Mock Version: 4.1
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1691026196.430821/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fbec302cd10>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.sz7janxt:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.sz7janxt:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'bc52e49e49fd4864b0ffff84a8eb6ddc', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1691026196.430821/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.sz7janxt:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1689897600
Wrote: /builddir/build/SRPMS/python-biopython-1.81-4.fc39.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1691026196.430821/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fbec302cd10>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.sz7janxt:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.sz7janxt:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'd41d567217504fd2bf2fb7e235e53efa', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1691026196.430821/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.sz7janxt:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1689897600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.fBUr6e
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf python-biopython-1.81
+ /usr/bin/mkdir -p python-biopython-1.81
+ cd python-biopython-1.81
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.81.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ rm -rf /builddir/build/BUILD/python-biopython-1.81-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/python-biopython-1.81-SPECPARTS
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ pushd biopython-1.81
~/build/BUILD/python-biopython-1.81/biopython-1.81 ~/build/BUILD/python-biopython-1.81
Patch #0 (python-biopython-fix_for_python312.patch):
+ echo 'Patch #0 (python-biopython-fix_for_python312.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0
patching file Tests/test_Entrez.py
Patch #1 (python-biopython-fix_compatibility_with_reportlab4.patch):
+ echo 'Patch #1 (python-biopython-fix_compatibility_with_reportlab4.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0
patching file Tests/test_GraphicsBitmaps.py
+ find Scripts -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec sed -i 's/\r//' '{}' ';'
+ find Bio -type f -exec chmod -x '{}' ';'
+ find Bio -type f -name '*.py' -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' '{}' ';'
+ popd
+ cp -a biopython-1.81 python3
~/build/BUILD/python-biopython-1.81
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.Yh4IEC
+ umask 022
+ cd /builddir/build/BUILD
~/build/BUILD/python-biopython-1.81/python3 ~/build/BUILD/python-biopython-1.81
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd python-biopython-1.81
+ pushd python3
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP'
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-312
creating build/lib.linux-x86_64-cpython-312/Bio
copying Bio/File.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/LogisticRegression.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/MarkovModel.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/MaxEntropy.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/NaiveBayes.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/Seq.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/SeqFeature.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/SeqRecord.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/_utils.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/bgzf.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/kNN.py -> build/lib.linux-x86_64-cpython-312/Bio
copying Bio/pairwise2.py -> build/lib.linux-x86_64-cpython-312/Bio
creating build/lib.linux-x86_64-cpython-312/Bio/Affy
copying Bio/Affy/CelFile.py -> build/lib.linux-x86_64-cpython-312/Bio/Affy
copying Bio/Affy/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Affy
creating build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/AlignInfo.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/a2m.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/bed.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/bigbed.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/bigmaf.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/bigpsl.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/clustal.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/emboss.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/exonerate.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/fasta.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/hhr.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/interfaces.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/maf.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/mauve.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/msf.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/nexus.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/phylip.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/psl.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/sam.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/stockholm.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
copying Bio/Align/tabular.py -> build/lib.linux-x86_64-cpython-312/Bio/Align
creating build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications
creating build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices
copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices
creating build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/MafIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/MauveIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/MsfIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO
creating build/lib.linux-x86_64-cpython-312/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Alphabet
creating build/lib.linux-x86_64-cpython-312/Bio/Application
copying Bio/Application/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Application
creating build/lib.linux-x86_64-cpython-312/Bio/Blast
copying Bio/Blast/Applications.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast
copying Bio/Blast/NCBIXML.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast
copying Bio/Blast/Record.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast
copying Bio/Blast/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast
creating build/lib.linux-x86_64-cpython-312/Bio/CAPS
copying Bio/CAPS/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/CAPS
creating build/lib.linux-x86_64-cpython-312/Bio/Cluster
copying Bio/Cluster/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Cluster
creating build/lib.linux-x86_64-cpython-312/Bio/codonalign
copying Bio/codonalign/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> build/lib.linux-x86_64-cpython-312/Bio/codonalign
copying Bio/codonalign/codonseq.py -> build/lib.linux-x86_64-cpython-312/Bio/codonalign
creating build/lib.linux-x86_64-cpython-312/Bio/Compass
copying Bio/Compass/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Compass
creating build/lib.linux-x86_64-cpython-312/Bio/Data
copying Bio/Data/CodonTable.py -> build/lib.linux-x86_64-cpython-312/Bio/Data
copying Bio/Data/IUPACData.py -> build/lib.linux-x86_64-cpython-312/Bio/Data
copying Bio/Data/PDBData.py -> build/lib.linux-x86_64-cpython-312/Bio/Data
copying Bio/Data/SCOPData.py -> build/lib.linux-x86_64-cpython-312/Bio/Data
copying Bio/Data/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Data
creating build/lib.linux-x86_64-cpython-312/Bio/Emboss
copying Bio/Emboss/Applications.py -> build/lib.linux-x86_64-cpython-312/Bio/Emboss
copying Bio/Emboss/Primer3.py -> build/lib.linux-x86_64-cpython-312/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-x86_64-cpython-312/Bio/Emboss
copying Bio/Emboss/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Emboss
creating build/lib.linux-x86_64-cpython-312/Bio/Entrez
copying Bio/Entrez/Parser.py -> build/lib.linux-x86_64-cpython-312/Bio/Entrez
copying Bio/Entrez/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Entrez
creating build/lib.linux-x86_64-cpython-312/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy
copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy
creating build/lib.linux-x86_64-cpython-312/Bio/GenBank
copying Bio/GenBank/Record.py -> build/lib.linux-x86_64-cpython-312/Bio/GenBank
copying Bio/GenBank/Scanner.py -> build/lib.linux-x86_64-cpython-312/Bio/GenBank
copying Bio/GenBank/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/GenBank
copying Bio/GenBank/utils.py -> build/lib.linux-x86_64-cpython-312/Bio/GenBank
creating build/lib.linux-x86_64-cpython-312/Bio/Geo
copying Bio/Geo/Record.py -> build/lib.linux-x86_64-cpython-312/Bio/Geo
copying Bio/Geo/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Geo
creating build/lib.linux-x86_64-cpython-312/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics
copying Bio/Graphics/Comparative.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics
copying Bio/Graphics/Distribution.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics
copying Bio/Graphics/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics
creating build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram
creating build/lib.linux-x86_64-cpython-312/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-x86_64-cpython-312/Bio/HMM
copying Bio/HMM/MarkovModel.py -> build/lib.linux-x86_64-cpython-312/Bio/HMM
copying Bio/HMM/Trainer.py -> build/lib.linux-x86_64-cpython-312/Bio/HMM
copying Bio/HMM/Utilities.py -> build/lib.linux-x86_64-cpython-312/Bio/HMM
copying Bio/HMM/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/HMM
creating build/lib.linux-x86_64-cpython-312/Bio/KEGG
copying Bio/KEGG/REST.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG
copying Bio/KEGG/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG
creating build/lib.linux-x86_64-cpython-312/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/Compound
creating build/lib.linux-x86_64-cpython-312/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/Enzyme
creating build/lib.linux-x86_64-cpython-312/Bio/KEGG/Gene
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creating build/lib.linux-x86_64-cpython-312/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/Map
creating build/lib.linux-x86_64-cpython-312/Bio/PDB
creating build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf
copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf
copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf
copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf
creating build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML
creating build/lib.linux-x86_64-cpython-312/Bio/Medline
copying Bio/Medline/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Medline
creating build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/alignace.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/clusterbuster.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/mast.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/matrix.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/meme.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/minimal.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/pfm.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/thresholds.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/transfac.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/motifs/xms.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs
creating build/lib.linux-x86_64-cpython-312/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs/applications
creating build/lib.linux-x86_64-cpython-312/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs/jaspar
creating build/lib.linux-x86_64-cpython-312/Bio/Nexus
copying Bio/Nexus/Nexus.py -> build/lib.linux-x86_64-cpython-312/Bio/Nexus
copying Bio/Nexus/Nodes.py -> build/lib.linux-x86_64-cpython-312/Bio/Nexus
copying Bio/Nexus/StandardData.py -> build/lib.linux-x86_64-cpython-312/Bio/Nexus
copying Bio/Nexus/Trees.py -> build/lib.linux-x86_64-cpython-312/Bio/Nexus
copying Bio/Nexus/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Nexus
creating build/lib.linux-x86_64-cpython-312/Bio/NMR
copying Bio/NMR/NOEtools.py -> build/lib.linux-x86_64-cpython-312/Bio/NMR
copying Bio/NMR/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/NMR
copying Bio/NMR/xpktools.py -> build/lib.linux-x86_64-cpython-312/Bio/NMR
creating build/lib.linux-x86_64-cpython-312/Bio/Pathway
copying Bio/Pathway/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Pathway
creating build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep
copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/Atom.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/Chain.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/DSSP.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/Dice.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/Entity.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/HSExposure.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/Model.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/NACCESS.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/PDBIO.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/PDBList.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/PDBParser.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/PICIO.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/PSEA.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/Polypeptide.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/Residue.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/SASA.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/SCADIO.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/Selection.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/Structure.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/StructureAlignment.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/Superimposer.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/cealign.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/ic_data.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/ic_rebuild.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/internal_coords.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/mmcifio.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/qcprot.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/vectors.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB
creating build/lib.linux-x86_64-cpython-312/Bio/phenotype
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copying Bio/phenotype/phen_micro.py -> build/lib.linux-x86_64-cpython-312/Bio/phenotype
copying Bio/phenotype/pm_fitting.py -> build/lib.linux-x86_64-cpython-312/Bio/phenotype
creating build/lib.linux-x86_64-cpython-312/Bio/PopGen
copying Bio/PopGen/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen
creating build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop
creating build/lib.linux-x86_64-cpython-312/Bio/Restriction
copying Bio/Restriction/PrintFormat.py -> build/lib.linux-x86_64-cpython-312/Bio/Restriction
copying Bio/Restriction/Restriction.py -> build/lib.linux-x86_64-cpython-312/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-x86_64-cpython-312/Bio/Restriction
copying Bio/Restriction/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Restriction
creating build/lib.linux-x86_64-cpython-312/Bio/SCOP
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copying Bio/SCOP/Des.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP
copying Bio/SCOP/Dom.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP
copying Bio/SCOP/Hie.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP
copying Bio/SCOP/Raf.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP
copying Bio/SCOP/Residues.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP
copying Bio/SCOP/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP
creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO
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copying Bio/SearchIO/FastaIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO
copying Bio/SearchIO/_index.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO
creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_legacy
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copying Bio/SearchIO/_legacy/ParserSupport.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_legacy
copying Bio/SearchIO/_legacy/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_legacy
creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model
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copying Bio/SearchIO/_model/_base.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hit.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model
copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model
copying Bio/SearchIO/_model/query.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model
creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO
creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HHsuiteIO
copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HHsuiteIO
creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO
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copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO
creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO
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copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO
creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/InterproscanIO
copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/InterproscanIO
creating build/lib.linux-x86_64-cpython-312/Bio/SeqIO
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copying Bio/SeqIO/AceIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/GckIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/Interfaces.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/NibIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/SwissIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
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copying Bio/SeqIO/_index.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
creating build/lib.linux-x86_64-cpython-312/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils
creating build/lib.linux-x86_64-cpython-312/Bio/Sequencing
copying Bio/Sequencing/Ace.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing
copying Bio/Sequencing/Phd.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing
creating build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications
creating build/lib.linux-x86_64-cpython-312/Bio/SVDSuperimposer
copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SVDSuperimposer
creating build/lib.linux-x86_64-cpython-312/Bio/PDB/QCPSuperimposer
copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB/QCPSuperimposer
creating build/lib.linux-x86_64-cpython-312/Bio/SwissProt
copying Bio/SwissProt/KeyWList.py -> build/lib.linux-x86_64-cpython-312/Bio/SwissProt
copying Bio/SwissProt/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SwissProt
creating build/lib.linux-x86_64-cpython-312/Bio/TogoWS
copying Bio/TogoWS/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/TogoWS
creating build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/BaseTree.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/CDAO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/CDAOIO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/Consensus.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/NeXML.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/Newick.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/NewickIO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/NexusIO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/PhyloXML.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/_io.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
copying Bio/Phylo/_utils.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo
creating build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications
creating build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML
copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML
copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML
creating build/lib.linux-x86_64-cpython-312/Bio/UniGene
copying Bio/UniGene/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/UniGene
creating build/lib.linux-x86_64-cpython-312/Bio/UniProt
copying Bio/UniProt/GOA.py -> build/lib.linux-x86_64-cpython-312/Bio/UniProt
copying Bio/UniProt/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/UniProt
creating build/lib.linux-x86_64-cpython-312/Bio/Wise
copying Bio/Wise/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Wise
copying Bio/Wise/dnal.py -> build/lib.linux-x86_64-cpython-312/Bio/Wise
copying Bio/Wise/psw.py -> build/lib.linux-x86_64-cpython-312/Bio/Wise
creating build/lib.linux-x86_64-cpython-312/BioSQL
copying BioSQL/__init__.py -> build/lib.linux-x86_64-cpython-312/BioSQL
copying BioSQL/Loader.py -> build/lib.linux-x86_64-cpython-312/BioSQL
copying BioSQL/DBUtils.py -> build/lib.linux-x86_64-cpython-312/BioSQL
copying BioSQL/BioSeqDatabase.py -> build/lib.linux-x86_64-cpython-312/BioSQL
copying BioSQL/BioSeq.py -> build/lib.linux-x86_64-cpython-312/BioSQL
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
/usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration.
!!
        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'Bio.Align.substitution_matrices.data' 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.data' 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.data' to be distributed and are
        already explicitly excluding 'Bio.Align.substitution_matrices.data' 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)
/usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration.
!!
        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'Bio.Entrez.DTDs' 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.Entrez.DTDs' 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.Entrez.DTDs' to be distributed and are
        already explicitly excluding 'Bio.Entrez.DTDs' 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)
/usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration.
!!
        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'Bio.Entrez.XSDs' 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.Entrez.XSDs' 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.Entrez.XSDs' to be distributed and are
        already explicitly excluding 'Bio.Entrez.XSDs' 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-x86_64-cpython-312/Bio
copying Bio/Align/_aligners.c -> build/lib.linux-x86_64-cpython-312/Bio/Align
creating build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data
copying Bio/Cluster/cluster.c -> build/lib.linux-x86_64-cpython-312/Bio/Cluster
copying Bio/Cluster/cluster.h -> build/lib.linux-x86_64-cpython-312/Bio/Cluster
copying Bio/Cluster/clustermodule.c -> build/lib.linux-x86_64-cpython-312/Bio/Cluster
creating build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs
creating build/lib.linux-x86_64-cpython-312/Bio/Entrez/XSDs
copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/XSDs
copying Bio/motifs/_pwm.c -> build/lib.linux-x86_64-cpython-312/Bio/motifs
copying Bio/Nexus/cnexus.c -> build/lib.linux-x86_64-cpython-312/Bio/Nexus
copying Bio/PDB/ccealignmodule.c -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/PDB/kdtrees.c -> build/lib.linux-x86_64-cpython-312/Bio/PDB
copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO
copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> build/lib.linux-x86_64-cpython-312/Bio/PDB/QCPSuperimposer
running build_ext
building 'Bio.Align._aligners' extension
creating build/temp.linux-x86_64-cpython-312
creating build/temp.linux-x86_64-cpython-312/Bio
creating build/temp.linux-x86_64-cpython-312/Bio/Align
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Align/_aligners.c -o build/temp.linux-x86_64-cpython-312/Bio/Align/_aligners.o
Bio/Align/_aligners.c: In function ‘Aligner_watermansmithbeyer_global_align_compare’:
Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized]
 5735 |         if (Ix_row) { \
      |            ^
Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here
 5405 |     double** Ix_row; \
      |              ^~~~~~
Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized]
 5737 |             if (Iy_row) { \
      |                ^
Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here
 5406 |     double** Iy_row; \
      |              ^~~~~~
Bio/Align/_aligners.c: In function ‘Aligner_watermansmithbeyer_local_align_compare’:
Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized]
 5737 |             if (Iy_row) { \
      |                ^
Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here
 5406 |     double** Iy_row; \
      |              ^~~~~~
Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized]
 5735 |         if (Ix_row) { \
      |            ^
Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here
 5405 |     double** Ix_row; \
      |              ^~~~~~
In function ‘Aligner_watermansmithbeyer_global_align_matrix’,
    inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6872:34:
Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized]
 5737 |             if (Iy_row) { \
      |                ^
Bio/Align/_aligners.c: In function ‘Aligner_align’:
Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here
 5406 |     double** Iy_row; \
      |              ^~~~~~
In function ‘Aligner_watermansmithbeyer_global_align_matrix’,
    inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6872:34:
Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized]
 5735 |         if (Ix_row) { \
      |            ^
Bio/Align/_aligners.c: In function ‘Aligner_align’:
Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here
 5405 |     double** Ix_row; \
      |              ^~~~~~
In function ‘Aligner_watermansmithbeyer_local_align_matrix’,
    inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6878:34:
Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized]
 5737 |             if (Iy_row) { \
      |                ^
Bio/Align/_aligners.c: In function ‘Aligner_align’:
Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here
 5406 |     double** Iy_row; \
      |              ^~~~~~
In function ‘Aligner_watermansmithbeyer_local_align_matrix’,
    inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6878:34:
Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized]
 5735 |         if (Ix_row) { \
      |            ^
Bio/Align/_aligners.c: In function ‘Aligner_align’:
Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here
 5405 |     double** Ix_row; \
      |              ^~~~~~
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/Align/_aligners.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/Align/_aligners.cpython-312-x86_64-linux-gnu.so
building 'Bio.cpairwise2' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/cpairwise2module.c -o build/temp.linux-x86_64-cpython-312/Bio/cpairwise2module.o
Bio/cpairwise2module.c: In function ‘_get_match_score’:
Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations]
   60 |     if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist)))
      |     ^~
In file included from /usr/include/python3.12/Python.h:95,
                 from Bio/cpairwise2module.c:16:
/usr/include/python3.12/ceval.h:27:43: note: declared here
   27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords(
      |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/cpairwise2.cpython-312-x86_64-linux-gnu.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-x86_64-cpython-312/Bio/Nexus
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Nexus/cnexus.c -o build/temp.linux-x86_64-cpython-312/Bio/Nexus/cnexus.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/Nexus/cnexus.cpython-312-x86_64-linux-gnu.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-x86_64-cpython-312/Bio/PDB
creating build/temp.linux-x86_64-cpython-312/Bio/PDB/QCPSuperimposer
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-x86_64-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-312-x86_64-linux-gnu.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-x86_64-cpython-312/Bio/motifs
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/motifs/_pwm.c -o build/temp.linux-x86_64-cpython-312/Bio/motifs/_pwm.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/motifs/_pwm.cpython-312-x86_64-linux-gnu.so
building 'Bio.Cluster._cluster' extension
creating build/temp.linux-x86_64-cpython-312/Bio/Cluster
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Cluster/cluster.c -o build/temp.linux-x86_64-cpython-312/Bio/Cluster/cluster.o
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Cluster/clustermodule.c -o build/temp.linux-x86_64-cpython-312/Bio/Cluster/clustermodule.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/Cluster/cluster.o build/temp.linux-x86_64-cpython-312/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/Cluster/_cluster.cpython-312-x86_64-linux-gnu.so
building 'Bio.PDB.kdtrees' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/PDB/kdtrees.c -o build/temp.linux-x86_64-cpython-312/Bio/PDB/kdtrees.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/PDB/kdtrees.cpython-312-x86_64-linux-gnu.so
building 'Bio.PDB.ccealign' extension
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-x86_64-cpython-312/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/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/PDB/ccealign.cpython-312-x86_64-linux-gnu.so
building 'Bio.SeqIO._twoBitIO' extension
creating build/temp.linux-x86_64-cpython-312/Bio/SeqIO
gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-x86_64-cpython-312/Bio/SeqIO/_twoBitIO.o
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/SeqIO/_twoBitIO.cpython-312-x86_64-linux-gnu.so
~/build/BUILD/python-biopython-1.81
+ popd
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.MZ6nxx
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64
++ dirname /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd python-biopython-1.81
+ pushd python3
~/build/BUILD/python-biopython-1.81/python3 ~/build/BUILD/python-biopython-1.81
+ /usr/bin/python3 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64 --install-data=/usr/share/python-biopython
running install
/usr/lib/python3.12/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, pypa/build or
        other standards-based tools.
