case.py", line 766, in assertRaises return context.handle('assertRaises', args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/unittest/case.py", line 237, in handle callable_obj(*args, **kwargs) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 470, in parse self.parser.Parse(data, False) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd' ====================================================================== ERROR: test_egquery1 (test_Entrez_parser.EGQueryTest.test_egquery1) Test parsing XML output returned by EGQuery (first test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 4240, in test_egquery1 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/egquery.dtd' ====================================================================== ERROR: test_egquery2 (test_Entrez_parser.EGQueryTest.test_egquery2) Test parsing XML output returned by EGQuery (second test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 4451, in test_egquery2 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/egquery.dtd' ====================================================================== ERROR: test_corrupted (test_Entrez_parser.EInfoTest.test_corrupted) Test if corrupted XML is handled correctly. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1255, in test_corrupted self.assertRaises(Parser.CorruptedXMLError, Entrez.read, stream) File "/usr/lib64/python3.11/unittest/case.py", line 766, in assertRaises return context.handle('assertRaises', args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/unittest/case.py", line 237, in handle callable_obj(*args, **kwargs) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd' ====================================================================== ERROR: test_list (test_Entrez_parser.EInfoTest.test_list) Test parsing database list returned by EInfo. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 106, in test_list record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd' ====================================================================== ERROR: test_pubmed1 (test_Entrez_parser.EInfoTest.test_pubmed1) Test parsing database info returned by EInfo. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 155, in test_pubmed1 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd' ====================================================================== ERROR: test_pubmed2 (test_Entrez_parser.EInfoTest.test_pubmed2) Test validating the XML against the DTD. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 196, in test_pubmed2 self.assertRaises(Parser.ValidationError, Entrez.read, stream) File "/usr/lib64/python3.11/unittest/case.py", line 766, in assertRaises return context.handle('assertRaises', args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/unittest/case.py", line 237, in handle callable_obj(*args, **kwargs) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd' ====================================================================== ERROR: test_pubmed3 (test_Entrez_parser.EInfoTest.test_pubmed3) Test non-validating parser on XML with an inconsistent DTD. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 205, in test_pubmed3 record = Entrez.read(stream, validate=False) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd' ====================================================================== ERROR: test_medline (test_Entrez_parser.ELinkTest.test_medline) Test parsing medline indexed articles returned by ELink. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 2988, in test_medline record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd' ====================================================================== ERROR: test_nucleotide (test_Entrez_parser.ELinkTest.test_nucleotide) Test parsing Nucleotide to Protein links returned by ELink. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 2571, in test_nucleotide record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd' ====================================================================== ERROR: test_pubmed1 (test_Entrez_parser.ELinkTest.test_pubmed1) Test parsing pubmed links returned by ELink (first test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 2362, in test_pubmed1 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd' ====================================================================== ERROR: test_pubmed2 (test_Entrez_parser.ELinkTest.test_pubmed2) Test parsing pubmed links returned by ELink (second test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 2610, in test_pubmed2 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd' ====================================================================== ERROR: test_pubmed3 (test_Entrez_parser.ELinkTest.test_pubmed3) Test parsing pubmed link returned by ELink (third test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 3220, in test_pubmed3 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd' ====================================================================== ERROR: test_pubmed4 (test_Entrez_parser.ELinkTest.test_pubmed4) Test parsing pubmed links returned by ELink (fourth test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 3283, in test_pubmed4 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd' ====================================================================== ERROR: test_pubmed5 (test_Entrez_parser.ELinkTest.test_pubmed5) Test parsing pubmed links returned by ELink (fifth test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 3485, in test_pubmed5 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd' ====================================================================== ERROR: test_pubmed6 (test_Entrez_parser.ELinkTest.test_pubmed6) Test parsing pubmed links returned by ELink (sixth test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 4218, in test_pubmed6 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd' ====================================================================== ERROR: test_epost (test_Entrez_parser.EPostTest.test_epost) Test parsing XML returned by EPost. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1763, in test_epost record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ePost_020511.dtd' ====================================================================== ERROR: test_invalid (test_Entrez_parser.EPostTest.test_invalid) Test parsing XML returned by EPost with invalid id (overflow tag). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1788, in test_invalid record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ePost_020511.dtd' ====================================================================== ERROR: test_wrong (test_Entrez_parser.EPostTest.test_wrong) Test parsing XML returned by EPost with incorrect arguments. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1775, in test_wrong self.assertRaises(RuntimeError, Entrez.read, stream) File "/usr/lib64/python3.11/unittest/case.py", line 766, in assertRaises return context.handle('assertRaises', args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/unittest/case.py", line 237, in handle callable_obj(*args, **kwargs) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ePost_020511.dtd' ====================================================================== ERROR: test_journals (test_Entrez_parser.ESearchTest.test_journals) Test parsing XML returned by ESearch from the Journals database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1514, in test_journals record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd' ====================================================================== ERROR: test_notfound (test_Entrez_parser.ESearchTest.test_notfound) Test parsing XML returned by ESearch when no items were found. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1730, in test_notfound record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd' ====================================================================== ERROR: test_nucleotide (test_Entrez_parser.ESearchTest.test_nucleotide) Test parsing XML returned by ESearch from the Nucleotide database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1670, in test_nucleotide record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd' ====================================================================== ERROR: test_pmc (test_Entrez_parser.ESearchTest.test_pmc) Test parsing XML returned by ESearch from PubMed Central. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1559, in test_pmc record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd' ====================================================================== ERROR: test_protein (test_Entrez_parser.ESearchTest.test_protein) Test parsing XML returned by ESearch from the Protein database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1704, in test_protein record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd' ====================================================================== ERROR: test_pubmed1 (test_Entrez_parser.ESearchTest.test_pubmed1) Test parsing XML returned by ESearch from PubMed (first test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1266, in test_pubmed1 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd' ====================================================================== ERROR: test_pubmed2 (test_Entrez_parser.ESearchTest.test_pubmed2) Test parsing XML returned by ESearch from PubMed (second test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1296, in test_pubmed2 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd' ====================================================================== ERROR: test_pubmed3 (test_Entrez_parser.ESearchTest.test_pubmed3) Test parsing XML returned by ESearch from PubMed (third test). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1472, in test_pubmed3 record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd' ====================================================================== ERROR: test_espell (test_Entrez_parser.ESpellTest.test_espell) Test parsing XML output returned by ESpell. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 4624, in test_espell record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSpell.dtd' ====================================================================== ERROR: test_journals (test_Entrez_parser.ESummaryTest.test_journals) Test parsing XML returned by ESummary from the Journals database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1897, in test_journals record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd' ====================================================================== ERROR: test_nucleotide (test_Entrez_parser.ESummaryTest.test_nucleotide) Test parsing XML returned by ESummary from the Nucleotide database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 2029, in test_nucleotide record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd' ====================================================================== ERROR: test_protein (test_Entrez_parser.ESummaryTest.test_protein) Test parsing XML returned by ESummary from the Protein database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1988, in test_protein record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd' ====================================================================== ERROR: test_pubmed (test_Entrez_parser.ESummaryTest.test_pubmed) Test parsing XML returned by ESummary from PubMed. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 1812, in test_pubmed record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd' ====================================================================== ERROR: test_structure (test_Entrez_parser.ESummaryTest.test_structure) Test parsing XML returned by ESummary from the Structure database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 2071, in test_structure record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd' ====================================================================== ERROR: test_taxonomy (test_Entrez_parser.ESummaryTest.test_taxonomy) Test parsing XML returned by ESummary from the Taxonomy database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 2124, in test_taxonomy record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd' ====================================================================== ERROR: test_unists (test_Entrez_parser.ESummaryTest.test_unists) Test parsing XML returned by ESummary from the UniSTS database. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 2163, in test_unists record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd' ====================================================================== ERROR: test_wrong (test_Entrez_parser.ESummaryTest.test_wrong) Test parsing XML returned by ESummary with incorrect arguments. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 2191, in test_wrong self.assertRaises(RuntimeError, Entrez.read, stream) File "/usr/lib64/python3.11/unittest/case.py", line 766, in assertRaises return context.handle('assertRaises', args, kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/unittest/case.py", line 237, in handle callable_obj(*args, **kwargs) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd' ====================================================================== ERROR: test_BytesIO (test_Entrez_parser.GeneralTests.test_BytesIO) Test parsing a BytesIO stream (bytes not string). ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 65, in test_BytesIO record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd' ====================================================================== ERROR: test_parse_bytes_stream (test_Entrez_parser.GeneralTests.test_parse_bytes_stream) Test parsing a file opened in binary mode. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 40, in test_parse_bytes_stream for record in records: File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 470, in parse self.parser.Parse(data, False) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_080101.dtd' ====================================================================== ERROR: test_pickle (test_Entrez_parser.GeneralTests.test_pickle) Test if records created by the parser can be pickled. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 90, in test_pickle record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/egquery.dtd' ====================================================================== ERROR: test_read_bytes_stream (test_Entrez_parser.GeneralTests.test_read_bytes_stream) Test reading a file opened in binary mode. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/biopython-1.86/Tests/test_Entrez_parser.py", line 31, in test_read_bytes_stream record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_080101.dtd' ERROR while importing Bio.Align: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.AlignInfo: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.a2m: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.analysis: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.bed: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.bigbed: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.bigmaf: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.bigpsl: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.chain: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.clustal: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.emboss: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.exonerate: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.fasta: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.hhr: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.interfaces: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.maf: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.mauve: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.msf: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.nexus: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.phylip: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.psl: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.sam: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.stockholm: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.substitution_matrices: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Align.tabular: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO.ClustalIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO.EmbossIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO.FastaIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO.Interfaces: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO.MafIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO.MauveIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO.MsfIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO.NexusIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO.PhylipIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.AlignIO.StockholmIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Blast: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Blast.NCBIWWW: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Blast.NCBIXML: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Blast._parser: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Blast._writers: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.CAPS: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Cluster: cannot import name '_cluster' from partially initialized module 'Bio.Cluster' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Cluster/__init__.py) ====================================================================== FAIL: Entrez (Bio) Doctest: Bio.Entrez ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Entrez File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 11, in Entrez ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 104, in Bio.Entrez Failed example: handle = Entrez.einfo() # or esearch, efetch, ... Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle = Entrez.einfo() # or esearch, efetch, ... ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 312, in einfo return _open(request) ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 634, in _open handle = urlopen(request) ^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 105, in Bio.Entrez Failed example: record = Entrez.read(handle) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = Entrez.read(handle) ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 106, in Bio.Entrez Failed example: handle.close() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle.close() ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 114, in Bio.Entrez Failed example: handle = Entrez.esummary(db="pubmed", id="19304878,14630660", retmode="xml") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle = Entrez.esummary(db="pubmed", id="19304878,14630660", retmode="xml") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 345, in esummary return _open(request) ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 634, in _open handle = urlopen(request) ^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 115, in Bio.Entrez Failed example: records = Entrez.parse(handle) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in records = Entrez.parse(handle) ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 116, in Bio.Entrez Failed example: for record in records: # each record is a Python dictionary or list. print(record['Title']) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in for record in records: ^^^^^^^ NameError: name 'records' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 121, in Bio.Entrez Failed example: handle.close() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle.close() ^^^^^^ NameError: name 'handle' is not defined ====================================================================== FAIL: ecitmatch (Bio.Entrez) Doctest: Bio.Entrez.ecitmatch ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Entrez.ecitmatch File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 444, in ecitmatch ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 460, in Bio.Entrez.ecitmatch Failed example: handle = Entrez.ecitmatch(db="pubmed", bdata=[citation_1]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle = Entrez.ecitmatch(db="pubmed", bdata=[citation_1]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 471, in ecitmatch return _open(request) ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 634, in _open handle = urlopen(request) ^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 461, in Bio.Entrez.ecitmatch Failed example: print(handle.read().strip().split("|")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(handle.read().strip().split("|")) ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 463, in Bio.Entrez.ecitmatch Failed example: handle.close() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle.close() ^^^^^^ NameError: name 'handle' is not defined ====================================================================== FAIL: efetch (Bio.Entrez) Doctest: Bio.Entrez.efetch ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Entrez.efetch File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 170, in efetch ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 183, in Bio.Entrez.efetch Failed example: handle = Entrez.efetch(db="nucleotide", id="AY851612", rettype="gb", retmode="text") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle = Entrez.efetch(db="nucleotide", id="AY851612", rettype="gb", retmode="text") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 201, in efetch return _open(request) ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 634, in _open handle = urlopen(request) ^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 184, in Bio.Entrez.efetch Failed example: print(handle.readline().strip()) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(handle.readline().strip()) ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 186, in Bio.Entrez.efetch Failed example: handle.close() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle.close() ^^^^^^ NameError: name 'handle' is not defined ====================================================================== FAIL: einfo (Bio.Entrez) Doctest: Bio.Entrez.einfo ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Entrez.einfo File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 288, in einfo ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 301, in Bio.Entrez.einfo Failed example: record = Entrez.read(Entrez.einfo()) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = Entrez.read(Entrez.einfo()) ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 312, in einfo return _open(request) ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 634, in _open handle = urlopen(request) ^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 302, in Bio.Entrez.einfo Failed example: 'pubmed' in record['DbList'] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in 'pubmed' in record['DbList'] ^^^^^^ NameError: name 'record' is not defined ====================================================================== FAIL: elink (Bio.Entrez) Doctest: Bio.Entrez.elink ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Entrez.elink File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 242, in elink ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 267, in Bio.Entrez.elink Failed example: handle = Entrez.elink(dbfrom="pubmed", id=pmid, linkname="pubmed_pubmed") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle = Entrez.elink(dbfrom="pubmed", id=pmid, linkname="pubmed_pubmed") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 285, in elink return _open(request) ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 634, in _open handle = urlopen(request) ^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 268, in Bio.Entrez.elink Failed example: record = Entrez.read(handle) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = Entrez.read(handle) ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 269, in Bio.Entrez.elink Failed example: handle.close() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle.close() ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 270, in Bio.Entrez.elink Failed example: print(record[0]["LinkSetDb"][0]["LinkName"]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record[0]["LinkSetDb"][0]["LinkName"]) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 272, in Bio.Entrez.elink Failed example: linked = [link["Id"] for link in record[0]["LinkSetDb"][0]["Link"]] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in linked = [link["Id"] for link in record[0]["LinkSetDb"][0]["Link"]] ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 273, in Bio.Entrez.elink Failed example: "14630660" in linked Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in "14630660" in linked ^^^^^^ NameError: name 'linked' is not defined ====================================================================== FAIL: esearch (Bio.Entrez) Doctest: Bio.Entrez.esearch ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Entrez.esearch File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 204, in esearch ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 218, in Bio.Entrez.esearch Failed example: handle = Entrez.esearch( db="nucleotide", retmax=10, idtype="acc", term="opuntia[ORGN] accD 2007[Publication Date]" ) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle = Entrez.esearch( ^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 239, in esearch return _open(request) ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 634, in _open handle = urlopen(request) ^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 223, in Bio.Entrez.esearch Failed example: record = Entrez.read(handle) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = Entrez.read(handle) ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 224, in Bio.Entrez.esearch Failed example: handle.close() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle.close() ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 225, in Bio.Entrez.esearch Failed example: int(record["Count"]) >= 2 Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in int(record["Count"]) >= 2 ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 227, in Bio.Entrez.esearch Failed example: "EF590893.1" in record["IdList"] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in "EF590893.1" in record["IdList"] ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 229, in Bio.Entrez.esearch Failed example: "EF590892.1" in record["IdList"] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in "EF590892.1" in record["IdList"] ^^^^^^ NameError: name 'record' is not defined ====================================================================== FAIL: espell (Bio.Entrez) Doctest: Bio.Entrez.espell ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Entrez.espell File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 388, in espell ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 400, in Bio.Entrez.espell Failed example: record = Entrez.read(Entrez.espell(term="biopythooon")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = Entrez.read(Entrez.espell(term="biopythooon")) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 413, in espell return _open(request) ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 634, in _open handle = urlopen(request) ^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 401, in Bio.Entrez.espell Failed example: print(record["Query"]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record["Query"]) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 403, in Bio.Entrez.espell Failed example: print(record["CorrectedQuery"]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record["CorrectedQuery"]) ^^^^^^ NameError: name 'record' is not defined ====================================================================== FAIL: esummary (Bio.Entrez) Doctest: Bio.Entrez.esummary ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Entrez.esummary File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 315, in esummary ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 329, in Bio.Entrez.esummary Failed example: handle = Entrez.esummary(db="structure", id="19923") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle = Entrez.esummary(db="structure", id="19923") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 345, in esummary return _open(request) ^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 634, in _open handle = urlopen(request) ^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 330, in Bio.Entrez.esummary Failed example: record = Entrez.read(handle) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = Entrez.read(handle) ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 331, in Bio.Entrez.esummary Failed example: handle.close() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle.close() ^^^^^^ NameError: name 'handle' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 332, in Bio.Entrez.esummary Failed example: print(record[0]["Id"]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record[0]["Id"]) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 334, in Bio.Entrez.esummary Failed example: print(record[0]["PdbDescr"]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record[0]["PdbDescr"]) ^^^^^^ NameError: name 'record' is not defined ====================================================================== FAIL: parse (Bio.Entrez) Doctest: Bio.Entrez.parse ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Entrez.parse File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 533, in parse ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 558, in Bio.Entrez.parse Failed example: for record in records: print(record['MedlineCitation']['Article']['Journal']['Title']) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in for record in records: File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 470, in parse self.parser.Parse(data, False) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_080101.dtd' ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 568, in Bio.Entrez.parse Failed example: for record in records: print(record['MedlineCitation']['Article']['Journal']['Title']) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in for record in records: File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 470, in parse self.parser.Parse(data, False) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_080101.dtd' ====================================================================== FAIL: read (Bio.Entrez) Doctest: Bio.Entrez.read ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Entrez.read File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 474, in read ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 492, in Bio.Entrez.read Failed example: record = Entrez.read(stream) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = Entrez.read(stream) ^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd' ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 493, in Bio.Entrez.read Failed example: print(record['QueryTranslation']) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record['QueryTranslation']) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 499, in Bio.Entrez.read Failed example: record = Entrez.read(path) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = Entrez.read(path) ^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 529, in read record = handler.read(source) ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 406, in read self.parser.ParseFile(stream) File "/builddir/build/BUILD/Python-3.11.6/Modules/pyexpat.c", line 659, in ExternalEntityRef File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1141, in externalEntityRefHandler self.verify_security(url, verify_hostname=not self.dtd_urls) File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/Parser.py", line 1110, in verify_security raise ValueError(f"Expected secure URL to NCBI, found {url!r}") ValueError: Expected secure URL to NCBI, found 'http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd' ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Entrez/__init__.py", line 500, in Bio.Entrez.read Failed example: print(record['QueryTranslation']) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record['QueryTranslation']) ^^^^^^ NameError: name 'record' is not defined ====================================================================== FAIL: get_prodoc_entry (Bio.ExPASy) Doctest: Bio.ExPASy.get_prodoc_entry ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.ExPASy.get_prodoc_entry File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 26, in get_prodoc_entry ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 31, in Bio.ExPASy.get_prodoc_entry Failed example: with ExPASy.get_prodoc_entry('PDOC00001') as in_handle: html = in_handle.read() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in with ExPASy.get_prodoc_entry('PDOC00001') as in_handle: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 42, in get_prodoc_entry return _open(f"{cgi}?{id}") ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 135, in _open handle = urlopen(url) ^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 34, in Bio.ExPASy.get_prodoc_entry Failed example: with open("myprodocrecord.html", "w") as out_handle: length = out_handle.write(html) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 2, in length = out_handle.write(html) ^^^^ NameError: name 'html' is not defined ====================================================================== FAIL: get_prosite_entry (Bio.ExPASy) Doctest: Bio.ExPASy.get_prosite_entry ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.ExPASy.get_prosite_entry File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 47, in get_prosite_entry ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 52, in Bio.ExPASy.get_prosite_entry Failed example: with ExPASy.get_prosite_entry('PS00001') as in_handle: html = in_handle.read() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in with ExPASy.get_prosite_entry('PS00001') as in_handle: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 63, in get_prosite_entry return _open(f"{cgi}?{id}") ^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 135, in _open handle = urlopen(url) ^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 55, in Bio.ExPASy.get_prosite_entry Failed example: with open("myprositerecord.html", "w") as out_handle: length = out_handle.write(html) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 2, in length = out_handle.write(html) ^^^^ NameError: name 'html' is not defined ====================================================================== FAIL: get_prosite_raw (Bio.ExPASy) Doctest: Bio.ExPASy.get_prosite_raw ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.ExPASy.get_prosite_raw File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 66, in get_prosite_raw ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 74, in Bio.ExPASy.get_prosite_raw Failed example: with ExPASy.get_prosite_raw('PS00001') as handle: record = Prosite.read(handle) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in with ExPASy.get_prosite_raw('PS00001') as handle: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 89, in get_prosite_raw handle = _open(f"https://prosite.expasy.org/{id}.txt") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 135, in _open handle = urlopen(url) ^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 77, in Bio.ExPASy.get_prosite_raw Failed example: print(record.accession) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.accession) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 82, in Bio.ExPASy.get_prosite_raw Failed example: handle = ExPASy.get_prosite_raw("DOES_NOT_EXIST") Expected: Traceback (most recent call last): ... ValueError: Failed to find entry 'DOES_NOT_EXIST' on ExPASy Got: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in handle = ExPASy.get_prosite_raw("DOES_NOT_EXIST") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 89, in get_prosite_raw handle = _open(f"https://prosite.expasy.org/{id}.txt") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 135, in _open handle = urlopen(url) ^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ====================================================================== FAIL: get_sprot_raw (Bio.ExPASy) Doctest: Bio.ExPASy.get_sprot_raw ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.ExPASy.get_sprot_raw File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 101, in get_sprot_raw ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 109, in Bio.ExPASy.get_sprot_raw Failed example: with ExPASy.get_sprot_raw("O23729") as handle: record = SwissProt.read(handle) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in with ExPASy.get_sprot_raw("O23729") as handle: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 124, in get_sprot_raw handle = _open(f"http://www.uniprot.org/uniprot/{id}.txt") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 135, in _open handle = urlopen(url) ^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1377, in http_open return self.do_open(http.client.HTTPConnection, req) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 112, in Bio.ExPASy.get_sprot_raw Failed example: print(record.entry_name) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.entry_name) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 117, in Bio.ExPASy.get_sprot_raw Failed example: ExPASy.get_sprot_raw("DOES_NOT_EXIST") Expected: Traceback (most recent call last): ... ValueError: Failed to find SwissProt entry 'DOES_NOT_EXIST' Got: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in ExPASy.get_sprot_raw("DOES_NOT_EXIST") File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 124, in get_sprot_raw handle = _open(f"http://www.uniprot.org/uniprot/{id}.txt") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/__init__.py", line 135, in _open handle = urlopen(url) ^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1377, in http_open return self.do_open(http.client.HTTPConnection, req) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ====================================================================== FAIL: cellosaurus (Bio.ExPASy) Doctest: Bio.ExPASy.cellosaurus ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.ExPASy.cellosaurus File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/cellosaurus.py", line 5, in cellosaurus ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/cellosaurus.py", line 31, in Bio.ExPASy.cellosaurus Failed example: bytestream = urlopen(url) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1555, in ftp_open host = socket.gethostbyname(host) ^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in bytestream = urlopen(url) ^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1557, in ftp_open raise URLError(msg) urllib.error.URLError: ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/cellosaurus.py", line 32, in Bio.ExPASy.cellosaurus Failed example: textstream = TextIOWrapper(bytestream, "UTF-8") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in textstream = TextIOWrapper(bytestream, "UTF-8") ^^^^^^^^^^ NameError: name 'bytestream' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/cellosaurus.py", line 36, in Bio.ExPASy.cellosaurus Failed example: records = cellosaurus.parse(textstream) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in records = cellosaurus.parse(textstream) ^^^^^^^^^^ NameError: name 'textstream' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/ExPASy/cellosaurus.py", line 37, in Bio.ExPASy.cellosaurus Failed example: for record in records: if 'Homo sapiens' in record['OX'][0]: print(record['ID']) # doctest:+ELLIPSIS Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in for record in records: ^^^^^^^ NameError: name 'records' is not defined ERROR while importing Bio.PDB: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.AbstractPropertyMap: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.Chain: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.DSSP: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.Dice: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.FragmentMapper: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.HSExposure: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.MMCIF2Dict: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.MMCIFParser: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.Model: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.NACCESS: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.NeighborSearch: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.PDBIO: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.PDBList: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.PDBMLParser: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.PDBParser: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.PICIO: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.PSEA: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.Polypeptide: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.ResidueDepth: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.SASA: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.SCADIO: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.Structure: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.StructureAlignment: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.StructureBuilder: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.Superimposer: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.alphafold_db: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.binary_cif: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.cealign: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.ic_data: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.ic_rebuild: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.internal_coords: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.mmcifio: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.mmtf: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.mmtf.DefaultParser: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.mmtf.mmtfio: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.parse_pdb_header: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.PDB.qcprot: No module named 'Bio.PDB.ccealign' ERROR while importing Bio.Phylo: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ====================================================================== FAIL: collapse_all (Bio.Phylo.BaseTree.TreeMixin) Doctest: Bio.Phylo.BaseTree.TreeMixin.collapse_all ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Phylo.BaseTree.TreeMixin.collapse_all File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 600, in collapse_all ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 609, in Bio.Phylo.BaseTree.TreeMixin.collapse_all Failed example: from Bio import Phylo Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import Phylo File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 610, in Bio.Phylo.BaseTree.TreeMixin.collapse_all Failed example: tree = Phylo.read('PhyloXML/apaf.xml', 'phyloxml') Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in tree = Phylo.read('PhyloXML/apaf.xml', 'phyloxml') ^^^^^ NameError: name 'Phylo' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 611, in Bio.Phylo.BaseTree.TreeMixin.collapse_all Failed example: print("Total branch length %0.2f" % tree.total_branch_length()) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("Total branch length %0.2f" % tree.total_branch_length()) ^^^^ NameError: name 'tree' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 613, in Bio.Phylo.BaseTree.TreeMixin.collapse_all Failed example: tree.collapse_all(lambda c: c.confidence is not None and c.confidence < 70) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in tree.collapse_all(lambda c: c.confidence is not None and c.confidence < 70) ^^^^ NameError: name 'tree' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 614, in Bio.Phylo.BaseTree.TreeMixin.collapse_all Failed example: print("Total branch length %0.2f" % tree.total_branch_length()) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("Total branch length %0.2f" % tree.total_branch_length()) ^^^^ NameError: name 'tree' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 623, in Bio.Phylo.BaseTree.TreeMixin.collapse_all Failed example: from Bio import Phylo Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import Phylo File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 624, in Bio.Phylo.BaseTree.TreeMixin.collapse_all Failed example: tree = Phylo.read('PhyloXML/apaf.xml', 'phyloxml') Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in tree = Phylo.read('PhyloXML/apaf.xml', 'phyloxml') ^^^^^ NameError: name 'Phylo' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 625, in Bio.Phylo.BaseTree.TreeMixin.collapse_all Failed example: print("Total branch length %0.2f" % tree.total_branch_length()) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("Total branch length %0.2f" % tree.total_branch_length()) ^^^^ NameError: name 'tree' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 627, in Bio.Phylo.BaseTree.TreeMixin.collapse_all Failed example: tree.collapse_all(lambda c: c.branch_length < 0.1) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in tree.collapse_all(lambda c: c.branch_length < 0.1) ^^^^ NameError: name 'tree' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 628, in Bio.Phylo.BaseTree.TreeMixin.collapse_all Failed example: print("Total branch length %0.2f" % tree.total_branch_length()) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("Total branch length %0.2f" % tree.total_branch_length()) ^^^^ NameError: name 'tree' is not defined ====================================================================== FAIL: find_elements (Bio.Phylo.BaseTree.TreeMixin) Doctest: Bio.Phylo.BaseTree.TreeMixin.find_elements ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.Phylo.BaseTree.TreeMixin.find_elements File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 307, in find_elements ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 341, in Bio.Phylo.BaseTree.TreeMixin.find_elements Failed example: from Bio import Phylo Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import Phylo File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/__init__.py", line 14, in from Bio.Phylo._io import convert File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/_io.py", line 19, in from Bio.Phylo import PhyloXMLIO File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXMLIO.py", line 24, in from Bio.Phylo import PhyloXML as PX File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/PhyloXML.py", line 23, in from Bio.Align import Alignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 342, in Bio.Phylo.BaseTree.TreeMixin.find_elements Failed example: phx = Phylo.PhyloXMLIO.read('PhyloXML/phyloxml_examples.xml') Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in phx = Phylo.PhyloXMLIO.read('PhyloXML/phyloxml_examples.xml') ^^^^^ NameError: name 'Phylo' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 343, in Bio.Phylo.BaseTree.TreeMixin.find_elements Failed example: matches = phx.phylogenies[5].find_elements(code='OCTVU') Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in matches = phx.phylogenies[5].find_elements(code='OCTVU') ^^^ NameError: name 'phx' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/Phylo/BaseTree.py", line 344, in Bio.Phylo.BaseTree.TreeMixin.find_elements Failed example: next(matches) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in next(matches) ^^^^^^^ NameError: name 'matches' is not defined ERROR while importing Bio.Phylo.CDAO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.CDAOIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.Consensus: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PAML: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PAML._paml: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PAML._parse_baseml: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PAML._parse_codeml: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PAML._parse_yn00: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PAML.baseml: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PAML.chi2: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PAML.codeml: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PAML.yn00: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PhyloXML: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.PhyloXMLIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo.TreeConstruction: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo._io: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.Phylo._utils: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SCOP: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SCOP.Cla: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SCOP.Des: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SCOP.Dom: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SCOP.Hie: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SCOP.Raf: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SCOP.Residues: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.BlastIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.BlastIO.blast_tab: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.BlastIO.blast_xml: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.BlatIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.ExonerateIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.ExonerateIO._base: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.ExonerateIO.exonerate_cigar: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.ExonerateIO.exonerate_text: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.ExonerateIO.exonerate_vulgar: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.FastaIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.HHsuiteIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.HHsuiteIO.hhsuite2_text: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.HmmerIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.HmmerIO._base: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.HmmerIO.hmmer2_text: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.HmmerIO.hmmer3_domtab: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.HmmerIO.hmmer3_tab: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.HmmerIO.hmmer3_text: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.InfernalIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.InfernalIO._base: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.InfernalIO.infernal_tab: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.InfernalIO.infernal_text: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.InterproscanIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO.InterproscanIO.interproscan_xml: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO._index: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO._model: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO._model.hit: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO._model.hsp: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SearchIO._model.query: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ====================================================================== FAIL: __contains__ (Bio.SeqFeature.SeqFeature) Doctest: Bio.SeqFeature.SeqFeature.__contains__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqFeature.SeqFeature.__contains__ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqFeature.py", line 494, in __contains__ ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqFeature.py", line 507, in Bio.SeqFeature.SeqFeature.__contains__ Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqFeature.py", line 508, in Bio.SeqFeature.SeqFeature.__contains__ Failed example: record = SeqIO.read("GenBank/NC_000932.gb", "gb") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = SeqIO.read("GenBank/NC_000932.gb", "gb") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqFeature.py", line 509, in Bio.SeqFeature.SeqFeature.__contains__ Failed example: for f in record.features: if 1750 in f: print("%s %s" % (f.type, f.location)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in for f in record.features: ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqFeature.py", line 522, in Bio.SeqFeature.SeqFeature.__contains__ Failed example: for f in record.features: if 1760 in f: print("%s %s" % (f.type, f.location)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in for f in record.features: ^^^^^^ NameError: name 'record' is not defined ERROR while importing Bio.SeqIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.AbiIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.AceIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.FastaIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.GckIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.GfaIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.IgIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.InsdcIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.Interfaces: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.NibIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.PdbIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.PhdIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.PirIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.QualityIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.SeqXmlIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.SffIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.SnapGeneIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.SwissIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.TabIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.TwoBitIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.UniprotIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO.XdnaIO: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.SeqIO._index: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ====================================================================== FAIL: SeqRecord (Bio.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 114, in SeqRecord ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 156, in Bio.SeqRecord.SeqRecord Failed example: print(record.format("fasta")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.format("fasta")) ^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 819, in format return self.__format__(format) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 848, in __format__ from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ====================================================================== FAIL: __add__ (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.__add__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.__add__ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 914, in __add__ ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 923, in Bio.SeqRecord.SeqRecord.__add__ Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 924, in Bio.SeqRecord.SeqRecord.__add__ Failed example: record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 925, in Bio.SeqRecord.SeqRecord.__add__ Failed example: print("%s %s" % (record.id, record.seq)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %s" % (record.id, record.seq)) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 927, in Bio.SeqRecord.SeqRecord.__add__ Failed example: print(list(record.letter_annotations)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(list(record.letter_annotations)) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 930, in Bio.SeqRecord.SeqRecord.__add__ Failed example: new = record + "ACT" Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new = record + "ACT" ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 931, in Bio.SeqRecord.SeqRecord.__add__ Failed example: print("%s %s" % (new.id, new.seq)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %s" % (new.id, new.seq)) ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 933, in Bio.SeqRecord.SeqRecord.__add__ Failed example: print(list(new.letter_annotations)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(list(new.letter_annotations)) ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 940, in Bio.SeqRecord.SeqRecord.__add__ Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 941, in Bio.SeqRecord.SeqRecord.__add__ Failed example: with open("GenBank/pBAD30.gb") as handle: plasmid = SeqIO.read(handle, "gb") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 2, in plasmid = SeqIO.read(handle, "gb") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 943, in Bio.SeqRecord.SeqRecord.__add__ Failed example: print("%s %i" % (plasmid.id, len(plasmid))) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %i" % (plasmid.id, len(plasmid))) ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 951, in Bio.SeqRecord.SeqRecord.__add__ Failed example: left = plasmid[:3765] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in left = plasmid[:3765] ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 952, in Bio.SeqRecord.SeqRecord.__add__ Failed example: right = plasmid[3765:] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in right = plasmid[3765:] ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 953, in Bio.SeqRecord.SeqRecord.__add__ Failed example: new = right + left Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new = right + left ^^^^^ NameError: name 'right' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 954, in Bio.SeqRecord.SeqRecord.__add__ Failed example: print("%s %i" % (new.id, len(new))) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %i" % (new.id, len(new))) ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 956, in Bio.SeqRecord.SeqRecord.__add__ Failed example: str(new.seq) == str(right.seq + left.seq) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in str(new.seq) == str(right.seq + left.seq) ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 958, in Bio.SeqRecord.SeqRecord.__add__ Failed example: len(new.features) == len(left.features) + len(right.features) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(new.features) == len(left.features) + len(right.features) ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 964, in Bio.SeqRecord.SeqRecord.__add__ Failed example: new.id == left.id == right.id == plasmid.id Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new.id == left.id == right.id == plasmid.id ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 966, in Bio.SeqRecord.SeqRecord.__add__ Failed example: new.name == left.name == right.name == plasmid.name Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new.name == left.name == right.name == plasmid.name ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 968, in Bio.SeqRecord.SeqRecord.__add__ Failed example: new.description == plasmid.description Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new.description == plasmid.description ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 970, in Bio.SeqRecord.SeqRecord.__add__ Failed example: new.annotations == left.annotations == right.annotations Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new.annotations == left.annotations == right.annotations ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 972, in Bio.SeqRecord.SeqRecord.__add__ Failed example: new.letter_annotations == plasmid.letter_annotations Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new.letter_annotations == plasmid.letter_annotations ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 974, in Bio.SeqRecord.SeqRecord.