        Follow the current Python packaging guidelines when building
        Python RPM packages.
        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html
        and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details.
        ********************************************************************************
!!
  self.initialize_options()
running install_lib
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL
copying build/lib.linux-x86_64-cpython-312/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL
copying build/lib.linux-x86_64-cpython-312/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL
copying build/lib.linux-x86_64-cpython-312/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL
copying build/lib.linux-x86_64-cpython-312/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL
copying build/lib.linux-x86_64-cpython-312/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/cpairwise2.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Wise
copying build/lib.linux-x86_64-cpython-312/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Wise
copying build/lib.linux-x86_64-cpython-312/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Wise
copying build/lib.linux-x86_64-cpython-312/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Wise
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/UniProt
copying build/lib.linux-x86_64-cpython-312/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/UniProt
copying build/lib.linux-x86_64-cpython-312/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/UniProt
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/UniGene
copying build/lib.linux-x86_64-cpython-312/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/UniGene
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/TogoWS
copying build/lib.linux-x86_64-cpython-312/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/TogoWS
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SwissProt
copying build/lib.linux-x86_64-cpython-312/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SwissProt
copying build/lib.linux-x86_64-cpython-312/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SwissProt
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SVDSuperimposer
copying build/lib.linux-x86_64-cpython-312/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SVDSuperimposer
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Sequencing
copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Sequencing
copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqUtils
copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqUtils
copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqUtils
copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqUtils
copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqUtils
copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqUtils
copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqUtils
copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqUtils
copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqUtils
copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqUtils
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/_twoBitIO.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/_twoBitIO.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/XdnaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/TwoBitIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/SnapGeneIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/NibIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/GckIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/InterproscanIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/InterproscanIO
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/HHsuiteIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HHsuiteIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/HHsuiteIO
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_legacy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_legacy/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_legacy/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO
copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SCOP
copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SCOP
copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SCOP
copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SCOP
copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SCOP
copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SCOP
copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SCOP
copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SCOP
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Restriction
copying build/lib.linux-x86_64-cpython-312/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Restriction
copying build/lib.linux-x86_64-cpython-312/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Restriction
copying build/lib.linux-x86_64-cpython-312/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Restriction
copying build/lib.linux-x86_64-cpython-312/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Restriction
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/phenotype
copying build/lib.linux-x86_64-cpython-312/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/phenotype
copying build/lib.linux-x86_64-cpython-312/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/phenotype
copying build/lib.linux-x86_64-cpython-312/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/phenotype
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep
copying build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep
copying build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep
copying build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep
copying build/lib.linux-x86_64-cpython-312/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/NMR
copying build/lib.linux-x86_64-cpython-312/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/NMR
copying build/lib.linux-x86_64-cpython-312/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/NMR
copying build/lib.linux-x86_64-cpython-312/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/NMR
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Nexus
copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/cnexus.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Nexus
copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Nexus
copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Nexus
copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Nexus
copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Nexus
copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Nexus
copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Nexus
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/_pwm.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs/jaspar
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs/jaspar
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs/jaspar
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs/applications
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs/applications
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs/applications
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/xms.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/pfm.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/clusterbuster.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
copying build/lib.linux-x86_64-cpython-312/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Medline
copying build/lib.linux-x86_64-cpython-312/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Medline
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/ccealign.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/kdtrees.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/ccealignmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/qcprot.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/internal_coords.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/ic_rebuild.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/ic_data.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/cealign.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/SCADIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/SASA.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PICIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf/mmtfio.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf
copying build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML
copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML
copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML
copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/Map
copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/Map
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/Gene
copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/Gene
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/Enzyme
copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/Enzyme
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/Compound
copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG/Compound
copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG
copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/HMM
copying build/lib.linux-x86_64-cpython-312/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/HMM
copying build/lib.linux-x86_64-cpython-312/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/HMM
copying build/lib.linux-x86_64-cpython-312/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/HMM
copying build/lib.linux-x86_64-cpython-312/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/HMM
copying build/lib.linux-x86_64-cpython-312/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/HMM
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics
copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Geo
copying build/lib.linux-x86_64-cpython-312/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Geo
copying build/lib.linux-x86_64-cpython-312/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Geo
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/GenBank
copying build/lib.linux-x86_64-cpython-312/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/GenBank
copying build/lib.linux-x86_64-cpython-312/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/GenBank
copying build/lib.linux-x86_64-cpython-312/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/GenBank
copying build/lib.linux-x86_64-cpython-312/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/GenBank
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy
copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy
copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy
copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy
copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy
copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy
copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/XSDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/XSDs
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/xhtml-table-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/esummary_gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/epost.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/elink.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
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copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
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copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
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copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
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copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
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copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-notat1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-math1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-list1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-link1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-funding1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-format1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-display1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-common1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-chars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/BITS-question-answer2.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez
copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Emboss
copying build/lib.linux-x86_64-cpython-312/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Emboss
copying build/lib.linux-x86_64-cpython-312/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Emboss
copying build/lib.linux-x86_64-cpython-312/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Emboss
copying build/lib.linux-x86_64-cpython-312/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Emboss
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data
copying build/lib.linux-x86_64-cpython-312/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data
copying build/lib.linux-x86_64-cpython-312/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data
copying build/lib.linux-x86_64-cpython-312/Bio/Data/PDBData.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data
copying build/lib.linux-x86_64-cpython-312/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data
copying build/lib.linux-x86_64-cpython-312/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Compass
copying build/lib.linux-x86_64-cpython-312/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Compass
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/codonalign
copying build/lib.linux-x86_64-cpython-312/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/codonalign
copying build/lib.linux-x86_64-cpython-312/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/codonalign
copying build/lib.linux-x86_64-cpython-312/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/codonalign
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Cluster
copying build/lib.linux-x86_64-cpython-312/Bio/Cluster/_cluster.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Cluster
copying build/lib.linux-x86_64-cpython-312/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Cluster
copying build/lib.linux-x86_64-cpython-312/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Cluster
copying build/lib.linux-x86_64-cpython-312/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Cluster
copying build/lib.linux-x86_64-cpython-312/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Cluster
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/CAPS
copying build/lib.linux-x86_64-cpython-312/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/CAPS
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast
copying build/lib.linux-x86_64-cpython-312/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast
copying build/lib.linux-x86_64-cpython-312/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast
copying build/lib.linux-x86_64-cpython-312/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast
copying build/lib.linux-x86_64-cpython-312/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast
copying build/lib.linux-x86_64-cpython-312/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast
copying build/lib.linux-x86_64-cpython-312/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Application
copying build/lib.linux-x86_64-cpython-312/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Application
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Alphabet
copying build/lib.linux-x86_64-cpython-312/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Alphabet
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/MsfIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/_aligners.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/_aligners.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/TRANS -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/STR -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/SCHNEIDER -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/RISLER -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/RAO -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/PAM70 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/PAM30 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/PAM250 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/NUC.4.4 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/MEGABLAST -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/MDM78 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/MCLACHLAN -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/LEVIN -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/JONES -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/JOHNSON -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/HOXD70 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/GONNET1992 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/GENETIC -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/FENG -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/DAYHOFF -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM90 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM80 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM62 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM50 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM45 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLASTP -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLASTN -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BENNER74 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BENNER6 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BENNER22 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data
copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications
copying build/lib.linux-x86_64-cpython-312/Bio/Align/tabular.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/stockholm.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/sam.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/psl.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/phylip.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/msf.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/mauve.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/maf.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/hhr.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/fasta.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/exonerate.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/emboss.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/clustal.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/bigpsl.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/bigmaf.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/bigbed.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/bed.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/a2m.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
copying build/lib.linux-x86_64-cpython-312/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Affy
copying build/lib.linux-x86_64-cpython-312/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Affy
copying build/lib.linux-x86_64-cpython-312/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Affy
copying build/lib.linux-x86_64-cpython-312/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
copying build/lib.linux-x86_64-cpython-312/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL/BioSeq.py to BioSeq.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL/DBUtils.py to DBUtils.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL/Loader.py to Loader.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/BioSQL/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Wise/psw.py to psw.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Wise/dnal.py to dnal.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Wise/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/UniProt/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/UniProt/GOA.py to GOA.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/UniGene/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-312.pyc
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byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/Distribution.py to Distribution.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/Comparative.py to Comparative.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Geo/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Geo/Record.py to Record.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/GenBank/utils.py to utils.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/GenBank/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/GenBank/Scanner.py to Scanner.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/GenBank/Record.py to Record.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy/cellosaurus.py to cellosaurus.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy/Prosite.py to Prosite.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy/Prodoc.py to Prodoc.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/ExPASy/Enzyme.py to Enzyme.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/Parser.py to Parser.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Emboss/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Emboss/Primer3.py to Primer3.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Emboss/Applications.py to Applications.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data/SCOPData.py to SCOPData.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data/PDBData.py to PDBData.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data/IUPACData.py to IUPACData.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Data/CodonTable.py to CodonTable.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Compass/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/codonalign/codonseq.py to codonseq.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/codonalign/codonalignment.py to codonalignment.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/codonalign/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Cluster/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/CAPS/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast/Record.py to Record.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast/ParseBlastTable.py to ParseBlastTable.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast/NCBIXML.py to NCBIXML.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast/NCBIWWW.py to NCBIWWW.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Blast/Applications.py to Applications.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Application/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Alphabet/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/StockholmIO.py to StockholmIO.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/PhylipIO.py to PhylipIO.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/NexusIO.py to NexusIO.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/MsfIO.py to MsfIO.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/MauveIO.py to MauveIO.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/MafIO.py to MafIO.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/Interfaces.py to Interfaces.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/FastaIO.py to FastaIO.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/EmbossIO.py to EmbossIO.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/AlignIO/ClustalIO.py to ClustalIO.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_TCoffee.py to _TCoffee.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Probcons.py to _Probcons.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Prank.py to _Prank.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Muscle.py to _Muscle.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Mafft.py to _Mafft.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_MSAProbs.py to _MSAProbs.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Dialign.py to _Dialign.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Clustalw.py to _Clustalw.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_ClustalOmega.py to _ClustalOmega.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/tabular.py to tabular.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/stockholm.py to stockholm.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/sam.py to sam.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/psl.py to psl.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/phylip.py to phylip.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/nexus.py to nexus.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/msf.py to msf.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/mauve.py to mauve.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/maf.py to maf.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/interfaces.py to interfaces.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/hhr.py to hhr.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/fasta.py to fasta.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/exonerate.py to exonerate.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/emboss.py to emboss.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/clustal.py to clustal.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/bigpsl.py to bigpsl.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/bigmaf.py to bigmaf.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/bigbed.py to bigbed.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/bed.py to bed.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/a2m.py to a2m.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Align/AlignInfo.py to AlignInfo.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Affy/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Affy/CelFile.py to CelFile.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/pairwise2.py to pairwise2.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/kNN.py to kNN.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/bgzf.py to bgzf.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/_utils.py to _utils.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/__init__.py to __init__.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqRecord.py to SeqRecord.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqFeature.py to SeqFeature.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Seq.py to Seq.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/MarkovModel.py to MarkovModel.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-312.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/File.py to File.cpython-312.pyc
writing byte-compilation script '/tmp/tmpbsscgtzw.py'
/usr/bin/python3 /tmp/tmpbsscgtzw.py
removing /tmp/tmpbsscgtzw.py
running install_egg_info
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
Copying biopython.egg-info to /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/biopython-1.81-py3.12.egg-info
running install_scripts
+ find Scripts -name '*.py'
+ xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3
Scripts/xbbtools/xbbtools.py: updating
Scripts/xbbtools/xbb_widget.py: updating
Scripts/xbbtools/xbb_utils.py: updating
Scripts/xbbtools/xbb_translations.py: updating
Scripts/xbbtools/xbb_search.py: updating
Scripts/xbbtools/xbb_help.py: updating
Scripts/xbbtools/xbb_blastbg.py: updating
Scripts/xbbtools/xbb_blast.py: updating
Scripts/xbbtools/nextorf.py: updating
Scripts/update_ncbi_codon_table.py: no change
Scripts/scop_pdb.py: updating
Scripts/query_pubmed.py: updating
Scripts/SeqGui/SeqGui.py: no change
Scripts/Restriction/rebase_update.py: updating
Scripts/Restriction/ranacompiler.py: updating
Scripts/Performance/biosql_performance_read.py: updating
Scripts/Performance/biosql_performance_load.py: updating
Scripts/PDB/hsexpo.py: updating
Scripts/PDB/generate_three_to_one_dict.py: no change
Scripts/GenBank/check_output_simple.py: updating
Scripts/GenBank/check_output.py: updating
+ popd
~/build/BUILD/python-biopython-1.81
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.81-4.fc39 --unique-debug-suffix -1.81-4.fc39.x86_64 --unique-debug-src-base python-biopython-1.81-4.fc39.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.81
find-debuginfo: starting
Extracting debug info from 9 files
DWARF-compressing 9 files
sepdebugcrcfix: Updated 9 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-1.81-4.fc39.x86_64
1192 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib/debug/usr/lib64/python3.12 using python3.12
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12 using python3.12
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.LFUSqK
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
~/build/BUILD/python-biopython-1.81/python3/Tests ~/build/BUILD/python-biopython-1.81
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd python-biopython-1.81
+ pushd python3/Tests
+ xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3
+ find . -name run_tests.py
./run_tests.py: updating
+ find ../ -name __init__.py
+ xargs rm -f
++ ls test_Ace.py test_Affy.py test_AlignIO.py test_AlignIO_ClustalIO.py test_AlignIO_EmbossIO.py test_AlignIO_FastaIO.py test_AlignIO_MauveIO.py test_AlignIO_PhylipIO.py test_AlignIO_convert.py test_AlignInfo.py test_Align_Alignment.py test_Align_a2m.py test_Align_bed.py test_Align_bigbed.py test_Align_bigmaf.py test_Align_bigpsl.py test_Align_clustal.py test_Align_emboss.py test_Align_exonerate.py test_Align_fasta.py test_Align_hhr.py test_Align_maf.py test_Align_mauve.py test_Align_msf.py test_Align_nexus.py test_Align_phylip.py test_Align_psl.py test_Align_sam.py test_Align_stockholm.py test_Align_tabular.py test_Application.py test_BWA_tool.py test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb_online.py test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector_online.py test_BioSQL_psycopg2.py test_BioSQL_psycopg2_online.py test_BioSQL_sqlite3.py test_BioSQL_sqlite3_online.py test_Blast_Record.py test_CAPS.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_ColorSpiral.py test_Compass.py test_Consensus.py test_Dialign_tool.py test_EMBL_unittest.py test_Emboss.py test_EmbossPhylipNew.py test_EmbossPrimer.py test_Entrez.py test_Entrez_online.py test_Entrez_parser.py test_Enzyme.py test_ExPASy.py test_Fasttree_tool.py test_File.py test_GenBank.py test_GenomeDiagram.py test_GraphicsBitmaps.py test_GraphicsChromosome.py test_GraphicsDistribution.py test_GraphicsGeneral.py test_HMMCasino.py test_HMMGeneral.py test_KEGG.py test_KEGG_online.py test_KGML_graphics.py test_KGML_graphics_online.py test_KGML_nographics.py test_KeyWList.py test_LogisticRegression.py test_MSAProbs_tool.py test_MafIO_index.py test_Mafft_tool.py test_MarkovModel.py test_Medline.py test_Muscle_tool.py test_NCBITextParser.py test_NCBIXML.py test_NCBI_BLAST_tools.py test_NCBI_qblast.py test_NMR.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDBList.py test_PDB_CEAligner.py test_PDB_DSSP.py test_PDB_Dice.py test_PDB_Disordered.py test_PDB_Exposure.py test_PDB_FragmentMapper.py test_PDB_KDTree.py test_PDB_MMCIF2Dict.py test_PDB_MMCIFIO.py test_PDB_MMCIFParser.py test_PDB_NACCESS.py test_PDB_PDBIO.py test_PDB_PDBParser.py test_PDB_PSEA.py test_PDB_Polypeptide.py test_PDB_QCSuperimposer.py test_PDB_ResidueDepth.py test_PDB_SASA.py test_PDB_SMCRA.py test_PDB_Selection.py test_PDB_StructureAlignment.py test_PDB_Superimposer.py test_PDB_internal_coords.py test_PDB_parse_pdb_header.py test_PDB_vectors.py test_PQR.py test_Pathway.py test_Phd.py test_Phylo.py test_PhyloXML.py test_Phylo_CDAO.py test_Phylo_NeXML.py test_Phylo_matplotlib.py test_Phylo_networkx.py test_PopGen_GenePop.py test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_nodepend.py test_Prank_tool.py test_Probcons_tool.py test_ProtParam.py test_RCSBFormats.py test_Restriction.py test_SCOP_Astral.py test_SCOP_Cla.py test_SCOP_Des.py test_SCOP_Dom.py test_SCOP_Hie.py test_SCOP_Raf.py test_SCOP_Residues.py test_SCOP_Scop.py test_SCOP_online.py test_SVDSuperimposer.py test_SearchIO_blast_tab.py test_SearchIO_blast_tab_index.py test_SearchIO_blast_text.py test_SearchIO_blast_xml.py test_SearchIO_blast_xml_index.py test_SearchIO_blat_psl.py test_SearchIO_blat_psl_index.py test_SearchIO_exonerate.py test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_vulgar_index.py test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10_index.py test_SearchIO_hhsuite2_text.py test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text_index.py test_SearchIO_interproscan_xml.py test_SearchIO_legacy.py test_SearchIO_model.py test_SearchIO_write.py test_SeqFeature.py test_SeqIO.py test_SeqIO_AbiIO.py test_SeqIO_FastaIO.py test_SeqIO_Gck.py test_SeqIO_Insdc.py test_SeqIO_NibIO.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_SnapGene.py test_SeqIO_TwoBitIO.py test_SeqIO_Xdna.py test_S++ grep -v SubsMat
++ grep -v pairwise_aligner
++ grep -v SearchIO_blast
++ grep -v bgzf
++ grep -v Phylo
++ grep -v Nexus
eqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_UniProt_GOA.py test_Uniprot.py test_Wise.py test_XXmotif_tool.py test_align.py test_align_substitution_matrices.py test_bgzf.py test_cellosaurus.py test_codonalign.py test_geo.py test_kNN.py test_mmtf.py test_mmtf_online.py test_motifs.py test_motifs_online.py test_pairwise2.py test_pairwise2_no_C.py test_pairwise_aligner.py test_pairwise_alignment_map.py test_phenotype.py test_phenotype_fit.py test_phyml_tool.py test_prodoc.py test_prosite.py test_raxml_tool.py test_samtools_tool.py test_seq.py test_translate.py
++ grep -v Tutorial
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Ace.py
test_Ace ... ok
test_check_ACEParser (test_Ace.AceTestOne.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestOne.test_check_record_parser)
Test to check that contig parser parses each contig into a contig. ... ok
test_check_ACEParser (test_Ace.AceTestThree.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestThree.test_check_record_parser)
Test to check that record parser parses each contig into a record. ... ok
test_check_ACEParser (test_Ace.AceTestTwo.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestTwo.test_check_record_parser)
Test to check that record parser parses each contig into a record. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.049 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Affy.py
test_Affy ... ok
testAffy3 (test_Affy.AffyTest.testAffy3) ... ok
testAffy4 (test_Affy.AffyTest.testAffy4) ... ok
testAffyBadHeader (test_Affy.AffyTest.testAffyBadHeader) ... ok
testAffyWrongModeReadV3 (test_Affy.AffyTest.testAffyWrongModeReadV3) ... ok
testAffyWrongModeReadV4 (test_Affy.AffyTest.testAffyWrongModeReadV4) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.017 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO.py
test_AlignIO ... ok
test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_parsing_empty_files)
Check that parsing an empty file returns an empty list. ... ok
test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions.test_phylip_reject_duplicate)
Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok
test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_writing_empty_files)
Check that writers can cope with no alignments. ... ok
test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions.test_writing_not_alignments)
Check that writers reject records that are not alignments. ... ok
test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal1) ... ok
test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal2) ... ok
test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal3) ... ok
test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal4) ... ok
test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal5) ... ok
test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal6) ... ok
test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss1) ... ok
test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss2) ... ok
test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss3) ... ok
test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss4) ... ok
test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss5) ... ok
test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss6) ... ok
test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss7) ... ok
test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss8) ... ok
test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta) ... ok
test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_1) ... ok
test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_2) ... ok
test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_3) ... ok
test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_4) ... ok
test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_5) ... ok
test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_6) ... ok
test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_7) ... ok
test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_8) ... ok
test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading.test_reading_alignments_ig) ... ok
test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf1) ... ok
test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf2) ... ok
test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf3) ... ok
test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf4) ... ok
test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading.test_reading_alignments_mauve) ... ok
test_reading_alignments_msf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf1) ... ok
test_reading_alignments_msf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf2) ... ok
test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus1) ... ok
test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus2) ... ok
test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip1) ... ok
test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip10) ... ok
test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip2) ... ok
test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip3) ... ok
test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip4) ... ok
test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip5) ... ok
test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip6) ... ok
test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip7) ... ok
test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip8) ... ok
test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip9) ... ok
test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading.test_reading_alignments_pir) ... ok
test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm1) ... ok
test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm2) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.471 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_ClustalIO.py
test_AlignIO_ClustalIO ... ok
test_biopython_header (test_AlignIO_ClustalIO.TestClustalIO.test_biopython_header)
Make sure we can parse the Biopython header. ... ok
test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO.test_cat_one_two) ... ok
test_empy (test_AlignIO_ClustalIO.TestClustalIO.test_empy)
Checking empty file. ... ok
test_kalign_header (test_AlignIO_ClustalIO.TestClustalIO.test_kalign_header)
Make sure we can parse the Kalign header. ... ok
test_one (test_AlignIO_ClustalIO.TestClustalIO.test_one) ... ok
test_three (test_AlignIO_ClustalIO.TestClustalIO.test_three) ... ok
test_two (test_AlignIO_ClustalIO.TestClustalIO.test_two) ... ok
test_write_read (test_AlignIO_ClustalIO.TestClustalIO.test_write_read)
Checking write/read. ... ok
test_write_read_single (test_AlignIO_ClustalIO.TestClustalIO.test_write_read_single)
Testing write/read when there is only one sequence. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.059 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_EmbossIO.py
test_AlignIO_EmbossIO ... ok
test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example) ... ok
test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example2) ... ok
test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example3) ... ok
test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_plus_simple) ... ok
test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO.test_simple_example) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.057 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_FastaIO.py
test_AlignIO_FastaIO ... ok
test_output001 (test_AlignIO_FastaIO.FastaIOTests.test_output001)
Check output001.m10 file. ... ok
test_output002 (test_AlignIO_FastaIO.FastaIOTests.test_output002)
Check output002.m10 file. ... ok
test_output003 (test_AlignIO_FastaIO.FastaIOTests.test_output003)
Check output003.m10 file. ... ok
test_output004 (test_AlignIO_FastaIO.FastaIOTests.test_output004)
Check output004.m10 file. ... ok
test_output005 (test_AlignIO_FastaIO.FastaIOTests.test_output005)
Check output005.m10 file. ... ok
test_output006 (test_AlignIO_FastaIO.FastaIOTests.test_output006)
Check output006.m10 file. ... ok
test_output007 (test_AlignIO_FastaIO.FastaIOTests.test_output007)
Check output007.m10 file. ... ok
test_output008 (test_AlignIO_FastaIO.FastaIOTests.test_output008)
Check output008.m10 file. ... ok
test_output009 (test_AlignIO_FastaIO.FastaIOTests.test_output009)
Check output009.m10 file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.072 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_MauveIO.py
test_AlignIO_MauveIO ... ok
test_one (test_AlignIO_MauveIO.TestMauveIO.test_one) ... ok
test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO.test_sequence_positions) ... ok
test_write_read (test_AlignIO_MauveIO.TestMauveIO.test_write_read) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_PhylipIO.py
test_AlignIO_PhylipIO ... ok
test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO.test_concatenation) ... ok
test_five (test_AlignIO_PhylipIO.TestPhylipIO.test_five) ... ok
test_four (test_AlignIO_PhylipIO.TestPhylipIO.test_four) ... ok
test_one (test_AlignIO_PhylipIO.TestPhylipIO.test_one) ... ok
test_six (test_AlignIO_PhylipIO.TestPhylipIO.test_six) ... ok
test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO.test_two_and_three) ... ok
test_write_read (test_AlignIO_PhylipIO.TestPhylipIO.test_write_read) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.057 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignIO_convert.py
test_AlignIO_convert ... ok
test_clustal_to_nexus_with_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_with_mol_type)
Converting Clustal to NEXUS with a molecule type. ... ok
test_clustal_to_nexus_without_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_without_mol_type)
Converting Clustal to NEXUS without a molecule type. ... ok
test_convert (test_AlignIO_convert.ConvertTests.test_convert) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.216 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_AlignInfo.py
test_AlignInfo ... ok
test_nucleotides (test_AlignInfo.AlignInfoTests.test_nucleotides) ... ok
test_proteins (test_AlignInfo.AlignInfoTests.test_proteins) ... ok
test_pseudo_count (test_AlignInfo.AlignInfoTests.test_pseudo_count) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_Alignment.py
test_Align_Alignment ... ok
test_nucleotide_nucleotide_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_nucleotide_nucleotide_str) ... ok
test_protein_nucleotide_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_protein_nucleotide_str) ... ok
test_aligned (test_Align_Alignment.TestAlign_out_of_order.test_aligned) ... ok
test_array (test_Align_Alignment.TestAlign_out_of_order.test_array) ... ok
test_indices (test_Align_Alignment.TestAlign_out_of_order.test_indices) ... ok
test_row (test_Align_Alignment.TestAlign_out_of_order.test_row) ... ok
test_row_col (test_Align_Alignment.TestAlign_out_of_order.test_row_col) ... ok
test_row_iterable (test_Align_Alignment.TestAlign_out_of_order.test_row_iterable) ... ok
test_row_slice (test_Align_Alignment.TestAlign_out_of_order.test_row_slice) ... ok
test_rows_col (test_Align_Alignment.TestAlign_out_of_order.test_rows_col) ... ok
test_rows_cols (test_Align_Alignment.TestAlign_out_of_order.test_rows_cols) ... ok
test_str (test_Align_Alignment.TestAlign_out_of_order.test_str) ... ok
test_substitutions (test_Align_Alignment.TestAlign_out_of_order.test_substitutions) ... ok
test_empty_alignment (test_Align_Alignment.TestAlignment.test_empty_alignment) ... ok
test_a2m (test_Align_Alignment.TestAlignment_format.test_a2m) ... ok
test_bed (test_Align_Alignment.TestAlignment_format.test_bed) ... ok
test_bigbed (test_Align_Alignment.TestAlignment_format.test_bigbed) ... ok
test_bigmaf (test_Align_Alignment.TestAlignment_format.test_bigmaf) ... ok
test_bigpsl (test_Align_Alignment.TestAlignment_format.test_bigpsl) ... ok
test_clustal (test_Align_Alignment.TestAlignment_format.test_clustal) ... ok
test_emboss (test_Align_Alignment.TestAlignment_format.test_emboss) ... ok
test_exonerate (test_Align_Alignment.TestAlignment_format.test_exonerate) ... ok
test_fasta (test_Align_Alignment.TestAlignment_format.test_fasta) ... ok
test_hhr (test_Align_Alignment.TestAlignment_format.test_hhr) ... ok
test_maf (test_Align_Alignment.TestAlignment_format.test_maf) ... ok
test_mauve (test_Align_Alignment.TestAlignment_format.test_mauve) ... ok
test_msf (test_Align_Alignment.TestAlignment_format.test_msf) ... ok
test_nexus (test_Align_Alignment.TestAlignment_format.test_nexus) ... ok
test_phylip (test_Align_Alignment.TestAlignment_format.test_phylip) ... ok
test_psl (test_Align_Alignment.TestAlignment_format.test_psl) ... ok
test_sam (test_Align_Alignment.TestAlignment_format.test_sam) ... ok
test_stockholm (test_Align_Alignment.TestAlignment_format.test_stockholm) ... ok
test_tabular (test_Align_Alignment.TestAlignment_format.test_tabular) ... ok
test_a2m (test_Align_Alignment.TestAlignment_pairwise_format.test_a2m) ... ok
test_bed (test_Align_Alignment.TestAlignment_pairwise_format.test_bed) ... ok
test_clustal (test_Align_Alignment.TestAlignment_pairwise_format.test_clustal) ... ok
test_exonerate (test_Align_Alignment.TestAlignment_pairwise_format.test_exonerate) ... ok
test_fasta (test_Align_Alignment.TestAlignment_pairwise_format.test_fasta) ... ok
test_maf (test_Align_Alignment.TestAlignment_pairwise_format.test_maf) ... ok
test_phylip (test_Align_Alignment.TestAlignment_pairwise_format.test_phylip) ... ok
test_psl (test_Align_Alignment.TestAlignment_pairwise_format.test_psl) ... ok
test_sam (test_Align_Alignment.TestAlignment_pairwise_format.test_sam) ... ok
test_comparison (test_Align_Alignment.TestMultipleAlignment.test_comparison) ... ok
test_indexing_slicing (test_Align_Alignment.TestMultipleAlignment.test_indexing_slicing) ... ok
test_sort (test_Align_Alignment.TestMultipleAlignment.test_sort) ... ok
test_substitutions (test_Align_Alignment.TestMultipleAlignment.test_substitutions) ... ok
test_target_query_properties (test_Align_Alignment.TestMultipleAlignment.test_target_query_properties) ... ok
test_aligned_indices (test_Align_Alignment.TestPairwiseAlignment.test_aligned_indices) ... ok
test_indexing_slicing (test_Align_Alignment.TestPairwiseAlignment.test_indexing_slicing) ... ok
test_sort (test_Align_Alignment.TestPairwiseAlignment.test_sort) ... ok
test_substitutions (test_Align_Alignment.TestPairwiseAlignment.test_substitutions) ... ok
test_target_query_properties (test_Align_Alignment.TestPairwiseAlignment.test_target_query_properties) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.388 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_a2m.py
test_Align_a2m ... ok
test_clustalw (test_Align_a2m.TestA2MReadingWriting.test_clustalw) ... ok
test_empty (test_Align_a2m.TestA2MReadingWriting.test_empty)
Checking empty file. ... ok
test_kalign (test_Align_a2m.TestA2MReadingWriting.test_kalign) ... ok
test_msaprobs (test_Align_a2m.TestA2MReadingWriting.test_msaprobs) ... ok