__add__ Failed example: new.dbxrefs == left.dbxrefs == right.dbxrefs Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new.dbxrefs == left.dbxrefs == right.dbxrefs ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 981, in Bio.SeqRecord.SeqRecord.__add__ Failed example: new.annotations = plasmid.annotations.copy() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new.annotations = plasmid.annotations.copy() ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 982, in Bio.SeqRecord.SeqRecord.__add__ Failed example: new.dbxrefs = plasmid.dbxrefs[:] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new.dbxrefs = plasmid.dbxrefs[:] ^^^^^^^ NameError: name 'plasmid' is not defined ====================================================================== FAIL: __contains__ (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.__contains__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.__contains__ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 660, in __contains__ ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 665, in Bio.SeqRecord.SeqRecord.__contains__ Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 666, in Bio.SeqRecord.SeqRecord.__contains__ Failed example: record = SeqIO.read("Fasta/sweetpea.nu", "fasta") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = SeqIO.read("Fasta/sweetpea.nu", "fasta") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 667, in Bio.SeqRecord.SeqRecord.__contains__ Failed example: "GAATTC" in record Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in "GAATTC" in record ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 669, in Bio.SeqRecord.SeqRecord.__contains__ Failed example: "AAA" in record Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in "AAA" in record ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 674, in Bio.SeqRecord.SeqRecord.__contains__ Failed example: "GAATTC" in record.seq Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in "GAATTC" in record.seq ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 676, in Bio.SeqRecord.SeqRecord.__contains__ Failed example: "AAA" in record.seq Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in "AAA" in record.seq ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 682, in Bio.SeqRecord.SeqRecord.__contains__ Failed example: Seq("AAA") in record Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in Seq("AAA") in record ^^^^^^ NameError: name 'record' is not defined ====================================================================== FAIL: __format__ (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.__format__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.__format__ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 821, in __format__ ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 835, in Bio.SeqRecord.SeqRecord.__format__ Failed example: format(record, "fasta") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in format(record, "fasta") File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 848, in __format__ from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 837, in Bio.SeqRecord.SeqRecord.__format__ Failed example: print(f"Here is {record.id} in FASTA format:\n{record:fasta}") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(f"Here is {record.id} in FASTA format:\n{record:fasta}") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 848, in __format__ from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ====================================================================== FAIL: __iter__ (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.__iter__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.__iter__ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 604, in __iter__ ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 609, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 610, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: record = SeqIO.read("Fasta/loveliesbleeding.pro", "fasta") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = SeqIO.read("Fasta/loveliesbleeding.pro", "fasta") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 611, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: for amino in record: print(amino) if amino == "L": break Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in for amino in record: ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 618, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: print(record.seq[3]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.seq[3]) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 623, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: for amino in record.seq: print(amino) if amino == "L": break Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in for amino in record.seq: ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 630, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: print(record.seq[3]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.seq[3]) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 638, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 639, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: rec = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in rec = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 640, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: print("%s %s" % (rec.id, rec.seq)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %s" % (rec.id, rec.seq)) ^^^ NameError: name 'rec' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 642, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: print(list(rec.letter_annotations)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(list(rec.letter_annotations)) ^^^ NameError: name 'rec' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 644, in Bio.SeqRecord.SeqRecord.__iter__ Failed example: for nuc, qual in zip(rec, rec.letter_annotations["solexa_quality"]): if qual > 35: print("%s %i" % (nuc, qual)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in for nuc, qual in zip(rec, rec.letter_annotations["solexa_quality"]): ^^^ NameError: name 'rec' is not defined ====================================================================== FAIL: __len__ (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.__len__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.__len__ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 859, in __len__ ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 864, in Bio.SeqRecord.SeqRecord.__len__ Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 865, in Bio.SeqRecord.SeqRecord.__len__ Failed example: record = SeqIO.read("Fasta/sweetpea.nu", "fasta") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = SeqIO.read("Fasta/sweetpea.nu", "fasta") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 866, in Bio.SeqRecord.SeqRecord.__len__ Failed example: len(record) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(record) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 868, in Bio.SeqRecord.SeqRecord.__len__ Failed example: len(record.seq) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(record.seq) ^^^^^^ NameError: name 'record' is not defined ====================================================================== FAIL: __radd__ (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.__radd__ ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.__radd__ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1040, in __radd__ ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1047, in Bio.SeqRecord.SeqRecord.__radd__ Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1048, in Bio.SeqRecord.SeqRecord.__radd__ Failed example: record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1049, in Bio.SeqRecord.SeqRecord.__radd__ Failed example: print("%s %s" % (record.id, record.seq)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %s" % (record.id, record.seq)) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1051, in Bio.SeqRecord.SeqRecord.__radd__ Failed example: print(list(record.letter_annotations)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(list(record.letter_annotations)) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1054, in Bio.SeqRecord.SeqRecord.__radd__ Failed example: new = "ACT" + record Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new = "ACT" + record ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1055, in Bio.SeqRecord.SeqRecord.__radd__ Failed example: print("%s %s" % (new.id, new.seq)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %s" % (new.id, new.seq)) ^^^ NameError: name 'new' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1057, in Bio.SeqRecord.SeqRecord.__radd__ Failed example: print(list(new.letter_annotations)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(list(new.letter_annotations)) ^^^ NameError: name 'new' is not defined ====================================================================== FAIL: format (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.format ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.format File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 789, in format ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 801, in Bio.SeqRecord.SeqRecord.format Failed example: record.format("fasta") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record.format("fasta") File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 819, in format return self.__format__(format) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 848, in __format__ from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 803, in Bio.SeqRecord.SeqRecord.format Failed example: print(record.format("fasta")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.format("fasta")) ^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 819, in format return self.__format__(format) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 848, in __format__ from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ====================================================================== FAIL: letter_annotations (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.letter_annotations ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.letter_annotations File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line unknown line number, in letter_annotations ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: print("%s %s" % (record.id, record.seq)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %s" % (record.id, record.seq)) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: print(list(record.letter_annotations)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(list(record.letter_annotations)) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: print(record.letter_annotations["solexa_quality"]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.letter_annotations["solexa_quality"]) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: sub_record = record[-10:] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in sub_record = record[-10:] ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: print("%s %s" % (sub_record.id, sub_record.seq)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %s" % (sub_record.id, sub_record.seq)) ^^^^^^^^^^ NameError: name 'sub_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: print(sub_record.letter_annotations["solexa_quality"]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(sub_record.letter_annotations["solexa_quality"]) ^^^^^^^^^^ NameError: name 'sub_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: len(sub_record.letter_annotations) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(sub_record.letter_annotations) ^^^^^^^^^^ NameError: name 'sub_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: sub_record.letter_annotations["dummy"] = "abcdefghij" Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in