test_muscle (test_Align_a2m.TestA2MReadingWriting.test_muscle) ... ok
test_probcons (test_Align_a2m.TestA2MReadingWriting.test_probcons) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bed.py
test_Align_bed ... ok
test_reading (test_Align_bed.TestAlign_bed12.test_reading)
Test parsing alignments in file formats BED3 through BED12. ... ok
test_writing (test_Align_bed.TestAlign_bed12.test_writing)
Test writing the alignments in bed12.bed as BED3 through BED12. ... ok
test_reading_psl_34_001 (test_Align_bed.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.bed. ... ok
test_reading_psl_34_003 (test_Align_bed.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.bed. ... ok
test_reading_psl_34_004 (test_Align_bed.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.bed. ... ok
test_reading_psl_34_005 (test_Align_bed.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.bed. ... ok
test_writing_psl_34_001 (test_Align_bed.TestAlign_dna.test_writing_psl_34_001)
Test writing the alignments in psl_34_001.bed. ... ok
test_writing_psl_34_003 (test_Align_bed.TestAlign_dna.test_writing_psl_34_003)
Test writing the alignments in psl_34_003.bed. ... ok
test_writing_psl_34_004 (test_Align_bed.TestAlign_dna.test_writing_psl_34_004)
Test writing the alignments in psl_34_004.bed. ... ok
test_writing_psl_34_005 (test_Align_bed.TestAlign_dna.test_writing_psl_34_005)
Test writing the alignments in psl_34_005.bed. ... ok
test_reading (test_Align_bed.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.bed. ... ok
test_writing (test_Align_bed.TestAlign_dna_rna.test_writing)
Test writing the alignments in dna_rna.bed. ... ok
test_reading_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.bed. ... ok
test_reading_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_002)
Test parsing psl_35_002.bed. ... ok
test_writing_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_001)
Test writing the alignments in psl_35_001.bed. ... ok
test_writing_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_002)
Test writing the alignments in psl_35_002.bed. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.161 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bigbed.py
test_Align_bigbed ... ok
test_reading (test_Align_bigbed.TestAlign_bed12.test_reading)
Test parsing alignments in file formats BED3 through BED12. ... ok
test_reading_psl_34_001 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.bb. ... ok
test_reading_psl_34_003 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.bb. ... ok
test_reading_psl_34_004 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.bb. ... ok
test_reading_psl_34_005 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.bb. ... ok
test_reading (test_Align_bigbed.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.bb. ... ok
test_reading_psl_35_001 (test_Align_bigbed.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.bb. ... ok
test_reading (test_Align_bigbed.TestAlign_extended_bed.test_reading)
Test parsing bigbed_extended.bb. ... ok
test_search_chromosome (test_Align_bigbed.TestAlign_searching.test_search_chromosome) ... ok
test_search_position (test_Align_bigbed.TestAlign_searching.test_search_position) ... ok
test_search_region (test_Align_bigbed.TestAlign_searching.test_search_region) ... ok
test_three_iterators (test_Align_bigbed.TestAlign_searching.test_three_iterators)
Create three iterators and use them concurrently. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.126 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bigmaf.py
test_Align_bigmaf ... ok
test_reading_bundle_without_target (test_Align_bigmaf.TestAlign_reading.test_reading_bundle_without_target)
Test parsing bundle_without_target.bb. ... ok
test_reading_ucsc_mm9_chr10 (test_Align_bigmaf.TestAlign_reading.test_reading_ucsc_mm9_chr10)
Test parsing MAF file ucsc_mm9_chr10.bb. ... ok
test_reading_ucsc_test (test_Align_bigmaf.TestAlign_reading.test_reading_ucsc_test)
Test parsing ucsc_test.bb. ... ok
test_search_chromosome (test_Align_bigmaf.TestAlign_searching.test_search_chromosome) ... ok
test_search_position (test_Align_bigmaf.TestAlign_searching.test_search_position) ... ok
test_search_region (test_Align_bigmaf.TestAlign_searching.test_search_region) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.314 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_bigpsl.py
test_Align_bigpsl ... ok
test_reading_bigpsl (test_Align_bigpsl.TestAlign_bigpsl.test_reading_bigpsl)
Test parsing bigPsl.bb. ... ok
test_reading_psl_34_001 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.psl.bb. ... ok
test_reading_psl_34_003 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.psl.bb. ... ok
test_reading_psl_34_004 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.psl.bb. ... ok
test_reading_psl_34_005 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.psl.bb. ... ok
test_reading (test_Align_bigpsl.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.psl.bb. ... ok
test_reading_psl_35_001 (test_Align_bigpsl.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.psl.bb. ... ok
test_reading_psl_35_002 (test_Align_bigpsl.TestAlign_dnax_prot.test_reading_psl_35_002)
Test parsing psl_35_002.psl.bb. ... ok
test_search_chromosome (test_Align_bigpsl.TestAlign_searching.test_search_chromosome) ... ok
test_search_position (test_Align_bigpsl.TestAlign_searching.test_search_position) ... ok
test_search_region (test_Align_bigpsl.TestAlign_searching.test_search_region) ... ok
test_three_iterators (test_Align_bigpsl.TestAlign_searching.test_three_iterators)
Create three iterators and use them concurrently. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.242 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_clustal.py
test_Align_clustal ... ok
test_clustalw (test_Align_clustal.TestClustalReadingWriting.test_clustalw) ... ok
test_empty (test_Align_clustal.TestClustalReadingWriting.test_empty)
Checking empty file. ... ok
test_kalign (test_Align_clustal.TestClustalReadingWriting.test_kalign)
Make sure we can parse the Kalign header. ... ok
test_msaprobs (test_Align_clustal.TestClustalReadingWriting.test_msaprobs) ... ok
test_muscle (test_Align_clustal.TestClustalReadingWriting.test_muscle) ... ok
test_probcons (test_Align_clustal.TestClustalReadingWriting.test_probcons) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.085 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_emboss.py
test_Align_emboss ... ok
test_local_water2 (test_Align_emboss.TestEmboss.test_local_water2)
Test parsing a local alignment. ... ok
test_matcher_pair (test_Align_emboss.TestEmboss.test_matcher_pair) ... ok
test_matcher_simple (test_Align_emboss.TestEmboss.test_matcher_simple) ... ok
test_needle_asis (test_Align_emboss.TestEmboss.test_needle_asis) ... ok
test_pair_aln_full_blank_line (test_Align_emboss.TestEmboss.test_pair_aln_full_blank_line) ... ok
test_pair_example (test_Align_emboss.TestEmboss.test_pair_example) ... ok
test_pair_example2 (test_Align_emboss.TestEmboss.test_pair_example2) ... ok
test_pair_example3 (test_Align_emboss.TestEmboss.test_pair_example3) ... ok
test_pair_example_nobrief (test_Align_emboss.TestEmboss.test_pair_example_nobrief) ... ok
test_water_reverse1 (test_Align_emboss.TestEmboss.test_water_reverse1) ... ok
test_water_reverse2 (test_Align_emboss.TestEmboss.test_water_reverse2) ... ok
test_water_reverse3 (test_Align_emboss.TestEmboss.test_water_reverse3) ... ok
test_water_reverse4 (test_Align_emboss.TestEmboss.test_water_reverse4) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.099 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_exonerate.py
test_Align_exonerate ... ok
test_exn_22_m_affine_local_cigar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_cigar)
Test parsing exn_22_m_affine_local_cigar.exn. ... ok
test_exn_22_m_affine_local_vulgar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_vulgar)
Test parsing exn_22_m_affine_local_vulgar.exn. ... ok
test_exn_22_m_cdna2genome_cigar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_cigar)
Test parsing exn_22_m_cdna2genome_cigar.exn. ... ok
test_exn_22_m_cdna2genome_vulgar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_vulgar)
Test parsing exn_22_m_cdna2genome_vulgar.exn. ... ok
test_exn_22_m_coding2coding_cigar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_cigar)
Test parsing exn_22_m_coding2coding_cigar.exn. ... ok
test_exn_22_m_coding2coding_vulgar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_vulgar)
Test parsing exn_22_m_coding2coding_vulgar.exn. ... ok
test_exn_22_m_coding2coding_fshifts_cigar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_cigar)
Test parsing exn_22_m_cigar_fshifts.exn). ... ok
test_exn_22_m_coding2coding_fshifts_vulgar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_vulgar)
Test parsing exn_22_o_vulgar_fshifts.exn. ... ok
test_exn_22_m_coding2genome_cigar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_cigar)
Test parsing exn_22_m_coding2genome_cigar.exn. ... ok
test_exn_22_m_coding2genome_vulgar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_vulgar)
Test parsing exn_22_m_coding2genome_vulgar.exn. ... ok
test_exn_22_m_dna2protein_cigar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_cigar)
Test parsing exn_22_m_dna2protein_cigar.exn. ... ok
test_exn_22_m_dna2protein_vulgar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_vulgar)
Test parsing exn_22_m_dna2protein_vulgar.exn. ... ok
test_exn_22_m_est2genome_cigar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_cigar)
Test parsing exn_22_m_est2genome_cigar.exn. ... ok
test_exn_22_m_est2genome_vulgar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_vulgar)
Test parsing exn_22_m_est2genome_vulgar.exn. ... ok
test_exn_22_m_genome2genome_cigar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_cigar)
Test parsing exn_22_o_vulgar_cigar.exn. ... ok
test_exn_22_m_genome2genome_vulgar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_vulgar)
Test parsing exn_22_o_vulgar.exn. ... ok
test_exn_22_q_multiple_cigar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_cigar)
Test parsing exn_22_q_multiple_cigar.exn. ... ok
test_exn_22_q_multiple_vulgar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_vulgar)
Test parsing exn_22_q_multiple_vulgar.exn. ... ok
test_exn_22_m_ner_cigar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_cigar)
Test parsing exonerate output (exn_22_m_ner_cigar.exn). ... ok
test_exn_22_m_ner_vulgar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_vulgar)
Test parsing exonerate output (exn_22_m_ner_vulgar.exn). ... ok
test_exn_22_q_none (test_Align_exonerate.Exonerate_none.test_exn_22_q_none)
Test parsing exonerate output (exn_22_q_none.exn). ... ok
test_exn_22_m_protein2dna_cigar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_cigar)
Test parsing exonerate output (exn_22_m_protein2dna_cigar.exn). ... ok
test_exn_22_m_protein2dna_vulgar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_vulgar)
Test parsing exonerate output (exn_22_m_protein2dna_vulgar.exn). ... ok
test_exn_22_m_protein2dna_fshifts_cigar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_cigar)
Test parsing exonerate output (exn_22_o_cigar_fshifts2.exn). ... ok
test_exn_22_m_protein2dna_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_vulgar)
Test parsing exonerate output (exn_22_o_vulgar_fshifts2.exn). ... ok
test_exn_22_m_protein2genome_cigar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_cigar)
Test parsing exn_22_m_protein2genome_cigar.exn. ... ok
test_exn_22_m_protein2genome_vulgar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_vulgar)
Test parsing exn_22_m_protein2genome_vulgar.exn. ... ok
test_exn_24_protein2genome_met_intron_cigar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_cigar)
Test parsing exn_24_m_protein2genome_met_intron_cigar.exn. ... ok
test_exn_24_protein2genome_met_intron_vulgar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_vulgar)
Test parsing exn_24_m_protein2genome_met_intron_vulgar.exn. ... ok
test_exn_24_m_protein2genome_revcomp_fshifts_cigar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_cigar)
Test parsing exn_24_m_protein2genome_revcomp_fshifts_cigar.exn. ... ok
test_exn_24_m_protein2genome_revcomp_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_vulgar)
Test parsing exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn. ... ok
test_exn_22_m_ungapped_cigar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_cigar)
Test parsing exn_22_m_ungapped_cigar.exn. ... ok
test_exn_22_m_ungapped_vulgar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_vulgar)
Test parsing exn_22_m_ungapped_vulgar.exn. ... ok
test_exn_22_m_ungapped_trans_cigar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_cigar)
Test parsing exn_22_m_ungapped_trans_cigar.exn. ... ok
test_exn_22_m_ungapped_trans_vulgar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_vulgar)
Test parsing exn_22_m_ungapped_trans_vulgar.exn. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.168 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_fasta.py
test_Align_fasta ... ok
test_clustalw (test_Align_fasta.TestFASTAReadingWriting.test_clustalw) ... ok
test_empty (test_Align_fasta.TestFASTAReadingWriting.test_empty)
Checking empty file. ... ok
test_kalign (test_Align_fasta.TestFASTAReadingWriting.test_kalign) ... ok
test_msaprobs (test_Align_fasta.TestFASTAReadingWriting.test_msaprobs) ... ok
test_muscle (test_Align_fasta.TestFASTAReadingWriting.test_muscle) ... ok
test_probcons (test_Align_fasta.TestFASTAReadingWriting.test_probcons) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_hhr.py
test_Align_hhr ... ok
test_length (test_Align_hhr.Align_hhr_2uvo_hhblits.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_reading) ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_onlyheader.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_allx.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_allx.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_hhpred_9590198.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_hhpred_9590198.test_reading) ... ok
test_length (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_length)
Test getting the number of alignments without parsing the file. ... ok
test_reading (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_reading) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.314 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_maf.py
test_Align_maf ... ok
test_reading_bug2453 (test_Align_maf.TestAlign_reading.test_reading_bug2453)
Test parsing bug2453.maf. ... ok
test_reading_bundle_without_target (test_Align_maf.TestAlign_reading.test_reading_bundle_without_target)
Test parsing bundle_without_target.maf. ... ok
test_reading_length_coords_mismatch (test_Align_maf.TestAlign_reading.test_reading_length_coords_mismatch)
Test parsing inconsistent MAF file length_coords_mismatch.maf. ... ok
test_reading_missing_signature (test_Align_maf.TestAlign_reading.test_reading_missing_signature)
Test parsing MAF file ucsc_mm9_chr10_big.maf with missing signature. ... ok
test_reading_ucsc_mm9_chr10 (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10)
Test parsing MAF file ucsc_mm9_chr10.maf. ... ok
test_reading_ucsc_mm9_chr10_bad (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10_bad)
Test parsing MAF file ucsc_mm9_chr10_bad.maf with incorrect sequence size. ... ok
test_reading_ucsc_test (test_Align_maf.TestAlign_reading.test_reading_ucsc_test)
Test parsing ucsc_test.maf. ... ok
test_writing_bug2453 (test_Align_maf.TestAlign_writing.test_writing_bug2453)
Test reading and writing bug2453.maf. ... ok
test_writing_bundle_without_target (test_Align_maf.TestAlign_writing.test_writing_bundle_without_target)
Test reading and writing bundle_without_target.maf. ... ok
test_writing_ucsc_mm9_chr10 (test_Align_maf.TestAlign_writing.test_writing_ucsc_mm9_chr10)
Test reading and writing ucsc_mm9_chr10.maf. ... ok
test_writing_ucsc_test (test_Align_maf.TestAlign_writing.test_writing_ucsc_test)
Test reading and writing ucsc_test.maf. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.469 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_mauve.py
test_Align_mauve ... ok
test_parse (test_Align_mauve.TestCombinedFile.test_parse) ... ok
test_write_read (test_Align_mauve.TestCombinedFile.test_write_read) ... ok
test_parse (test_Align_mauve.TestDSeparateFiles.test_parse) ... ok
test_write_read (test_Align_mauve.TestDSeparateFiles.test_write_read) ... ok
test_empty (test_Align_mauve.TestMauveBasic.test_empty) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.097 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_msf.py
test_Align_msf ... ok
test_protein1 (test_Align_msf.TestMSF.test_protein1) ... ok
test_protein2 (test_Align_msf.TestMSF.test_protein2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.060 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_nexus.py
test_Align_nexus ... ok
test_empty (test_Align_nexus.TestNexusBasic.test_empty) ... ok
test_nexus1 (test_Align_nexus.TestNexusReading.test_nexus1) ... ok
test_nexus2 (test_Align_nexus.TestNexusReading.test_nexus2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.086 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_phylip.py
test_Align_phylip ... ok
test_five_and_six (test_Align_phylip.TestPhylipReading.test_five_and_six) ... ok
test_four (test_Align_phylip.TestPhylipReading.test_four) ... ok
test_one (test_Align_phylip.TestPhylipReading.test_one) ... ok
test_two_and_three (test_Align_phylip.TestPhylipReading.test_two_and_three) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_psl.py
test_Align_psl ... ok
test_reading_psl_34_001 (test_Align_psl.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.psl and pslx_34_001.pslx. ... ok
test_reading_psl_34_002 (test_Align_psl.TestAlign_dna.test_reading_psl_34_002)
Test parsing psl_34_002.psl and pslx_34_002.pslx. ... ok
test_reading_psl_34_003 (test_Align_psl.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.psl and pslx_34_003.pslx. ... ok
test_reading_psl_34_004 (test_Align_psl.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.psl and pslx_34_004.pslx. ... ok
test_reading_psl_34_005 (test_Align_psl.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.psl and pslx_34_005.pslx. ... ok
test_writing_psl_34_001 (test_Align_psl.TestAlign_dna.test_writing_psl_34_001)
Test writing the alignments in psl_34_001.psl. ... ok
test_writing_psl_34_002 (test_Align_psl.TestAlign_dna.test_writing_psl_34_002)
Test writing the alignments in psl_34_002.psl. ... ok
test_writing_psl_34_003 (test_Align_psl.TestAlign_dna.test_writing_psl_34_003)
Test writing the alignments in psl_34_003.psl. ... ok
test_writing_psl_34_004 (test_Align_psl.TestAlign_dna.test_writing_psl_34_004)
Test writing the alignments in psl_34_004.psl. ... ok
test_writing_psl_34_005 (test_Align_psl.TestAlign_dna.test_writing_psl_34_005)
Test writing the alignments in psl_34_005.psl. ... ok
test_reading (test_Align_psl.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.psl. ... ok
test_writing (test_Align_psl.TestAlign_dna_rna.test_writing)
Test writing the alignments in dna_rna.psl. ... ok
test_reading_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_001)
Test parsing psl_35_001.psl and pslx_35_001.pslx. ... ok
test_reading_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_002)
Test parsing psl_35_002.psl. ... ok
test_writing_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_001)
Test writing the alignments in psl_35_001.psl. ... ok
test_writing_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_002)
Test writing the alignments in psl_35_002.psl. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.319 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_sam.py
test_Align_sam ... ok
test_4D8I6M (test_Align_sam.TestAlign_clippping.test_4D8I6M)
Test alignment starting with deletion followed by insertion. ... ok
test_4I8D6M (test_Align_sam.TestAlign_clippping.test_4I8D6M)
Test alignment starting with insertion followed by deletion. ... ok
test_4S6M (test_Align_sam.TestAlign_clippping.test_4S6M)
Test alignment starting with soft clip at non-zero position. ... ok
test_4S8D6M (test_Align_sam.TestAlign_clippping.test_4S8D6M)
Test alignment starting with soft clip followed by deletion. ... ok
test_4S8I6M (test_Align_sam.TestAlign_clippping.test_4S8I6M)
Test alignment starting with soft clip followed by insertion. ... ok
test_6M (test_Align_sam.TestAlign_clippping.test_6M)
Test alignment starting at non-zero position. ... ok
test_8D6M_ex1 (test_Align_sam.TestAlign_clippping.test_8D6M_ex1)
Test alignment starting with deletion. ... ok
test_8D6M_ex2 (test_Align_sam.TestAlign_clippping.test_8D6M_ex2)
Test alignment starting with deletion at non-zero position. ... ok
test_8I6M_ex1 (test_Align_sam.TestAlign_clippping.test_8I6M_ex1)
Test alignment starting with insertion. ... ok
test_8I6M_ex2 (test_Align_sam.TestAlign_clippping.test_8I6M_ex2)
Test alignment starting with insertion at non-zero position. ... ok
test_8S6M (test_Align_sam.TestAlign_clippping.test_8S6M)
Test alignment starting with soft clip. ... ok
test_reading_psl_34_001 (test_Align_sam.TestAlign_dna.test_reading_psl_34_001)
Test parsing psl_34_001.sam. ... ok
test_reading_psl_34_003 (test_Align_sam.TestAlign_dna.test_reading_psl_34_003)
Test parsing psl_34_003.sam. ... ok
test_reading_psl_34_004 (test_Align_sam.TestAlign_dna.test_reading_psl_34_004)
Test parsing psl_34_004.sam. ... ok
test_reading_psl_34_005 (test_Align_sam.TestAlign_dna.test_reading_psl_34_005)
Test parsing psl_34_005.sam. ... ok
test_writing_psl_34_001 (test_Align_sam.TestAlign_dna.test_writing_psl_34_001)
Test writing the alignments in psl_34_001.sam. ... ok
test_writing_psl_34_003 (test_Align_sam.TestAlign_dna.test_writing_psl_34_003)
Test writing the alignments in psl_34_003.sam. ... ok
test_writing_psl_34_004 (test_Align_sam.TestAlign_dna.test_writing_psl_34_004)
Test writing the alignments in psl_34_004.sam. ... ok
test_writing_psl_34_005 (test_Align_sam.TestAlign_dna.test_writing_psl_34_005)
Test writing the alignments in psl_34_005.sam. ... ok
test_reading (test_Align_sam.TestAlign_dna_rna.test_reading)
Test parsing dna_rna.sam. ... ok
test_reading_psl_comparison (test_Align_sam.TestAlign_dna_rna.test_reading_psl_comparison)
Test parsing dna_rna.sam and comparing to dna_rna.psl. ... ok
test_writing (test_Align_sam.TestAlign_dna_rna.test_writing)
Test writing the alignments in dna_rna.sam. ... ok
test_ex1 (test_Align_sam.TestAlign_sambam.test_ex1) ... ok
test_ex1_header (test_Align_sam.TestAlign_sambam.test_ex1_header) ... ok
test_sam1 (test_Align_sam.TestAlign_sambam.test_sam1) ... ok
test_sam2 (test_Align_sam.TestAlign_sambam.test_sam2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.379 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_stockholm.py
test_Align_stockholm ... ok
test_reading_alignments_cath1 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath1)
Test parsing CATH record 3.30.160.60/FF/004774. ... ok
test_reading_alignments_cath2 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath2)
Test parsing CATH record 2.105.10.10/FF/000002. ... ok
test_reading_alignments_cath3 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath3)
Test parsing CATH record 1.10.275.10/FF/000026. ... ok
test_reading_example (test_Align_stockholm.TestStockholm_reading.test_reading_example)
Test parsing Pfam record HAT as the docstring example. ... ok
test_reading_writing_alignments_globins45 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_globins45)
Test parsing hmmalign output. ... ok
test_reading_writing_alignments_pfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam1)
Test parsing Pfam record 120_Rick_ant. ... ok
test_reading_writing_alignments_pfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam2)
Test parsing Pfam record 7kD_DNA_binding. ... ok
test_reading_writing_alignments_pfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam3)
Test parsing Pfam record 12TM_1. ... ok
test_reading_writing_alignments_pfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam4)
Test parsing Pfam record 3Beta_HSD. ... ok
test_reading_writing_alignments_pfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam5)
Test parsing Pfam record ArsP_1. ... ok
test_reading_writing_alignments_pfam6 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam6)
Test parsing Pfam record COX2_TM. ... ok
test_reading_writing_alignments_pfam7 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam7)
Test parsing Pfam record Alpha_E1_glycop. ... ok
test_reading_writing_alignments_pfam8 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam8)
Test parsing Pfam record Cyclin_N. ... ok
test_reading_writing_alignments_pfam9 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam9)
Test parsing Pfam record SH3_11. ... ok
test_reading_writing_alignments_rfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam1)
Test parsing Rfam record BTnc005. ... ok
test_reading_writing_alignments_rfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam2)
Test parsing Rfam record SraC_RyeA. ... ok
test_reading_writing_alignments_rfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam3)
Test parsing Rfam record McaS. ... ok
test_reading_writing_alignments_rfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam4)
Test parsing Rfam record IRES_KSHV. ... ok
test_reading_writing_alignments_rfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam5)
Test parsing Rfam record BMV3_UPD-PK3. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.746 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Align_tabular.py
test_Align_tabular ... ok
test_2226_tblastn_001 (test_Align_tabular.TestBlast.test_2226_tblastn_001) ... ok
test_2226_tblastn_002 (test_Align_tabular.TestBlast.test_2226_tblastn_002) ... ok
test_2226_tblastn_003 (test_Align_tabular.TestBlast.test_2226_tblastn_003) ... ok
test_2226_tblastn_004 (test_Align_tabular.TestBlast.test_2226_tblastn_004) ... ok
test_2226_tblastn_005 (test_Align_tabular.TestBlast.test_2226_tblastn_005) ... ok
test_2226_tblastn_007 (test_Align_tabular.TestBlast.test_2226_tblastn_007) ... ok
test_2226_tblastn_008 (test_Align_tabular.TestBlast.test_2226_tblastn_008) ... ok
test_2226_tblastn_009 (test_Align_tabular.TestBlast.test_2226_tblastn_009) ... ok
test_2226_tblastn_010 (test_Align_tabular.TestBlast.test_2226_tblastn_010) ... ok
test_2226_tblastn_011 (test_Align_tabular.TestBlast.test_2226_tblastn_011) ... ok
test_2226_tblastn_012 (test_Align_tabular.TestBlast.test_2226_tblastn_012) ... ok
test_2228_tblastn_001 (test_Align_tabular.TestBlast.test_2228_tblastn_001) ... ok
test_2228_tblastx_001 (test_Align_tabular.TestBlast.test_2228_tblastx_001) ... ok
test_empty (test_Align_tabular.TestFastaBasic.test_empty) ... ok
test_m8CB (test_Align_tabular.TestFastaNucleotide.test_m8CB) ... ok
test_m8CC (test_Align_tabular.TestFastaNucleotide.test_m8CC) ... ok
test_m8CB (test_Align_tabular.TestFastaProtein.test_m8CB) ... ok
test_m8CC (test_Align_tabular.TestFastaProtein.test_m8CC) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.457 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Application.py
test_Application ... ok
test_echo (test_Application.TestApp.test_echo) ... ok
test_echo_capture_both (test_Application.TestApp.test_echo_capture_both) ... ok
test_echo_capture_neither (test_Application.TestApp.test_echo_capture_neither) ... ok
test_echo_capture_stderr (test_Application.TestApp.test_echo_capture_stderr) ... ok
test_echo_capture_stdout (test_Application.TestApp.test_echo_capture_stdout) ... ok
test_echo_file_both (test_Application.TestApp.test_echo_file_both) ... ok
test_echo_file_same (test_Application.TestApp.test_echo_file_same) ... ok
test_echo_file_stderr (test_Application.TestApp.test_echo_file_stderr) ... ok
test_echo_file_stdout (test_Application.TestApp.test_echo_file_stdout) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.054 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BWA_tool.py
test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.023 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb.py
test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.135 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb_online.py
test_BioSQL_MySQLdb_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.092 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector.py
test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector_online.py
test_BioSQL_mysql_connector_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.092 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2.py
test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.093 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2_online.py
test_BioSQL_psycopg2_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.099 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3.py
test_BioSQL_sqlite3 ... ok
test_SeqIO_loading (common_BioSQL.AutoSeqIOTests.test_SeqIO_loading) ... ok
test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest.test_backwards_compatibility)
Check can re-use an old BioSQL SQLite3 database. ... ok
test_NC_000932 (common_BioSQL.ClosedLoopTest.test_NC_000932)
From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok
test_NC_005816 (common_BioSQL.ClosedLoopTest.test_NC_005816)
From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok
test_NT_019265 (common_BioSQL.ClosedLoopTest.test_NT_019265)
From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok
test_arab1 (common_BioSQL.ClosedLoopTest.test_arab1)
From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok
test_cor6_6 (common_BioSQL.ClosedLoopTest.test_cor6_6)
From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok
test_no_ref (common_BioSQL.ClosedLoopTest.test_no_ref)
From GenBank file to BioSQL and back to a GenBank file, noref. ... ok
test_one_of (common_BioSQL.ClosedLoopTest.test_one_of)
From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok
test_protein_refseq2 (common_BioSQL.ClosedLoopTest.test_protein_refseq2)
From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok
test_del_db_items (common_BioSQL.DeleteTest.test_del_db_items)
Check all associated data is deleted from an item. ... ok
test_server (common_BioSQL.DeleteTest.test_server)
Check BioSeqDatabase methods. ... ok
test_duplicate_id_load (common_BioSQL.DupLoadTest.test_duplicate_id_load)
Make sure can't import records with same ID (in one go). ... ok
test_duplicate_load (common_BioSQL.DupLoadTest.test_duplicate_load)
Make sure can't import a single record twice (in one go). ... ok
test_duplicate_load2 (common_BioSQL.DupLoadTest.test_duplicate_load2)
Make sure can't import a single record twice (in steps). ... ok
test_record_loading (common_BioSQL.InDepthLoadTest.test_record_loading)
Make sure all records are correctly loaded. ... ok
test_reload (common_BioSQL.InDepthLoadTest.test_reload)
Make sure can't reimport existing records. ... ok
test_seq_feature (common_BioSQL.InDepthLoadTest.test_seq_feature)
In depth check that SeqFeatures are transmitted through the db. ... ok
test_transfer (common_BioSQL.InDepthLoadTest.test_transfer)
Make sure can load record into another namespace. ... ok
test_load_database (common_BioSQL.LoaderTest.test_load_database)
Load SeqRecord objects into a BioSQL database. ... ok
test_cross_retrieval_of_items (common_BioSQL.MultiReadTest.test_cross_retrieval_of_items)
Test that valid ids can't be retrieved between namespaces. ... ok
test_get_db_items (common_BioSQL.MultiReadTest.test_get_db_items)
Check list, keys, length etc. ... ok
test_server (common_BioSQL.MultiReadTest.test_server)
Check BioSeqDatabase methods. ... ok
test_get_db_items (common_BioSQL.ReadTest.test_get_db_items)
Check list, keys, length etc. ... ok
test_lookup_items (common_BioSQL.ReadTest.test_lookup_items)
Test retrieval of items using various ids. ... ok
test_server (common_BioSQL.ReadTest.test_server)
Check BioSeqDatabase methods. ... ok
test_addition (common_BioSQL.SeqInterfaceTest.test_addition)
Check can add Seq objects from BioSQL together. ... ok
test_convert (common_BioSQL.SeqInterfaceTest.test_convert)
Check can turn a Seq object from BioSQL into a Seq or MutableSeq. ... ok
test_eq (common_BioSQL.SeqInterfaceTest.test_eq) ... ok
test_ge (common_BioSQL.SeqInterfaceTest.test_ge) ... ok
test_gt (common_BioSQL.SeqInterfaceTest.test_gt) ... ok
test_le (common_BioSQL.SeqInterfaceTest.test_le) ... ok
test_lt (common_BioSQL.SeqInterfaceTest.test_lt) ... ok
test_multiplication (common_BioSQL.SeqInterfaceTest.test_multiplication)
Check can multiply Seq objects from BioSQL by integers. ... ok
test_ne (common_BioSQL.SeqInterfaceTest.test_ne) ... ok
test_record_slicing (common_BioSQL.SeqInterfaceTest.test_record_slicing)
Check that slices of DBSeqRecord are retrieved properly. ... ok
test_seq (common_BioSQL.SeqInterfaceTest.test_seq)
Make sure Seqs from BioSQL implement the right interface. ... ok
test_seq_features (common_BioSQL.SeqInterfaceTest.test_seq_features)
Check SeqFeatures of a sequence. ... ok
test_seq_record (common_BioSQL.SeqInterfaceTest.test_seq_record)
Make sure SeqRecords from BioSQL implement the right interface. ... ok
test_seq_slicing (common_BioSQL.SeqInterfaceTest.test_seq_slicing)
Check that slices of sequences are retrieved properly. ... ok
test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest.test_ambiguous_location)
Loaded uniprot-xml with ambiguous location in BioSQL. ... ok
test_add (common_BioSQL.TestBaseClassMethods.test_add) ... ok
test_bytes (common_BioSQL.TestBaseClassMethods.test_bytes) ... ok
test_contains (common_BioSQL.TestBaseClassMethods.test_contains) ... ok
test_count (common_BioSQL.TestBaseClassMethods.test_count) ... ok
test_endswith (common_BioSQL.TestBaseClassMethods.test_endswith) ... ok
test_find (common_BioSQL.TestBaseClassMethods.test_find) ... ok
test_hash (common_BioSQL.TestBaseClassMethods.test_hash) ... ok
test_index (common_BioSQL.TestBaseClassMethods.test_index) ... ok
test_lower (common_BioSQL.TestBaseClassMethods.test_lower) ... ok
test_lstrip (common_BioSQL.TestBaseClassMethods.test_lstrip) ... ok
test_mul (common_BioSQL.TestBaseClassMethods.test_mul) ... ok
test_radd (common_BioSQL.TestBaseClassMethods.test_radd) ... ok
test_replace (common_BioSQL.TestBaseClassMethods.test_replace) ... ok
test_repr (common_BioSQL.TestBaseClassMethods.test_repr) ... ok
test_rfind (common_BioSQL.TestBaseClassMethods.test_rfind) ... ok
test_rindex (common_BioSQL.TestBaseClassMethods.test_rindex) ... ok
test_rsplit (common_BioSQL.TestBaseClassMethods.test_rsplit) ... ok
test_rstrip (common_BioSQL.TestBaseClassMethods.test_rstrip) ... ok
test_split (common_BioSQL.TestBaseClassMethods.test_split) ... ok
test_startswith (common_BioSQL.TestBaseClassMethods.test_startswith) ... ok
test_str (common_BioSQL.TestBaseClassMethods.test_str) ... ok
test_strip (common_BioSQL.TestBaseClassMethods.test_strip) ... ok
test_translate (common_BioSQL.TestBaseClassMethods.test_translate) ... ok
test_upper (common_BioSQL.TestBaseClassMethods.test_upper) ... ok
test_NC_000932 (common_BioSQL.TransferTest.test_NC_000932)
From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok
test_NC_005816 (common_BioSQL.TransferTest.test_NC_005816)
From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok
test_NT_019265 (common_BioSQL.TransferTest.test_NT_019265)
From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok
test_arab1 (common_BioSQL.TransferTest.test_arab1)
From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok
test_cor6_6 (common_BioSQL.TransferTest.test_cor6_6)
From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok
test_no_ref (common_BioSQL.TransferTest.test_no_ref)
From GenBank file to BioSQL, then again to a new namespace, noref. ... ok
test_one_of (common_BioSQL.TransferTest.test_one_of)
From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok
test_protein_refseq2 (common_BioSQL.TransferTest.test_protein_refseq2)
From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.273 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3_online.py
test_BioSQL_sqlite3_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.099 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Blast_Record.py
test_Blast_Record ... ok
test_str (test_Blast_Record.TestHsp.test_str) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.052 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CAPS.py
test_CAPS ... ok
test (test_CAPS.TestCAPS.test) ... ok
testNoCAPS (test_CAPS.TestCAPS.testNoCAPS) ... ok
testNoCAPS_msa (test_CAPS.TestCAPS.testNoCAPS_msa) ... ok
test_msa (test_CAPS.TestCAPS.test_msa) ... ok
test_trivial (test_CAPS.TestCAPS.test_trivial) ... ok
test_trivial_msa (test_CAPS.TestCAPS.test_trivial_msa) ... ok
test_uneven (test_CAPS.TestCAPS.test_uneven) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.190 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Chi2.py
test_Chi2 ... ok
test_cdf_chi2 (test_Chi2.ModTest.test_cdf_chi2) ... ok
test_incomplete_gamma (test_Chi2.ModTest.test_incomplete_gamma) ... ok
test_ln_gamma (test_Chi2.ModTest.test_ln_gamma) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.102 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ClustalOmega_tool.py
test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Clustalw_tool.py
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Cluster.py
test_Cluster ... ok
test_clusterdistance (test_Cluster.TestCluster.test_clusterdistance) ... ok
test_clusterdistance_arguments (test_Cluster.TestCluster.test_clusterdistance_arguments) ... ok
test_distancematrix_arguments (test_Cluster.TestCluster.test_distancematrix_arguments) ... ok
test_distancematrix_kmedoids (test_Cluster.TestCluster.test_distancematrix_kmedoids) ... ok
test_kcluster (test_Cluster.TestCluster.test_kcluster) ... ok
test_kcluster_arguments (test_Cluster.TestCluster.test_kcluster_arguments) ... ok
test_kmedoids_arguments (test_Cluster.TestCluster.test_kmedoids_arguments) ... ok
test_mask_parse (test_Cluster.TestCluster.test_mask_parse) ... ok
test_matrix_parse (test_Cluster.TestCluster.test_matrix_parse) ... ok
test_pca (test_Cluster.TestCluster.test_pca) ... ok
test_pca_arguments (test_Cluster.TestCluster.test_pca_arguments) ... ok
test_somcluster (test_Cluster.TestCluster.test_somcluster) ... ok
test_somcluster_arguments (test_Cluster.TestCluster.test_somcluster_arguments) ... ok
test_tree (test_Cluster.TestCluster.test_tree) ... ok
test_tree_arguments (test_Cluster.TestCluster.test_tree_arguments) ... ok
test_treecluster (test_Cluster.TestCluster.test_treecluster) ... ok
test_treecluster_arguments (test_Cluster.TestCluster.test_treecluster_arguments) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.044 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_CodonTable.py
test_CodonTable ... ok
test_coding (test_CodonTable.AmbiguousCodonsTests.test_coding)
Check a few ambiguous codons for correct coding. ... ok
test_list_ambiguous_codons (test_CodonTable.AmbiguousCodonsTests.test_list_ambiguous_codons)
Check if stop codons are properly extended. ... ok
test_start_codons (test_CodonTable.AmbiguousCodonsTests.test_start_codons)
Test various ambiguous codons as start codon. ... ok
test_stop_codons (test_CodonTable.AmbiguousCodonsTests.test_stop_codons)
Test various ambiguous codons as stop codon. ... ok
test_ambiguous_tables (test_CodonTable.BasicSanityTests.test_ambiguous_tables)
Check if all IDs and all names are present in ambiguous tables. ... ok
test_complete_tables (test_CodonTable.BasicSanityTests.test_complete_tables)
Check if all unambiguous codon tables have all entries. ... ok
test_number_of_tables (test_CodonTable.BasicSanityTests.test_number_of_tables)
Check if we have the same number of tables for each type. ... ok
test_ambiguous_forward_table (test_CodonTable.ErrorConditions.test_ambiguous_forward_table)
Raise errors in AmbiguousForwardTable. ... ok
test_list_possible_proteins (test_CodonTable.ErrorConditions.test_list_possible_proteins)
Raise errors in list_possible proteins. ... ok
test_print_table (test_CodonTable.PrintTable.test_print_table)
Test output of __str__ function. ... ok
test_table01 (test_CodonTable.SingleTableTests.test_table01)
Check table 1: Standard. ... ok
test_table02 (test_CodonTable.SingleTableTests.test_table02)
Check table 2: Vertebrate Mitochondrial. ... ok
test_table03 (test_CodonTable.SingleTableTests.test_table03)
Check table 3: Yeast Mitochondrial. ... ok
test_table04 (test_CodonTable.SingleTableTests.test_table04)
Check table 4: Mold Mitochondrial and others. ... ok
test_table05 (test_CodonTable.SingleTableTests.test_table05)
Check table 5: Invertebrate Mitochondrial. ... ok
test_table06 (test_CodonTable.SingleTableTests.test_table06)
Check table 6: Ciliate and Other Nuclear. ... ok
test_table09 (test_CodonTable.SingleTableTests.test_table09)
Check table 9: Echinoderm and Flatworm Mitochondrial. ... ok
test_table10 (test_CodonTable.SingleTableTests.test_table10)
Check table 10: Euplotid Nuclear. ... ok
test_table11 (test_CodonTable.SingleTableTests.test_table11)
Check table 11: Bacterial, Archaeal and Plant Plastid. ... ok
test_table12 (test_CodonTable.SingleTableTests.test_table12)
Check table 12: Alternative Yeast Nuclear. ... ok
test_table13 (test_CodonTable.SingleTableTests.test_table13)
Check table 13: Ascidian Mitochondrial. ... ok
test_table14 (test_CodonTable.SingleTableTests.test_table14)
Check table 14: Alternative Flatworm Mitochondrial. ... ok
test_table16 (test_CodonTable.SingleTableTests.test_table16)
Check table 16: Chlorophycean Mitochondrial. ... ok
test_table21 (test_CodonTable.SingleTableTests.test_table21)
Check table 21: Trematode Mitochondrial. ... ok
test_table22 (test_CodonTable.SingleTableTests.test_table22)
Check table 22: Scenedesmus obliquus Mitochondrial. ... ok
test_table23 (test_CodonTable.SingleTableTests.test_table23)
Check table 9: Thraustochytrium Mitochondrial. ... ok
test_table24 (test_CodonTable.SingleTableTests.test_table24)
Check table 24: Pterobranchia Mitochondrial. ... ok
test_table25 (test_CodonTable.SingleTableTests.test_table25)
Check table 25: Candidate Division SR1 and Gracilibacteria. ... ok
test_table26 (test_CodonTable.SingleTableTests.test_table26)
Check table 26: Pachysolen tannophilus Nuclear. ... ok
test_table27 (test_CodonTable.SingleTableTests.test_table27)
Check table 27: Karyorelict Nuclear. ... ok
test_table28 (test_CodonTable.SingleTableTests.test_table28)
Check table 28: Condylostoma Nuclear. ... ok
test_table29 (test_CodonTable.SingleTableTests.test_table29)
Check table 29: Mesodinium Nuclear. ... ok
test_table30 (test_CodonTable.SingleTableTests.test_table30)
Check table 30: Peritrich Nuclear. ... ok
test_table31 (test_CodonTable.SingleTableTests.test_table31)
Check table 31: Blastocrithidia Nuclear. ... ok
test_table32 (test_CodonTable.SingleTableTests.test_table32)
Check table 32: Balanophoraceae Plastid. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.057 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ColorSpiral.py
test_ColorSpiral ... ok
test_dict (test_ColorSpiral.DictTest.test_dict)
get_color_dict() for classes A-D, no jitter. ... ok
test_colorlist (test_ColorSpiral.SpiralTest.test_colorlist)
Get set of eight colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SpiralTest.test_colorspiral)
Get set of 16 colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SquareTest.test_colorspiral)
Set of 625 colours, with jitter, using get_colors(). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.072 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Compass.py
test_Compass ... ok
testAlignmentParsingOne (test_Compass.CompassTest.testAlignmentParsingOne) ... ok
testAlignmentParsingTwo (test_Compass.CompassTest.testAlignmentParsingTwo) ... ok
testCompassIteratorEasy (test_Compass.CompassTest.testCompassIteratorEasy) ... ok
testCompassIteratorHard (test_Compass.CompassTest.testCompassIteratorHard) ... ok
testCompassParser (test_Compass.CompassTest.testCompassParser) ... ok
testCompassScanAndConsume (test_Compass.CompassTest.testCompassScanAndConsume) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.017 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Consensus.py
test_Consensus ... ok
test_bitstring (test_Consensus.BitStringTest.test_bitstring) ... ok
test_bootstrap (test_Consensus.BootstrapTest.test_bootstrap) ... ok
test_bootstrap_consensus (test_Consensus.BootstrapTest.test_bootstrap_consensus) ... ok
test_bootstrap_consensus_msa (test_Consensus.BootstrapTest.test_bootstrap_consensus_msa) ... ok
test_bootstrap_trees (test_Consensus.BootstrapTest.test_bootstrap_trees) ... ok
test_bootstrap_trees_msa (test_Consensus.BootstrapTest.test_bootstrap_trees_msa) ... ok
test_adam_consensus (test_Consensus.ConsensusTest.test_adam_consensus) ... ok
test_count_clades (test_Consensus.ConsensusTest.test_count_clades) ... ok
test_get_support (test_Consensus.ConsensusTest.test_get_support) ... ok
test_majority_consensus (test_Consensus.ConsensusTest.test_majority_consensus) ... ok
test_strict_consensus (test_Consensus.ConsensusTest.test_strict_consensus) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.756 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Dialign_tool.py
test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.061 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EMBL_unittest.py
test_EMBL_unittest ... ok
test_embl_0_line (test_EMBL_unittest.EMBLTests.test_embl_0_line)
Test SQ line with 0 length sequence. ... ok
test_embl_content_after_co (test_EMBL_unittest.EMBLTests.test_embl_content_after_co)
Test a ValueError is thrown by content after a CO line. ... ok
test_embl_no_coords (test_EMBL_unittest.EMBLTests.test_embl_no_coords)
Test sequence lines without coordinates. ... ok
test_embl_wrong_dr_line (test_EMBL_unittest.EMBLTests.test_embl_wrong_dr_line)
Test files with wrong DR lines. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Emboss.py
test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss.
----------------------------------------------------------------------
Ran 1 test in 0.114 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPhylipNew.py
test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools.
----------------------------------------------------------------------
Ran 1 test in 0.103 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_EmbossPrimer.py
test_EmbossPrimer ... ok
test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest.test_in_depth_single_parse)
Make sure we get info right from a single primer find. ... ok
test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest.test_indepth_regular_parse)
Make sure we get the data from normal primer3 files okay. ... ok
test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest.test_internal_oligo_single_parse)
Make sure we can parse an internal oligo file correctly. ... ok
test_multi_record_full (test_EmbossPrimer.Primer3ParseTest.test_multi_record_full)
Test parsing multiple primer sets (NirK full). ... ok
test_multi_record_fwd (test_EmbossPrimer.Primer3ParseTest.test_multi_record_fwd)
Test parsing multiple primer sets (NirK forward). ... ok
test_simple_parse (test_EmbossPrimer.Primer3ParseTest.test_simple_parse)
Make sure that we can use all single target primer3 files. ... ok
test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest.test_primer_representation)
Make sure we can output primer information correctly. ... ok
test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest.test_in_depth_normal_parse)
Make sure the output from a simple primersearch file is correct. ... ok
test_simple_parse (test_EmbossPrimer.PrimersearchParseTest.test_simple_parse)
Make sure that we can parse all primersearch files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.020 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez.py
C
test_Entrez ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Entrez/__init__.py:694: UserWarning: 
            Email address is not specified.