sub_record.letter_annotations["dummy"] = "abcdefghij" ^^^^^^^^^^ NameError: name 'sub_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: len(sub_record.letter_annotations) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(sub_record.letter_annotations) ^^^^^^^^^^ NameError: name 'sub_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: del sub_record.letter_annotations["solexa_quality"] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in del sub_record.letter_annotations["solexa_quality"] ^^^^^^^^^^ NameError: name 'sub_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: sub_record.letter_annotations Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in sub_record.letter_annotations ^^^^^^^^^^ NameError: name 'sub_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: sub_record.letter_annotations = {} Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in sub_record.letter_annotations = {} ^^^^^^^^^^ NameError: name 'sub_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line ?, in Bio.SeqRecord.SeqRecord.letter_annotations Failed example: sub_record.letter_annotations Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in sub_record.letter_annotations ^^^^^^^^^^ NameError: name 'sub_record' is not defined ====================================================================== FAIL: lower (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.lower ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.lower File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1137, in lower ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1142, in Bio.SeqRecord.SeqRecord.lower Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1143, in Bio.SeqRecord.SeqRecord.lower Failed example: record = SeqIO.read("Fasta/aster.pro", "fasta") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = SeqIO.read("Fasta/aster.pro", "fasta") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1144, in Bio.SeqRecord.SeqRecord.lower Failed example: print(record.format("fasta")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.format("fasta")) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1149, in Bio.SeqRecord.SeqRecord.lower Failed example: print(record.lower().format("fasta")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.lower().format("fasta")) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1157, in Bio.SeqRecord.SeqRecord.lower Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1158, in Bio.SeqRecord.SeqRecord.lower Failed example: old = SeqIO.read("EMBL/TRBG361.embl", "embl") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in old = SeqIO.read("EMBL/TRBG361.embl", "embl") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1159, in Bio.SeqRecord.SeqRecord.lower Failed example: len(old.features) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(old.features) ^^^ NameError: name 'old' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1161, in Bio.SeqRecord.SeqRecord.lower Failed example: new = old.lower() Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in new = old.lower() ^^^ NameError: name 'old' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1162, in Bio.SeqRecord.SeqRecord.lower Failed example: len(old.features) == len(new.features) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(old.features) == len(new.features) ^^^ NameError: name 'old' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1164, in Bio.SeqRecord.SeqRecord.lower Failed example: old.annotations["organism"] == new.annotations["organism"] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in old.annotations["organism"] == new.annotations["organism"] ^^^ NameError: name 'old' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1166, in Bio.SeqRecord.SeqRecord.lower Failed example: old.dbxrefs == new.dbxrefs Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in old.dbxrefs == new.dbxrefs ^^^ NameError: name 'old' is not defined ====================================================================== FAIL: reverse_complement (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.reverse_complement ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.reverse_complement File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1211, in reverse_complement ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1235, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1236, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1237, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print("%s %s" % (record.id, record.seq)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %s" % (record.id, record.seq)) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1239, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print(list(record.letter_annotations)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(list(record.letter_annotations)) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1241, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print(record.letter_annotations["solexa_quality"]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.letter_annotations["solexa_quality"]) ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1247, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: rc_record = record.reverse_complement(id=record.id + "_rc") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in rc_record = record.reverse_complement(id=record.id + "_rc") ^^^^^^ NameError: name 'record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1248, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print("%s %s" % (rc_record.id, rc_record.seq)) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %s" % (rc_record.id, rc_record.seq)) ^^^^^^^^^ NameError: name 'rc_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1254, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print(rc_record.letter_annotations["solexa_quality"]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(rc_record.letter_annotations["solexa_quality"]) ^^^^^^^^^ NameError: name 'rc_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1261, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1262, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: with open("GenBank/pBAD30.gb") as handle: plasmid = SeqIO.read(handle, "gb") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 2, in plasmid = SeqIO.read(handle, "gb") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1264, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print("%s %i" % (plasmid.id, len(plasmid))) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %i" % (plasmid.id, len(plasmid))) ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1266, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: plasmid.seq Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in plasmid.seq ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1268, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: len(plasmid.features) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(plasmid.features) ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1273, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: rc_plasmid = plasmid.reverse_complement(id=plasmid.id+"_rc") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in rc_plasmid = plasmid.reverse_complement(id=plasmid.id+"_rc") ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1274, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print("%s %i" % (rc_plasmid.id, len(rc_plasmid))) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print("%s %i" % (rc_plasmid.id, len(rc_plasmid))) ^^^^^^^^^^ NameError: name 'rc_plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1276, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: rc_plasmid.seq Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in rc_plasmid.seq ^^^^^^^^^^ NameError: name 'rc_plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1278, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: len(rc_plasmid.features) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(rc_plasmid.features) ^^^^^^^^^^ NameError: name 'rc_plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1285, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print(plasmid.features[1]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(plasmid.features[1]) ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1293, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print(rc_plasmid.features[-2]) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(rc_plasmid.features[-2]) ^^^^^^^^^^ NameError: name 'rc_plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1304, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: len(plasmid) - 1081 Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(plasmid) - 1081 ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1306, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: len(plasmid) - 1960 Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in len(plasmid) - 1960 ^^^^^^^ NameError: name 'plasmid' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1332, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print(rna1.reverse_complement(id="RC", description="unk").format("fasta")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(rna1.reverse_complement(id="RC", description="unk").format("fasta")) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 819, in format return self.__format__(format) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 848, in __format__ from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1336, in Bio.SeqRecord.SeqRecord.reverse_complement Failed example: print(rna2.reverse_complement(id="RC", description="RNA").format("fasta")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(rna2.reverse_complement(id="RC", description="RNA").format("fasta")) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 819, in format return self.__format__(format) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 848, in __format__ from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ====================================================================== FAIL: translate (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.translate ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.translate File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1437, in translate ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1459, in Bio.SeqRecord.SeqRecord.translate Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1460, in Bio.SeqRecord.SeqRecord.translate Failed example: gene_record = SeqIO.read("Fasta/sweetpea.nu", "fasta") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in gene_record = SeqIO.read("Fasta/sweetpea.nu", "fasta") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1461, in Bio.SeqRecord.SeqRecord.translate Failed example: print(gene_record.format("fasta")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(gene_record.format("fasta")) ^^^^^^^^^^^ NameError: name 'gene_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1473, in Bio.SeqRecord.SeqRecord.translate Failed example: protein_record = gene_record.translate(table=11, id="phya", description="translation") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in protein_record = gene_record.translate(table=11, ^^^^^^^^^^^ NameError: name 'gene_record' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1476, in Bio.SeqRecord.SeqRecord.translate Failed example: print(protein_record.format("fasta")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(protein_record.format("fasta")) ^^^^^^^^^^^^^^ NameError: name 'protein_record' is not defined ====================================================================== FAIL: upper (Bio.SeqRecord.SeqRecord) Doctest: Bio.SeqRecord.SeqRecord.upper ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.SeqRecord.SeqRecord.upper File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1092, in upper ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1102, in Bio.SeqRecord.SeqRecord.upper Failed example: print(record.upper().format("fastq")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.upper().format("fastq")) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 819, in format return self.