            To make use of NCBI's E-utilities, NCBI requires you to specify your
            email address with each request.  As an example, if your email address
            is A.N.Other@example.com, you can specify it as follows:
               from Bio import Entrez
               Entrez.email = 'A.N.Other@example.com'
            In case of excessive usage of the E-utilities, NCBI will attempt to contact
            a user at the email address provided before blocking access to the
            E-utilities.
  warnings.warn(
ok
test_custom_directory (test_Entrez.CustomDirectoryTest.test_custom_directory) ... ok
test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction.test_construct_cgi_ecitmatch) ... ok
test_construct_cgi_efetch (test_Entrez.TestURLConstruction.test_construct_cgi_efetch) ... ok
test_construct_cgi_einfo (test_Entrez.TestURLConstruction.test_construct_cgi_einfo)
Test constructed url for request to Entrez. ... ok
test_construct_cgi_elink1 (test_Entrez.TestURLConstruction.test_construct_cgi_elink1) ... ok
test_construct_cgi_elink2 (test_Entrez.TestURLConstruction.test_construct_cgi_elink2)
Commas: Link from protein to gene. ... ok
test_construct_cgi_elink3 (test_Entrez.TestURLConstruction.test_construct_cgi_elink3)
Multiple ID entries: Find one-to-one links from protein to gene. ... ok
test_construct_cgi_epost1 (test_Entrez.TestURLConstruction.test_construct_cgi_epost1) ... ok
test_construct_cgi_epost2 (test_Entrez.TestURLConstruction.test_construct_cgi_epost2) ... ok
test_default_params (test_Entrez.TestURLConstruction.test_default_params)
Test overriding default values for the "email", "api_key", and "tool" parameters. ... ok
test_email_warning (test_Entrez.TestURLConstruction.test_email_warning)
Test issuing warning when user does not specify email address. ... ok
test_format_ids (test_Entrez.TestURLConstruction.test_format_ids) ... ok
test_has_api_key (test_Entrez.TestURLConstruction.test_has_api_key)
Test checking whether a Request object specifies an API key. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.155 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez_online.py
test_Entrez_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.072 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Entrez_parser.py
test_Entrez_parser ... ok
test_efetch_schemas (test_Entrez_parser.EFetchTest.test_efetch_schemas)
Test parsing XML using Schemas. ... ok
test_fasta (test_Entrez_parser.EFetchTest.test_fasta)
Test error handling when presented with Fasta non-XML data. ... ok
test_genbank (test_Entrez_parser.EFetchTest.test_genbank)
Test error handling when presented with GenBank non-XML data. ... ok
test_nucleotide1 (test_Entrez_parser.EFetchTest.test_nucleotide1)
Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok
test_nucleotide2 (test_Entrez_parser.EFetchTest.test_nucleotide2)
Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok
test_omim (test_Entrez_parser.EFetchTest.test_omim)
Test parsing XML returned by EFetch, OMIM database. ... ok
test_pmc (test_Entrez_parser.EFetchTest.test_pmc)
Test parsing XML returned by EFetch from PubMed Central. ... ok
test_protein (test_Entrez_parser.EFetchTest.test_protein)
Test parsing XML returned by EFetch, Protein database. ... ok
test_pubmed1 (test_Entrez_parser.EFetchTest.test_pubmed1)
Test parsing XML returned by EFetch, PubMed database (first test). ... ok
test_pubmed2 (test_Entrez_parser.EFetchTest.test_pubmed2)
Test parsing XML returned by EFetch, PubMed database (second test). ... ok
test_pubmed_html (test_Entrez_parser.EFetchTest.test_pubmed_html)
Test error handling when presented with HTML (so XML-like) data. ... ok
test_pubmed_html_escaping (test_Entrez_parser.EFetchTest.test_pubmed_html_escaping)
Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok
test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_mathml_tags)
Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok
test_pubmed_html_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_tags)
Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok
test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_mathml_tags)
Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok
test_taxonomy (test_Entrez_parser.EFetchTest.test_taxonomy)
Test parsing XML returned by EFetch, Taxonomy database. ... ok
test_truncated_xml (test_Entrez_parser.EFetchTest.test_truncated_xml)
Test error handling for a truncated XML declaration. ... ok
test_xml_without_declaration (test_Entrez_parser.EFetchTest.test_xml_without_declaration)
Test error handling for a missing XML declaration. ... ok
test_xml_without_definition (test_Entrez_parser.EFetchTest.test_xml_without_definition)
Test error handling for a missing DTD or XML Schema. ... ok
test_egquery1 (test_Entrez_parser.EGQueryTest.test_egquery1)
Test parsing XML output returned by EGQuery (first test). ... ok
test_egquery2 (test_Entrez_parser.EGQueryTest.test_egquery2)
Test parsing XML output returned by EGQuery (second test). ... ok
test_corrupted (test_Entrez_parser.EInfoTest.test_corrupted)
Test if corrupted XML is handled correctly. ... ok
test_list (test_Entrez_parser.EInfoTest.test_list)
Test parsing database list returned by EInfo. ... ok
test_pubmed1 (test_Entrez_parser.EInfoTest.test_pubmed1)
Test parsing database info returned by EInfo. ... ok
test_pubmed2 (test_Entrez_parser.EInfoTest.test_pubmed2)
Test validating the XML against the DTD. ... ok
test_pubmed3 (test_Entrez_parser.EInfoTest.test_pubmed3)
Test non-validating parser on XML with an inconsistent DTD. ... ok
test_medline (test_Entrez_parser.ELinkTest.test_medline)
Test parsing medline indexed articles returned by ELink. ... ok
test_nucleotide (test_Entrez_parser.ELinkTest.test_nucleotide)
Test parsing Nucleotide to Protein links returned by ELink. ... ok
test_pubmed1 (test_Entrez_parser.ELinkTest.test_pubmed1)
Test parsing pubmed links returned by ELink (first test). ... ok
test_pubmed2 (test_Entrez_parser.ELinkTest.test_pubmed2)
Test parsing pubmed links returned by ELink (second test). ... ok
test_pubmed3 (test_Entrez_parser.ELinkTest.test_pubmed3)
Test parsing pubmed link returned by ELink (third test). ... ok
test_pubmed4 (test_Entrez_parser.ELinkTest.test_pubmed4)
Test parsing pubmed links returned by ELink (fourth test). ... ok
test_pubmed5 (test_Entrez_parser.ELinkTest.test_pubmed5)
Test parsing pubmed links returned by ELink (fifth test). ... ok
test_pubmed6 (test_Entrez_parser.ELinkTest.test_pubmed6)
Test parsing pubmed links returned by ELink (sixth test). ... ok
test_epost (test_Entrez_parser.EPostTest.test_epost)
Test parsing XML returned by EPost. ... ok
test_invalid (test_Entrez_parser.EPostTest.test_invalid)
Test parsing XML returned by EPost with invalid id (overflow tag). ... ok
test_wrong (test_Entrez_parser.EPostTest.test_wrong)
Test parsing XML returned by EPost with incorrect arguments. ... ok
test_journals (test_Entrez_parser.ESearchTest.test_journals)
Test parsing XML returned by ESearch from the Journals database. ... ok
test_notfound (test_Entrez_parser.ESearchTest.test_notfound)
Test parsing XML returned by ESearch when no items were found. ... ok
test_nucleotide (test_Entrez_parser.ESearchTest.test_nucleotide)
Test parsing XML returned by ESearch from the Nucleotide database. ... ok
test_pmc (test_Entrez_parser.ESearchTest.test_pmc)
Test parsing XML returned by ESearch from PubMed Central. ... ok
test_protein (test_Entrez_parser.ESearchTest.test_protein)
Test parsing XML returned by ESearch from the Protein database. ... ok
test_pubmed1 (test_Entrez_parser.ESearchTest.test_pubmed1)
Test parsing XML returned by ESearch from PubMed (first test). ... ok
test_pubmed2 (test_Entrez_parser.ESearchTest.test_pubmed2)
Test parsing XML returned by ESearch from PubMed (second test). ... ok
test_pubmed3 (test_Entrez_parser.ESearchTest.test_pubmed3)
Test parsing XML returned by ESearch from PubMed (third test). ... ok
test_espell (test_Entrez_parser.ESpellTest.test_espell)
Test parsing XML output returned by ESpell. ... ok
test_integer_none (test_Entrez_parser.ESummaryTest.test_integer_none)
Test parsing ESummary XML where an Integer is not defined. ... ok
test_journals (test_Entrez_parser.ESummaryTest.test_journals)
Test parsing XML returned by ESummary from the Journals database. ... ok
test_nucleotide (test_Entrez_parser.ESummaryTest.test_nucleotide)
Test parsing XML returned by ESummary from the Nucleotide database. ... ok
test_protein (test_Entrez_parser.ESummaryTest.test_protein)
Test parsing XML returned by ESummary from the Protein database. ... ok
test_pubmed (test_Entrez_parser.ESummaryTest.test_pubmed)
Test parsing XML returned by ESummary from PubMed. ... ok
test_structure (test_Entrez_parser.ESummaryTest.test_structure)
Test parsing XML returned by ESummary from the Structure database. ... ok
test_taxonomy (test_Entrez_parser.ESummaryTest.test_taxonomy)
Test parsing XML returned by ESummary from the Taxonomy database. ... ok
test_unists (test_Entrez_parser.ESummaryTest.test_unists)
Test parsing XML returned by ESummary from the UniSTS database. ... ok
test_wrong (test_Entrez_parser.ESummaryTest.test_wrong)
Test parsing XML returned by ESummary with incorrect arguments. ... ok
test_BytesIO (test_Entrez_parser.GeneralTests.test_BytesIO)
Test parsing a BytesIO handle (bytes not string). ... ok
test_closed_handle (test_Entrez_parser.GeneralTests.test_closed_handle)
Test parsing closed handle fails gracefully. ... ok
test_parse_bytes_handle (test_Entrez_parser.GeneralTests.test_parse_bytes_handle)
Test parsing a handle opened in binary mode. ... ok
test_parse_text_handle (test_Entrez_parser.GeneralTests.test_parse_text_handle)
Test parsing a handle opened in text mode. ... ok
test_pickle (test_Entrez_parser.GeneralTests.test_pickle)
Test if records created by the parser can be pickled. ... ok
test_read_bytes_handle (test_Entrez_parser.GeneralTests.test_read_bytes_handle)
Test reading a handle opened in binary mode. ... ok
test_read_text_handle (test_Entrez_parser.GeneralTests.test_read_text_handle)
Test reading a handle opened in text mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.563 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Enzyme.py
test_Enzyme ... ok
test_lactate (test_Enzyme.TestEnzyme.test_lactate)
Parsing ENZYME record for lactate racemase (5.1.2.1). ... ok
test_lipoprotein (test_Enzyme.TestEnzyme.test_lipoprotein)
Parsing ENZYME record for lipoprotein lipase (3.1.1.34). ... ok
test_parse_many (test_Enzyme.TestEnzyme.test_parse_many)
Check parse function with multiple records. ... ok
test_parse_one (test_Enzyme.TestEnzyme.test_parse_one)
Check parse function with one record. ... ok
test_parse_zero (test_Enzyme.TestEnzyme.test_parse_zero) ... ok
test_proline (test_Enzyme.TestEnzyme.test_proline)
Parsing ENZYME record for proline racemase (5.1.1.4). ... ok
test_valine (test_Enzyme.TestEnzyme.test_valine)
Parsing ENZYME record for valine decarboxylase (4.1.1.14). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ExPASy.py
test_ExPASy ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.008 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_Fasttree_tool.py
test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.130 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_File.py
C
test_File ... ok
test_custom_path_like_object (test_File.AsHandleTestCase.test_custom_path_like_object)
Test as_handle with a custom path-like object. ... ok
test_handle (test_File.AsHandleTestCase.test_handle)
Test as_handle with a file-like object argument. ... ok
test_path_object (test_File.AsHandleTestCase.test_path_object)
Test as_handle with a pathlib.Path object. ... ok
test_string_path (test_File.AsHandleTestCase.test_string_path)
Test as_handle with a string path argument. ... ok
test_stringio (test_File.AsHandleTestCase.test_stringio)
Testing passing StringIO handles. ... ok
test_instance_exception (test_File.BaseClassTests.test_instance_exception) ... ok
test_bgzf (test_File.RandomAccess.test_bgzf)
Test BGZF compressed file. ... ok
test_gzip (test_File.RandomAccess.test_gzip)
Test gzip compressed file. ... ok
test_plain (test_File.RandomAccess.test_plain)
Test plain text file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenBank.py
C
test_GenBank ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_embl_cds_interaction (test_GenBank.GenBankScannerTests.test_embl_cds_interaction)
Test EMBL CDS interaction, parse CDS features on embl files. ... ok
test_embl_record_interaction (test_GenBank.GenBankScannerTests.test_embl_record_interaction)
Test EMBL Record interaction on embl files. ... ok
test_genbank_cds_interaction (test_GenBank.GenBankScannerTests.test_genbank_cds_interaction)
Test CDS interaction, parse CDS features on gb(k) files. ... ok
test_genbank_interaction (test_GenBank.GenBankScannerTests.test_genbank_interaction)
Test GenBank records interaction on gbk files. ... ok
test_000_genbank_bad_loc_wrap_warning (test_GenBank.GenBankTests.test_000_genbank_bad_loc_wrap_warning)
Feature line wrapping warning. ... ok
test_001_genbank_bad_origin_wrapping_location (test_GenBank.GenBankTests.test_001_genbank_bad_origin_wrapping_location)
Bad origin wrapping. ... ok
test_001_implicit_orign_wrap_fix (test_GenBank.GenBankTests.test_001_implicit_orign_wrap_fix)
Attempt to fix implied origin wrapping. ... ok
test_001_negative_location_warning (test_GenBank.GenBankTests.test_001_negative_location_warning)
Un-parsable feature location warning. ... ok
test_compound_complex_origin_wrap (test_GenBank.GenBankTests.test_compound_complex_origin_wrap)
Test the attempts to fix compound complex origin wrapping. ... ok
test_dbline_embl_gb (test_GenBank.GenBankTests.test_dbline_embl_gb)
Parse GenBank/EMBL paired records with PR project entry: EMBL. ... ok
test_dbline_gb_embl (test_GenBank.GenBankTests.test_dbline_gb_embl)
Parse GenBank/EMBL paired records with PR project entry: GenBank. ... ok
test_dblink (test_GenBank.GenBankTests.test_dblink)
Parse GenBank record with old DBLINK project entry. ... ok
test_dblink_two (test_GenBank.GenBankTests.test_dblink_two)
Parse GenBank record with old and new DBLINK project entries. ... ok
test_dot_lineage (test_GenBank.GenBankTests.test_dot_lineage)
Missing taxonomy lineage. ... ok
test_extremely_long_sequence (test_GenBank.GenBankTests.test_extremely_long_sequence)
Tests if extremely long sequences can be read. ... ok
test_fuzzy_origin_wrap (test_GenBank.GenBankTests.test_fuzzy_origin_wrap)
Test features that wrap an origin, and have fuzzy location. ... ok
test_genbank_bad_loc_wrap_parsing (test_GenBank.GenBankTests.test_genbank_bad_loc_wrap_parsing)
Bad location wrapping. ... ok
test_genbank_date_correct (test_GenBank.GenBankTests.test_genbank_date_correct)
Check if user provided date is inserted correctly. ... ok
test_genbank_date_datetime (test_GenBank.GenBankTests.test_genbank_date_datetime)
Check if datetime objects are handled correctly. ... ok
test_genbank_date_default (test_GenBank.GenBankTests.test_genbank_date_default)
Check if default date is handled correctly. ... ok
test_genbank_date_invalid (test_GenBank.GenBankTests.test_genbank_date_invalid)
Check if invalid dates are treated as default. ... ok
test_genbank_date_list (test_GenBank.GenBankTests.test_genbank_date_list)
Check if date lists are handled correctly. ... ok
test_genbank_read (test_GenBank.GenBankTests.test_genbank_read)
GenBank.read(...) simple test. ... ok
test_genbank_read_invalid (test_GenBank.GenBankTests.test_genbank_read_invalid)
GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok
test_genbank_read_multirecord (test_GenBank.GenBankTests.test_genbank_read_multirecord)
GenBank.read(...) error on multiple record input. ... ok
test_genbank_read_no_origin_no_end (test_GenBank.GenBankTests.test_genbank_read_no_origin_no_end)
GenBank.read(...) error on malformed file. ... ok
test_implicit_orign_wrap_extract_and_translate (test_GenBank.GenBankTests.test_implicit_orign_wrap_extract_and_translate)
Test that features wrapped around origin give expected data. ... ok
test_invalid_product_line_raises_value_error (test_GenBank.GenBankTests.test_invalid_product_line_raises_value_error)
Parsing invalid product line. ... ok
test_locus_line_topogoly (test_GenBank.GenBankTests.test_locus_line_topogoly)
Test if chromosome topology is conserved. ... ok
test_long_names (test_GenBank.GenBankTests.test_long_names)
Various GenBank names which push the column based LOCUS line. ... ok
test_longer_locus_line (test_GenBank.GenBankTests.test_longer_locus_line)
Check that we can read and write files with longer locus lines. ... ok
test_malformed_structured_comment_parsing (test_GenBank.GenBankTests.test_malformed_structured_comment_parsing)
Test malformed structured comment gives warning. ... ok
test_multiline_structured_comment_parsing (test_GenBank.GenBankTests.test_multiline_structured_comment_parsing)
Multiline structured comment parsing. ... ok
test_negative_location (test_GenBank.GenBankTests.test_negative_location)
Negative feature locations. ... ok
test_qualifier_escaping_read (test_GenBank.GenBankTests.test_qualifier_escaping_read)
Check qualifier escaping is preserved when parsing. ... ok
test_qualifier_escaping_write (test_GenBank.GenBankTests.test_qualifier_escaping_write)
Check qualifier escaping is preserved when writing. ... ok
test_qualifier_order (test_GenBank.GenBankTests.test_qualifier_order)
Check the qualifier order is preserved. ... ok
test_structured_comment_parsing (test_GenBank.GenBankTests.test_structured_comment_parsing)
Structured comment parsing. ... ok
test_tsa (test_GenBank.GenBankTests.test_tsa)
Test TSA annotation parsing. ... ok
test_first_line_imgt (test_GenBank.LineOneTests.test_first_line_imgt)
Check IMGT ID line parsing. ... ok
test_topology_embl (test_GenBank.LineOneTests.test_topology_embl)
Check EMBL ID line parsing. ... ok
test_topology_genbank (test_GenBank.LineOneTests.test_topology_genbank)
Check GenBank LOCUS line parsing. ... ok
test_000_write_invalid_but_parsed_locus_line (test_GenBank.OutputTests.test_000_write_invalid_but_parsed_locus_line)
Make sure we survive writing slightly invalid LOCUS lines we could parse. ... ok
test_mad_dots (test_GenBank.OutputTests.test_mad_dots)
Writing and reading back accesssion.version variants. ... ok
test_seqrecord_default_description (test_GenBank.OutputTests.test_seqrecord_default_description)
Read in file using SeqRecord default description. ... ok
test_write_tsa_data_division (test_GenBank.OutputTests.test_write_tsa_data_division)
Make sure we don't kill the TSA data_file_division for TSA files. ... ok
test_cleaning_features (test_GenBank.TestBasics.test_cleaning_features)
Test the ability to clean up feature values. ... ok
test_ensembl_locus (test_GenBank.TestBasics.test_ensembl_locus)
Test the ENSEMBL locus line. ... ok
test_write_format (test_GenBank.TestBasics.test_write_format)
Test writing to the difference formats. ... ok
test_feature_parser_01 (test_GenBank.TestFeatureParser.test_feature_parser_01) ... ok
test_feature_parser_02 (test_GenBank.TestFeatureParser.test_feature_parser_02) ... ok
test_feature_parser_03 (test_GenBank.TestFeatureParser.test_feature_parser_03) ... ok
test_feature_parser_04 (test_GenBank.TestFeatureParser.test_feature_parser_04) ... ok
test_feature_parser_05 (test_GenBank.TestFeatureParser.test_feature_parser_05) ... ok
test_feature_parser_06 (test_GenBank.TestFeatureParser.test_feature_parser_06) ... ok
test_feature_parser_07 (test_GenBank.TestFeatureParser.test_feature_parser_07) ... ok
test_feature_parser_08 (test_GenBank.TestFeatureParser.test_feature_parser_08) ... ok
test_feature_parser_09 (test_GenBank.TestFeatureParser.test_feature_parser_09) ... ok
test_feature_parser_10 (test_GenBank.TestFeatureParser.test_feature_parser_10) ... ok
test_feature_parser_11 (test_GenBank.TestFeatureParser.test_feature_parser_11) ... ok
test_feature_parser_12 (test_GenBank.TestFeatureParser.test_feature_parser_12) ... ok
test_feature_parser_13 (test_GenBank.TestFeatureParser.test_feature_parser_13) ... ok
test_feature_parser_14 (test_GenBank.TestFeatureParser.test_feature_parser_14) ... ok
test_feature_parser_15 (test_GenBank.TestFeatureParser.test_feature_parser_15) ... ok
test_feature_parser_16 (test_GenBank.TestFeatureParser.test_feature_parser_16) ... ok
test_feature_parser_17 (test_GenBank.TestFeatureParser.test_feature_parser_17) ... ok
test_feature_parser_18 (test_GenBank.TestFeatureParser.test_feature_parser_18) ... ok
test_feature_parser_19 (test_GenBank.TestFeatureParser.test_feature_parser_19) ... ok
test_feature_parser_20 (test_GenBank.TestFeatureParser.test_feature_parser_20) ... ok
test_features_spanning_origin (test_GenBank.TestFeatureParser.test_features_spanning_origin)
Test that features that span the origin on circular DNA are included correctly for different ways of specifying the topology. ... ok
test_record_parser_01 (test_GenBank.TestRecordParser.test_record_parser_01) ... ok
test_record_parser_02 (test_GenBank.TestRecordParser.test_record_parser_02) ... ok
test_record_parser_03 (test_GenBank.TestRecordParser.test_record_parser_03) ... ok
test_record_parser_04 (test_GenBank.TestRecordParser.test_record_parser_04) ... ok
test_record_parser_05 (test_GenBank.TestRecordParser.test_record_parser_05) ... ok
test_record_parser_06 (test_GenBank.TestRecordParser.test_record_parser_06) ... ok
test_record_parser_07 (test_GenBank.TestRecordParser.test_record_parser_07) ... ok
test_record_parser_08 (test_GenBank.TestRecordParser.test_record_parser_08) ... ok
test_record_parser_09 (test_GenBank.TestRecordParser.test_record_parser_09) ... ok
test_record_parser_10 (test_GenBank.TestRecordParser.test_record_parser_10) ... ok
test_record_parser_11 (test_GenBank.TestRecordParser.test_record_parser_11) ... ok
test_record_parser_12 (test_GenBank.TestRecordParser.test_record_parser_12) ... ok
test_record_parser_13 (test_GenBank.TestRecordParser.test_record_parser_13) ... ok
test_record_parser_14 (test_GenBank.TestRecordParser.test_record_parser_14) ... ok
test_record_parser_15 (test_GenBank.TestRecordParser.test_record_parser_15) ... ok
test_record_parser_16 (test_GenBank.TestRecordParser.test_record_parser_16) ... ok
test_record_parser_17 (test_GenBank.TestRecordParser.test_record_parser_17) ... ok
test_record_parser_18 (test_GenBank.TestRecordParser.test_record_parser_18) ... ok
test_record_parser_19 (test_GenBank.TestRecordParser.test_record_parser_19) ... ok
test_record_parser_20 (test_GenBank.TestRecordParser.test_record_parser_20) ... ok
test_record_parser_tls (test_GenBank.TestRecordParser.test_record_parser_tls) ... ok
test_record_parser_tsa (test_GenBank.TestRecordParser.test_record_parser_tsa) ... ok
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.333 seconds
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GenomeDiagram.py
test_GenomeDiagram ... ok
test_color_conversions (test_GenomeDiagram.ColorsTest.test_color_conversions)
Test color translations. ... ok
test_add_track (test_GenomeDiagram.DiagramTest.test_add_track)
Add track. ... ok
test_add_track_error (test_GenomeDiagram.DiagramTest.test_add_track_error)
Test adding unspecified track. ... ok
test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest.test_add_track_to_occupied_level)
Add track to occupied level. ... ok
test_del_tracks (test_GenomeDiagram.DiagramTest.test_del_tracks)
Delete track. ... ok
test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_methods_pdf)
Construct and draw PDF using method approach. ... ok
test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_object_pdf)
Construct and draw PDF using object approach. ... ok
test_get_tracks (test_GenomeDiagram.DiagramTest.test_get_tracks)
Get track. ... ok
test_move_track (test_GenomeDiagram.DiagramTest.test_move_track)
Move a track. ... ok
test_partial_diagram (test_GenomeDiagram.DiagramTest.test_partial_diagram)
Construct and draw SVG and PDF for just part of a SeqRecord. ... ok
test_renumber (test_GenomeDiagram.DiagramTest.test_renumber)
Test renumbering tracks. ... ok
test_str (test_GenomeDiagram.DiagramTest.test_str)
Test diagram's info as string. ... ok
test_write_arguments (test_GenomeDiagram.DiagramTest.test_write_arguments)
Check how the write methods respond to output format arguments. ... ok
test_limits (test_GenomeDiagram.GraphTest.test_limits)
Check line graphs. ... ok
test_slicing (test_GenomeDiagram.GraphTest.test_slicing)
Check GraphData slicing. ... ok
test_label_default (test_GenomeDiagram.LabelTest.test_label_default)
Feature labels - default. ... ok
test_all_sigils (test_GenomeDiagram.SigilsTest.test_all_sigils)
All sigils. ... ok
test_arrow_heads (test_GenomeDiagram.SigilsTest.test_arrow_heads)
Feature arrow sigils, varying heads. ... ok
test_arrow_shafts (test_GenomeDiagram.SigilsTest.test_arrow_shafts)
Feature arrow sigils, varying shafts. ... ok
test_big_arrow_shafts (test_GenomeDiagram.SigilsTest.test_big_arrow_shafts)
Feature big-arrow sigils, varying shafts. ... ok
test_labels (test_GenomeDiagram.SigilsTest.test_labels)
Feature labels. ... ok
test_long_arrow_heads (test_GenomeDiagram.SigilsTest.test_long_arrow_heads)
Feature ARROW sigil heads within bounding box. ... ok
test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest.test_long_bigarrow_heads)
Feature BIGARROW sigil heads within bounding box. ... ok
test_long_jaggy (test_GenomeDiagram.SigilsTest.test_long_jaggy)
Feature JAGGY sigil heads within bounding box. ... ok
test_long_octo_heads (test_GenomeDiagram.SigilsTest.test_long_octo_heads)
Feature OCTO sigil heads within bounding box. ... ok
test_short_arrow (test_GenomeDiagram.SigilsTest.test_short_arrow)
Feature arrow sigil heads within bounding box. ... ok
test_short_bigarrow (test_GenomeDiagram.SigilsTest.test_short_bigarrow)
Feature big-arrow sigil heads within bounding box. ... ok
test_short_jaggy (test_GenomeDiagram.SigilsTest.test_short_jaggy)
Feature arrow sigil heads within bounding box. ... ok
test_short_octo (test_GenomeDiagram.SigilsTest.test_short_octo)
Feature big-arrow sigil heads within bounding box. ... ok
----------------------------------------------------------------------
Ran 1 test in 3.683 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsBitmaps.py
test_GraphicsBitmaps ... skipping. Reportlab module rlPyCairo unavailable
cannot import desired renderPM backend rlPyCairo
Seek advice at the users list see
https://pairlist2.pair.net/mailman/listinfo/reportlab-users
----------------------------------------------------------------------
Ran 1 test in 0.149 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsChromosome.py
test_GraphicsChromosome ... ok
test_add_count (test_GraphicsChromosome.ChromosomeCountTest.test_add_count)
Add counts to specific chromosome segments. ... ok
test_add_label (test_GraphicsChromosome.ChromosomeCountTest.test_add_label)
Add labels to chromosome segments. ... ok
test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest.test_color_from_count)
Retrieve a color from a count number with the default color scheme. ... ok
test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest.test_fill_chromosome)
Test filling out the information on a chromosome. ... ok
test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest.test_get_segment_info)
Test retrieval of segment information. ... ok
test_set_scale (test_GraphicsChromosome.ChromosomeCountTest.test_set_scale)
Set the scale for a chromosome segment. ... ok
test_random_organism (test_GraphicsChromosome.OrganismGraphicTest.test_random_organism)
Generate an organism with random chromosome info. ... ok
test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism)
Test the basic functionality of drawing an organism. ... ok
test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_pdf)
Output a simple organism to a PDF file. ... ok
test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_ps)
Output a simple organism to a postscript file. ... ok
test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_svg)
Output a simple organism to an SVG file. ... ok
test_widget (test_GraphicsChromosome.OrganismGraphicTest.test_widget)
Try widget derived functionality. ... ok
test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_seqfeatures)
Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis. ... ok
test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_tuples)
Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.860 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsDistribution.py
test_GraphicsDistribution ... ok
test_multi_page (test_GraphicsDistribution.BarChartTest.test_multi_page)
Create a page with multiple distributions on it. ... ok
test_simple_page (test_GraphicsDistribution.BarChartTest.test_simple_page)
Test displaying a page with single distribution. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.188 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_GraphicsGeneral.py
test_GraphicsGeneral ... ok
test_simple_scatter_plot_1 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_1)
Test creation of a simple ScatterPlot with one list. ... ok
test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_7)
Test creation of a simple ScatterPlot with more lists. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.221 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMCasino.py
test_HMMCasino ... ok
test_baum_welch_training_standard (test_HMMCasino.TestHMMCasino.test_baum_welch_training_standard)
Standard Training with known states. ... ok
test_baum_welch_training_without (test_HMMCasino.TestHMMCasino.test_baum_welch_training_without)
Baum-Welch training without known state sequences. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.609 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_HMMGeneral.py
test_HMMGeneral ... ok
test_log_likelihood (test_HMMGeneral.AbstractTrainerTest.test_log_likelihood)
Calculate log likelihood. ... ok
test_ml_estimator (test_HMMGeneral.AbstractTrainerTest.test_ml_estimator)
Test the maximum likelihood estimator for simple cases. ... ok
test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest.test_allow_transition)
Testing allow_transition. ... ok
test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest.test_non_ergodic)
Non-ergodic model (meaning that some transitions are not allowed). ... ok
test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest.test_simple_hmm)
Test a simple model with 2 states and 2 symbols. ... ok
test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_from)
Testing the calculation of transitions_from. ... ok
test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_to)
Testing the calculation of transitions_to. ... ok
test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest.test_allow_all_transitions)
Testing allow_all_transitions. ... ok
test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_equal_probabilities) ... ok
test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_initial_probabilities) ... ok
test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_random_probabilities) ... ok
test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest.test_test_initialize)
Making sure MarkovModelBuilder is initialized correctly. ... ok
test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest.test_calculate_s_value)
Testing the calculation of s values. ... ok
test_empty_state_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_empty_state_training_sequence) ... ok
test_invalid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_invalid_training_sequence) ... ok
test_valid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_valid_training_sequence) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.059 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG.py
test_KEGG ... ok
test_irregular (test_KEGG.CompoundTests.test_irregular)
compound.irregular tests. ... ok
test_mass (test_KEGG.CompoundTests.test_mass)
record.mass tests. ... ok
test_sample (test_KEGG.CompoundTests.test_sample)
compound.sample tests. ... ok
test_4letter (test_KEGG.EnzymeTests.test_4letter)
enzyme.4letter tests. ... ok
test_exceptions (test_KEGG.EnzymeTests.test_exceptions)
enzyme.exceptions tests. ... ok
test_irregular (test_KEGG.EnzymeTests.test_irregular)
enzyme.irregular tests. ... ok
test_new (test_KEGG.EnzymeTests.test_new)
enzyme.new tests. ... ok
test_sample (test_KEGG.EnzymeTests.test_sample)
enzyme.sample tests. ... ok
test_map00950 (test_KEGG.MapTests.test_map00950)
map00950.rea tests. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.126 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KEGG_online.py
test_KEGG_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.077 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics.py
test_KGML_graphics ... ok
test_render_KGML_basic (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_basic)
Basic rendering of KGML: write to PDF without modification. ... ok
test_render_KGML_modify (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_modify)
Rendering of KGML to PDF, with modification. ... ok
test_render_KGML_transparency (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_transparency)
Rendering of KGML to PDF, with color alpha channel. ... ok
----------------------------------------------------------------------
Ran 1 test in 7.091 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics_online.py
test_KGML_graphics_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.051 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KGML_nographics.py
test_KGML_nographics ... ok
test_read_and_write_KGML_files (test_KGML_nographics.KGMLPathwayTest.test_read_and_write_KGML_files)
Read KGML from, and write KGML to, local files. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.071 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_KeyWList.py
test_KeyWList ... ok
test_parse (test_KeyWList.KeyWListTest.test_parse)
Test parsing keywlist.txt works. ... ok
test_parse2 (test_KeyWList.KeyWListTest.test_parse2)
Parsing keywlist2.txt (without header and footer). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.056 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_LogisticRegression.py
test_LogisticRegression ... ok
test_calculate_model (test_LogisticRegression.TestLogisticRegression.test_calculate_model) ... ok
test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression.test_calculate_model_with_update_callback) ... ok
test_calculate_probability (test_LogisticRegression.TestLogisticRegression.test_calculate_probability) ... ok
test_classify (test_LogisticRegression.TestLogisticRegression.test_classify) ... ok
test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression.test_dimensionality_of_input_xs) ... ok
test_leave_one_out (test_LogisticRegression.TestLogisticRegression.test_leave_one_out) ... ok
test_model_accuracy (test_LogisticRegression.TestLogisticRegression.test_model_accuracy) ... ok
test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression.test_xs_and_ys_input_parameter_lengths) ... ok
test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression.test_ys_input_class_assignments) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.055 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MSAProbs_tool.py
test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MafIO_index.py
test_MafIO_index ... ok
test_bundle_without_target (test_MafIO_index.NewIndexTest.test_bundle_without_target) ... ok
test_good_big (test_MafIO_index.NewIndexTest.test_good_big) ... ok
test_good_small (test_MafIO_index.NewIndexTest.test_good_small) ... ok
test_length_coords_mismatch (test_MafIO_index.NewIndexTest.test_length_coords_mismatch) ... ok
test_old (test_MafIO_index.PreBuiltIndexTest.test_old) ... ok
test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest.test_old_corrupt_index) ... ok
test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest.test_old_file_not_found) ... ok
test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest.test_old_invalid_sqlite) ... ok
test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest.test_old_unfinished_index) ... ok
test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_filename) ... ok
test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_target_seqname) ... ok
test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_version) ... ok
test_region2bin (test_MafIO_index.StaticMethodTest.test_region2bin) ... ok
test_ucscbin (test_MafIO_index.StaticMethodTest.test_ucscbin) ... ok
test_records_begin (test_MafIO_index.TestGetRecord.test_records_begin) ... ok
test_records_end (test_MafIO_index.TestGetRecord.test_records_end) ... ok
test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF.test_incorrect_bundle_coords) ... ok
test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF.test_correct_block_boundary)
Following issues 504 and 1086. ... ok
test_correct_block_length (test_MafIO_index.TestSearchGoodMAF.test_correct_block_length)
Following issues 504 and 1086. ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_1)
Correct retrieval of Cnksr3 in mouse. ... ok
test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_2) ... ok
test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_3)
Following issue 1083. ... ok
test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_1)
Checking that spliced sequences are correct. ... ok
test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_2)
Checking that spliced sequences are correct. ... ok
test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_count) ... ok
test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_schema) ... ok
test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_1) ... ok
test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_2) ... ok
test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF.test_bundle_without_target) ... ok
test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF.test_inconsistent_strand) ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF.test_correct_retrieval_1)
Correct retrieval of Cnksr3 in mouse. ... ok
test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF.test_invalid_strand) ... ok
test_no_alignment (test_MafIO_index.TestSpliceGoodMAF.test_no_alignment) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.098 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Mafft_tool.py
test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.064 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_MarkovModel.py
test_MarkovModel ... ok
test_argmaxes (test_MarkovModel.TestMarkovModel.test_argmaxes) ... ok
test_backward (test_MarkovModel.TestMarkovModel.test_backward) ... ok
test_baum_welch (test_MarkovModel.TestMarkovModel.test_baum_welch) ... ok
test_forward (test_MarkovModel.TestMarkovModel.test_forward) ... ok
test_logsum_and_exp_logsum (test_MarkovModel.TestMarkovModel.test_logsum_and_exp_logsum) ... ok
test_logvecadd (test_MarkovModel.TestMarkovModel.test_logvecadd) ... ok
test_mle (test_MarkovModel.TestMarkovModel.test_mle) ... ok
test_normalize_and_copy_and_check (test_MarkovModel.TestMarkovModel.test_normalize_and_copy_and_check) ... ok
test_random_norm (test_MarkovModel.TestMarkovModel.test_random_norm) ... ok
test_readline_and_check_start (test_MarkovModel.TestMarkovModel.test_readline_and_check_start) ... ok
test_save_and_load (test_MarkovModel.TestMarkovModel.test_save_and_load) ... ok
test_topcoder1 (test_MarkovModel.TestMarkovModel.test_topcoder1) ... ok
test_topcoder2 (test_MarkovModel.TestMarkovModel.test_topcoder2) ... ok
test_topcoder3 (test_MarkovModel.TestMarkovModel.test_topcoder3) ... ok
test_topcoder4 (test_MarkovModel.TestMarkovModel.test_topcoder4) ... ok
test_topcoder5 (test_MarkovModel.TestMarkovModel.test_topcoder5) ... ok
test_train_bw (test_MarkovModel.TestMarkovModel.test_train_bw) ... ok
test_train_visible (test_MarkovModel.TestMarkovModel.test_train_visible) ... ok
test_uniform_norm (test_MarkovModel.TestMarkovModel.test_uniform_norm) ... ok
test_viterbi (test_MarkovModel.TestMarkovModel.test_viterbi) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.210 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Medline.py
test_Medline ... ok
test_multiline_mesh (test_Medline.TestMedline.test_multiline_mesh) ... ok
test_parse (test_Medline.TestMedline.test_parse) ... ok
test_read (test_Medline.TestMedline.test_read) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.012 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Muscle_tool.py
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.097 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBITextParser.py
test_NCBITextParser ... ok
test_conversion (test_NCBITextParser.TestBlastRecord.test_conversion)
Converting a Blast record multiple alignment. ... ok
test_text_2010L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_001)
Parsing BLASTN 2.0.10 output (text_2010L_blastn_001). ... ok
test_text_2010L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_002)
Parsing BLASTN 2.0.10 output without alignments (text_2010L_blastn_002). ... ok
test_text_2010L_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_003)
Parsing BLASTN 2.0.10 output without descriptions (text_2010L_blastn_003). ... ok
test_text_2010L_blastn_004 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_004)
Parsing BLASTN 2.0.10 output (text_2010L_blastn_004). ... ok
test_text_2010L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_001)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_001). ... ok
test_text_2010L_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_002)
Parsing BLASTP 2.0.10 output without hits (text_2010L_blastp_002). ... ok