__format__(format) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 848, in __format__ from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 1111, in Bio.SeqRecord.SeqRecord.upper Failed example: print(record.lower().format("fastq")) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.lower().format("fastq")) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 819, in format return self.__format__(format) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/SeqRecord.py", line 848, in __format__ from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ====================================================================== FAIL: search_iter (Bio.TogoWS) Doctest: Bio.TogoWS.search_iter ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.TogoWS.search_iter File "/builddir/build/BUILD/biopython-1.86/Bio/TogoWS/__init__.py", line 188, in search_iter ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/TogoWS/__init__.py", line 201, in Bio.TogoWS.search_iter Failed example: for id in TogoWS.search_iter("pubmed", "diabetes+human", limit=10): print("PubMed ID: %s" %id) # maybe fetch data with entry? Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in for id in TogoWS.search_iter("pubmed", "diabetes+human", limit=10): File "/builddir/build/BUILD/biopython-1.86/Bio/TogoWS/__init__.py", line 208, in search_iter count = search_count(db, query) ^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/TogoWS/__init__.py", line 166, in search_count _search_db_names = _get_fields(_BASE_URL + "/search") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/TogoWS/__init__.py", line 54, in _get_fields handle = _open(url) ^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/TogoWS/__init__.py", line 358, in _open handle = urlopen(url) ^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1377, in http_open return self.do_open(http.client.HTTPConnection, req) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ====================================================================== FAIL: search (Bio.UniProt) Doctest: Bio.UniProt.search ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.UniProt.search File "/builddir/build/BUILD/biopython-1.86/Bio/UniProt/__init__.py", line 119, in search ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/UniProt/__init__.py", line 130, in Bio.UniProt.search Failed example: results = UniProt.search("(organism_id:2697049) AND (reviewed:true)")[:10] Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/urllib/request.py", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/usr/lib64/python3.11/http/client.py", line 1306, in request self._send_request(method, url, body, headers, encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1352, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1301, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/usr/lib64/python3.11/http/client.py", line 1061, in _send_output self.send(msg) File "/usr/lib64/python3.11/http/client.py", line 999, in send self.connect() File "/usr/lib64/python3.11/http/client.py", line 1471, in connect super().connect() File "/usr/lib64/python3.11/http/client.py", line 965, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 844, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/socket.py", line 979, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in results = UniProt.search("(organism_id:2697049) AND (reviewed:true)")[:10] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/UniProt/__init__.py", line 150, in search return _UniProtSearchResults(url) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/UniProt/__init__.py", line 70, in __init__ response = self._fetch_next_batch() ^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILD/biopython-1.86/Bio/UniProt/__init__.py", line 61, in _fetch_next_batch with urlopen(self.next_url) as response: # type: ignore ^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1391, in https_open return self.do_open(http.client.HTTPSConnection, req, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.11/urllib/request.py", line 1351, in do_open raise URLError(err) urllib.error.URLError: ====================================================================== FAIL: bgzf (Bio) Doctest: Bio.bgzf ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for Bio.bgzf File "/builddir/build/BUILD/biopython-1.86/Bio/bgzf.py", line 8, in bgzf ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/bgzf.py", line 210, in Bio.bgzf Failed example: from Bio import SeqIO Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in from Bio import SeqIO File "/builddir/build/BUILD/biopython-1.86/Bio/SeqIO/__init__.py", line 384, in from Bio import AlignIO File "/builddir/build/BUILD/biopython-1.86/Bio/AlignIO/__init__.py", line 141, in from Bio.Align import MultipleSeqAlignment File "/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py", line 37, in from Bio.Align import _aligncore # type: ignore ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/bgzf.py", line 212, in Bio.bgzf Failed example: record = SeqIO.read(handle, "genbank") Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in record = SeqIO.read(handle, "genbank") ^^^^^ NameError: name 'SeqIO' is not defined ---------------------------------------------------------------------- File "/builddir/build/BUILD/biopython-1.86/Bio/bgzf.py", line 214, in Bio.bgzf Failed example: print(record.id) Exception raised: Traceback (most recent call last): File "/usr/lib64/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(record.id) ^^^^^^ NameError: name 'record' is not defined ERROR while importing Bio.codonalign: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.codonalign.codonalignment: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.codonalign.codonseq: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.alignace: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.clusterbuster: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.jaspar: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.jaspar.db: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.mast: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.matrix: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.meme: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.minimal: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.pfm: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.thresholds: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.transfac: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.motifs.xms: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ERROR while importing Bio.pairwise2: cannot import name '_aligncore' from partially initialized module 'Bio.Align' (most likely due to a circular import) (/builddir/build/BUILD/biopython-1.86/Bio/Align/__init__.py) ---------------------------------------------------------------------- Ran 505 tests in 565.514 seconds FAILED (failures = 351) Python version: 3.11.6 (main, Feb 28 2026, 00:00:00) [GCC 12.3.0 20230508 (Anolis OS 12.3.0-16)] Operating system: posix linux + RPM_EC=0 ++ jobs -p + exit 0 Processing files: python3-biopython-1.86-1.an23.loongarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Wj4Inj + umask 022 + cd /builddir/build/BUILD + cd biopython-1.86 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + cp -pr README.rst /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + cp -pr Tests/Blast/README.txt /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + cp -pr Tests/Blat/README.txt /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + cp -pr Tests/Exonerate/README.txt /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + cp -pr Tests/HHsuite/README.txt /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + cp -pr Tests/Hmmer/README.txt /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + cp -pr Tests/PAML/Control_files/README.txt /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + cp -pr Tests/Roche/README.txt /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + cp -pr Tests/SamBam/readme.txt /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/doc/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.84qGw4 + umask 022 + cd /builddir/build/BUILD + cd biopython-1.86 + LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/licenses/python3-biopython + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/licenses/python3-biopython + cp -pr LICENSE /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/licenses/python3-biopython + cp -pr LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64/usr/share/licenses/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 warning: File listed twice: /usr/share/doc/python3-biopython/README.txt warning: File listed twice: /usr/share/doc/python3-biopython/README.txt warning: File listed twice: /usr/share/doc/python3-biopython/README.txt warning: File listed twice: /usr/share/doc/python3-biopython/README.txt warning: File listed twice: /usr/share/doc/python3-biopython/README.txt warning: File listed twice: /usr/share/doc/python3-biopython/README.txt Provides: python-biopython = 1.86-1.an23 python3-biopython = 1.86-1.an23 python3-biopython(loongarch-64) = 1.86-1.an23 python3.11-biopython = 1.86-1.an23 python3.11dist(biopython) = 1.86 python3dist(biopython) = 1.86 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-loongarch-lp64d.so.1()(64bit) ld-linux-loongarch-lp64d.so.1(GLIBC_2.36)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.36)(64bit) python(abi) = 3.11 python3.11dist(numpy) rtld(GNU_HASH) Obsoletes: python-biopython < 1.86-1.an23 Processing files: python-biopython-debugsource-1.86-1.an23.loongarch64 Provides: python-biopython-debugsource = 1.86-1.an23 python-biopython-debugsource(loongarch-64) = 1.86-1.an23 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-biopython-debuginfo-1.86-1.an23.loongarch64 Provides: debuginfo(build-id) = 19bae2b067c7f10445c85a4626bc9c2063dc326d debuginfo(build-id) = 1b618ebcaef46fea139244b4bc48da964d59f7fd debuginfo(build-id) = 1d29e62f74ae1e91d8f18d381f2b72820ef17d2e debuginfo(build-id) = 24ffd7d3160e1e08273cdbf00d3f09959183b62e debuginfo(build-id) = 37710f74f38d4146d9467ee446f7ba4a8364105f debuginfo(build-id) = 3b420231c52965bb1a97b28b3167151da13ab097 debuginfo(build-id) = 5193ddcfb9b4e90b29a40f0808a3bf04c357df8e debuginfo(build-id) = 5218a30dcd80cdff5fae539419d4f164baf2bedf debuginfo(build-id) = 729116358a6970e7bdeaf2e6ae51299d8bc81344 debuginfo(build-id) = d3b2bf39bc99a5ca965d6fd9d91e0ef5bd657ade debuginfo(build-id) = e1c247282a51563430cbca73214bd910cf19b3ae debuginfo(build-id) = e5b2f78b51808bb9754e6d09beb4622b1d110034 debuginfo(build-id) = f9231d26e9c42f37447ef0210b85a630d3660276 python-biopython-debuginfo = 1.86-1.an23 python3-biopython-debuginfo = 1.86-1.an23 python3-biopython-debuginfo(loongarch-64) = 1.86-1.an23 python3.11-biopython-debuginfo = 1.86-1.an23 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-biopython-debugsource(loongarch-64) = 1.86-1.an23 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.86-1.an23.loongarch64 Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.86-1.an23.loongarch64.rpm Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.86-1.an23.loongarch64.rpm Wrote: /builddir/build/RPMS/python3-biopython-1.86-1.an23.loongarch64.rpm RPM build warnings: File listed twice: /usr/share/doc/python3-biopython/README.txt File listed twice: /usr/share/doc/python3-biopython/README.txt File listed twice: /usr/share/doc/python3-biopython/README.txt File listed twice: /usr/share/doc/python3-biopython/README.txt File listed twice: /usr/share/doc/python3-biopython/README.txt File listed twice: /usr/share/doc/python3-biopython/README.txt Child return code was: 0