test_text_2010L_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_003)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_003). ... ok
test_text_2010L_blastp_004 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_004)
Parsing BLASTP 2.0.10 output without descriptions (text_2010L_blastp_004). ... ok
test_text_2010L_blastp_005 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_005)
Parsing BLASTP 2.0.10 output without alignments (text_2010L_blastp_005). ... ok
test_text_2010L_blastp_006 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_006)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_006). ... ok
test_text_2010L_blastp_007 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_007)
Parsing BLASTP 2.0.10 output (text_2010L_blastp_007). ... ok
test_text_2010L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastx_001)
Parsing BLASTX 2.0.10 output (text_2010L_blastx_001). ... ok
test_text_2010L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastx_002)
Parsing BLASTX 2.0.10 output without hits (text_2010L_blastx_002). ... ok
test_text_2010L_phiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_001)
Parsing PHI-BLAST, BLASTP 2.0.10 output, one round (text_2010L_phiblast_001). ... ok
test_text_2010L_phiblast_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_002)
Parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (text_2010L_phiblast_002). ... ok
test_text_2010L_phiblast_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_003)
Parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (text_2010L_phiblast_003). ... ok
test_text_2010L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastn_001)
Parsing TBLASTN 2.0.10 output (text_2010L_tblastn_001). ... ok
test_text_2010L_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastn_002)
Parsing TBLASTN 2.0.10 output without hits (text_2010L_tblastn_002). ... ok
test_text_2010L_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastx_001)
Parsing TBLASTX 2.0.10 output (text_2010L_tblastx_001). ... ok
test_text_2011L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_001)
Parsing BLASTN 2.0.11 output (text_2011L_blastn_001). ... ok
test_text_2011L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_002)
Parsing BLASTN 2.0.11 output without alignments (text_2011L_blastn_002). ... ok
test_text_2011L_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_003)
Parsing BLASTN 2.0.11 output without descriptions (text_2011L_blastn_003). ... ok
test_text_2011L_blastn_004 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_004)
Parsing BLASTN 2.0.11 output (text_2011L_blastn_004). ... ok
test_text_2011L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_001)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_001). ... ok
test_text_2011L_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_002)
Parsing BLASTP 2.0.11 output without hits (text_2011L_blastp_002). ... ok
test_text_2011L_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_003)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_003). ... ok
test_text_2011L_blastp_004 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_004)
Parsing BLASTP 2.0.11 output without descriptions (text_2011L_blastp_004). ... ok
test_text_2011L_blastp_005 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_005)
Parsing BLASTP 2.0.11 output without alignments (text_2011L_blastp_005). ... ok
test_text_2011L_blastp_006 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_006)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_006). ... ok
test_text_2011L_blastp_007 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_007)
Parsing BLASTP 2.0.11 output (text_2011L_blastp_007). ... ok
test_text_2011L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastx_001)
Parsing BLASTX 2.0.11 output (text_2011L_blastx_001). ... ok
test_text_2011L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastx_002)
Parsing BLASTX 2.0.11 output without hits (text_2011L_blastx_002). ... ok
test_text_2011L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_001)
Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_001). ... ok
test_text_2011L_psiblast_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_002)
Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_002). ... ok
test_text_2011L_psiblast_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_003)
Parsing BLASTP 2.0.11 output (text_2011L_psiblast_003). ... ok
test_text_2011L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastn_001)
Parsing TBLASTN 2.0.11 output (text_2011L_tblastn_001). ... ok
test_text_2011L_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastn_002)
Parsing TBLASTN 2.0.11 output without hits (text_2011L_tblastn_002). ... ok
test_text_2011L_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastx_001)
Parsing TBLASTX 2.0.11 output (text_2011L_tblastx_001). ... ok
test_text_2012L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2012L_psiblast_001)
Parsing BLASTP 2.0.12 output (text_2012L_psiblast_001). ... ok
test_text_2014L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2014L_blastn_001)
Parsing BLASTN 2.0.14 output (text_2014L_blastn_001). ... ok
test_text_2014L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2014L_psiblast_001)
Parsing BLASTP 2.0.14 output (text_2014L_psiblast_001). ... ok
test_text_2201L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2201L_blastx_001)
Parsing BLASTX 2.2.1 output (text_2201L_blastx_001). ... ok
test_text_2202L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastn_001)
Parsing BLASTN 2.2.2 output with error messages (text_2202L_blastn_001). ... ok
test_text_2202L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastn_002)
Parsing BLASTN 2.2.2 output with missing error messages (text_2202L_blastn_002). ... ok
test_text_2202L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastp_001)
Parsing BLASTP 2.2.2 output with multiple records (text_2202L_blastp_001). ... ok
test_text_2208L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2208L_psiblast_001)
Parsing BLASTP 2.2.8 output (text_2208L_psiblast_001). ... ok
test_text_2215L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2215L_blastx_001)
Parsing BLASTX 2.2.15 output with no hits (text_2215L_blastx_001). ... ok
test_text_2216L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2216L_tblastn_001)
Parsing TBLASTN 2.2.16 output (text_2216L_tblastn_001). ... ok
test_text_2220L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2220L_blastx_001)
Parsing BLASTX 2.2.20 output (text_2220L_blastx_001). ... ok
test_text_2220L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2220L_blastx_002)
Parsing BLASTX 2.2.20 output with multiple queries (text_2220L_blastx_002). ... ok
test_text_2221L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2221L_blastp_001)
Parsing BLASTP 2.2.21 output with multiple queries (text_2221L_blastp_001). ... ok
test_text_2222L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2222L_blastx_001)
Parsing BLASTX 2.2.22 output with multiple queries (text_2222L_blastx_001). ... ok
test_text_2222_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2222_blastx_001)
Parsing BLASTX 2.2.22+ output with multiple queries (text_2222_blastx_001). ... ok
test_text_2226_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_001)
Parsing BLASTN 2.2.26+ output with no results. ... ok
test_text_2226_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_002)
Parsing BLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_003)
Parsing BLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_001)
Parsing BLASTP 2.2.26+ with no results. ... ok
test_text_2226_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_002)
Parsing BLASTP 2.2.26+ with single hsp results. ... ok
test_text_2226_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_003)
Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_001)
Parsing BLASTX 2.2.26+ with no results. ... ok
test_text_2226_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_002)
Parsing BLASTX 2.2.26+ with single hsp results. ... ok
test_text_2226_blastx_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_003)
Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_001)
Parsing TBLASTN 2.2.26+ output with no results. ... ok
test_text_2226_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_002)
Parsing TBLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_003)
Parsing TBLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_001)
Parsing TBLASTX 2.2.26+ output with no results. ... ok
test_text_2226_tblastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_002)
Parsing TBLASTX 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastx_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_003)
Parsing TBLASTX 2.2.26+ output with multiple hsp results present. ... ok
test_text_2230_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2230_blastp_001)
Parsing BLASTP 2.2.30+ output with line of dashes. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.479 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBIXML.py
test_NCBIXML ... ok
test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastn_001)
Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001). ... ok
test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastp_001)
Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001). ... ok
test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastx_001)
Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001). ... ok
test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastn_001)
Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001). ... ok
test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastx_001)
Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001). ... ok
test_xml_2218L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_blastp_001)
Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001). ... ok
test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_rpsblast_001)
Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001). ... ok
test_xml_2218_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_001)
Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001). ... ok
test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_002)
Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002). ... ok
test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastp_001)
Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001). ... ok
test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastx_001)
Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001). ... ok
test_xml_2900_blastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v1) ... ok
test_xml_2900_blastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v2) ... ok
test_xml_2900_blastp_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v1) ... ok
test_xml_2900_blastp_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v2) ... ok
test_xml_2900_blastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v1) ... ok
test_xml_2900_blastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v2) ... ok
test_xml_2900_tblastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v1) ... ok
test_xml_2900_tblastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v2) ... ok
test_xml_2900_tblastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v1) ... ok
test_xml_2900_tblastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.625 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBI_BLAST_tools.py
test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NCBI_qblast.py
test_NCBI_qblast ... ok
test_blastp_nr_actin (test_NCBI_qblast.TestQblast.test_blastp_nr_actin) ... ok
test_discomegablast (test_NCBI_qblast.TestQblast.test_discomegablast) ... ok
test_error_conditions (test_NCBI_qblast.TestQblast.test_error_conditions)
Test if exceptions were properly handled. ... ok
test_orchid_est (test_NCBI_qblast.TestQblast.test_orchid_est) ... ok
test_parse_qblast_ref_page (test_NCBI_qblast.TestQblast.test_parse_qblast_ref_page) ... ok
test_pcr_primers (test_NCBI_qblast.TestQblast.test_pcr_primers) ... ok
test_short_query (test_NCBI_qblast.TestQblast.test_short_query)
Test SHORT_QUERY_ADJUST parameter. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NMR.py
test_NMR ... ok
test_noetools (test_NMR.NmrTests.test_noetools)
Self test for NMR.NOEtools. ... ok
test_xpktools (test_NMR.NmrTests.test_xpktools)
Self test for NMR.xpktools. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.015 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_NaiveBayes.py
test_NaiveBayes ... ok
test_car_data (test_NaiveBayes.CarTest.test_car_data)
Simple example using car data. ... ok
test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest.test_calculate_function_with_scale) ... ok
test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest.test_calculate_function_wrong_dimensionality) ... ok
test_classify_function (test_NaiveBayes.NaiveBayesTest.test_classify_function) ... ok
test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest.test_train_function_input_lengths) ... ok
test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_no_training_set) ... ok
test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_uneven_dimension_of_training_set) ... ok
test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest.test_train_function_with_priors) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.012 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_baseml.py
test_PAML_baseml ... ok
testAlignmentExists (test_PAML_baseml.ModTest.testAlignmentExists) ... ok
testAlignmentFileIsValid (test_PAML_baseml.ModTest.testAlignmentFileIsValid) ... ok
testAlignmentSpecified (test_PAML_baseml.ModTest.testAlignmentSpecified) ... ok
testCtlFileExistsOnRead (test_PAML_baseml.ModTest.testCtlFileExistsOnRead) ... ok
testCtlFileExistsOnRun (test_PAML_baseml.ModTest.testCtlFileExistsOnRun) ... ok
testCtlFileValidOnRead (test_PAML_baseml.ModTest.testCtlFileValidOnRead) ... ok
testCtlFileValidOnRun (test_PAML_baseml.ModTest.testCtlFileValidOnRun) ... ok
testOptionExists (test_PAML_baseml.ModTest.testOptionExists) ... ok
testOutputFileSpecified (test_PAML_baseml.ModTest.testOutputFileSpecified) ... ok
testPamlErrorsCaught (test_PAML_baseml.ModTest.testPamlErrorsCaught) ... ok
testParseAllVersions (test_PAML_baseml.ModTest.testParseAllVersions) ... ok
testParseAlpha1Rho1 (test_PAML_baseml.ModTest.testParseAlpha1Rho1) ... ok
testParseModel (test_PAML_baseml.ModTest.testParseModel) ... ok
testParseNhomo (test_PAML_baseml.ModTest.testParseNhomo) ... ok
testParseSEs (test_PAML_baseml.ModTest.testParseSEs) ... ok
testResultsExist (test_PAML_baseml.ModTest.testResultsExist) ... ok
testResultsParsable (test_PAML_baseml.ModTest.testResultsParsable) ... ok
testResultsValid (test_PAML_baseml.ModTest.testResultsValid) ... ok
testTreeExists (test_PAML_baseml.ModTest.testTreeExists) ... ok
testTreeFileValid (test_PAML_baseml.ModTest.testTreeFileValid) ... ok
testTreeSpecified (test_PAML_baseml.ModTest.testTreeSpecified) ... ok
testWorkingDirValid (test_PAML_baseml.ModTest.testWorkingDirValid) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.181 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_codeml.py
test_PAML_codeml ... ok
testAlignmentExists (test_PAML_codeml.ModTest.testAlignmentExists) ... ok
testAlignmentFileIsValid (test_PAML_codeml.ModTest.testAlignmentFileIsValid) ... ok
testAlignmentSpecified (test_PAML_codeml.ModTest.testAlignmentSpecified) ... ok
testCtlFileExistsOnRead (test_PAML_codeml.ModTest.testCtlFileExistsOnRead) ... ok
testCtlFileExistsOnRun (test_PAML_codeml.ModTest.testCtlFileExistsOnRun) ... ok
testCtlFileValidOnRead (test_PAML_codeml.ModTest.testCtlFileValidOnRead) ... ok
testCtlFileValidOnRun (test_PAML_codeml.ModTest.testCtlFileValidOnRun) ... ok
testOptionExists (test_PAML_codeml.ModTest.testOptionExists) ... ok
testOutputFileSpecified (test_PAML_codeml.ModTest.testOutputFileSpecified) ... ok
testPamlErrorsCaught (test_PAML_codeml.ModTest.testPamlErrorsCaught) ... ok
testParseAA (test_PAML_codeml.ModTest.testParseAA) ... ok
testParseAAPairwise (test_PAML_codeml.ModTest.testParseAAPairwise) ... ok
testParseAllNSsites (test_PAML_codeml.ModTest.testParseAllNSsites) ... ok
testParseBranchSiteA (test_PAML_codeml.ModTest.testParseBranchSiteA) ... ok
testParseCladeModelC (test_PAML_codeml.ModTest.testParseCladeModelC) ... ok
testParseFreeRatio (test_PAML_codeml.ModTest.testParseFreeRatio) ... ok
testParseM2arel (test_PAML_codeml.ModTest.testParseM2arel) ... ok
testParseNSsite3 (test_PAML_codeml.ModTest.testParseNSsite3) ... ok
testParseNgene2Mgene02 (test_PAML_codeml.ModTest.testParseNgene2Mgene02) ... ok
testParseNgene2Mgene1 (test_PAML_codeml.ModTest.testParseNgene2Mgene1) ... ok
testParseNgene2Mgene34 (test_PAML_codeml.ModTest.testParseNgene2Mgene34) ... ok
testParsePairwise (test_PAML_codeml.ModTest.testParsePairwise) ... ok
testParseSEs (test_PAML_codeml.ModTest.testParseSEs) ... ok
testParseSitesParamsForPairwise (test_PAML_codeml.ModTest.testParseSitesParamsForPairwise)
Verify that pairwise site estimates are indeed parsed. Fixes #483. ... ok
testResultsExist (test_PAML_codeml.ModTest.testResultsExist) ... ok
testResultsParsable (test_PAML_codeml.ModTest.testResultsParsable) ... ok
testResultsValid (test_PAML_codeml.ModTest.testResultsValid) ... ok
testTreeExists (test_PAML_codeml.ModTest.testTreeExists) ... ok
testTreeFileValid (test_PAML_codeml.ModTest.testTreeFileValid) ... ok
testTreeParseVersatility (test_PAML_codeml.ModTest.testTreeParseVersatility)
Test finding trees in the results. ... ok
testTreeSpecified (test_PAML_codeml.ModTest.testTreeSpecified) ... ok
testWorkingDirValid (test_PAML_codeml.ModTest.testWorkingDirValid) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.868 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_tools.py
test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.107 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PAML_yn00.py
test_PAML_yn00 ... ok
testAlignmentExists (test_PAML_yn00.ModTest.testAlignmentExists) ... ok
testAlignmentFileIsValid (test_PAML_yn00.ModTest.testAlignmentFileIsValid) ... ok
testAlignmentSpecified (test_PAML_yn00.ModTest.testAlignmentSpecified) ... ok
testCtlFileExistsOnRead (test_PAML_yn00.ModTest.testCtlFileExistsOnRead) ... ok
testCtlFileExistsOnRun (test_PAML_yn00.ModTest.testCtlFileExistsOnRun) ... ok
testCtlFileValidOnRead (test_PAML_yn00.ModTest.testCtlFileValidOnRead) ... ok
testCtlFileValidOnRun (test_PAML_yn00.ModTest.testCtlFileValidOnRun) ... ok
testOptionExists (test_PAML_yn00.ModTest.testOptionExists) ... ok
testOutputFileSpecified (test_PAML_yn00.ModTest.testOutputFileSpecified) ... ok
testParseAllVersions (test_PAML_yn00.ModTest.testParseAllVersions) ... ok
testParseDottedNames (test_PAML_yn00.ModTest.testParseDottedNames) ... ok
testParseDottedNumNames (test_PAML_yn00.ModTest.testParseDottedNumNames) ... ok
testParseLongNames (test_PAML_yn00.ModTest.testParseLongNames) ... ok
testResultsExist (test_PAML_yn00.ModTest.testResultsExist) ... ok
testResultsParsable (test_PAML_yn00.ModTest.testResultsParsable) ... ok
testResultsValid (test_PAML_yn00.ModTest.testResultsValid) ... ok
testWorkingDirValid (test_PAML_yn00.ModTest.testWorkingDirValid) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.121 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDBList.py
test_PDBList ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.067 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_CEAligner.py
test_PDB_CEAligner ... ok
test_cealigner (test_PDB_CEAligner.CEAlignerTests.test_cealigner)
Test aligning 7CFN on 6WQA. ... ok
test_cealigner_no_transform (test_PDB_CEAligner.CEAlignerTests.test_cealigner_no_transform)
Test aligning 7CFN on 6WQA without transforming 7CFN. ... ok
test_cealigner_nucleic (test_PDB_CEAligner.CEAlignerTests.test_cealigner_nucleic)
Test aligning 1LCD on 1LCD. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.550 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_DSSP.py
test_PDB_DSSP ... ok
test_DSSP_RSA (test_PDB_DSSP.DSSP_test.test_DSSP_RSA)
Tests the usage of different ASA tables. ... ok
test_DSSP_file (test_PDB_DSSP.DSSP_test.test_DSSP_file)
Test parsing of pregenerated DSSP. ... ok
test_DSSP_hbonds (test_PDB_DSSP.DSSP_test.test_DSSP_hbonds)
Test parsing of DSSP hydrogen bond information. ... ok
test_DSSP_in_model_obj (test_PDB_DSSP.DSSP_test.test_DSSP_in_model_obj)
All elements correctly added to xtra attribute of input model object. ... ok
test_DSSP_noheader_file (test_PDB_DSSP.DSSP_test.test_DSSP_noheader_file)
Test parsing of pregenerated DSSP missing header information. ... ok
setUpClass (test_PDB_DSSP.DSSP_tool_test) ... skipped 'Install dssp if you want to use it from Biopython.'
----------------------------------------------------------------------
Ran 1 test in 0.210 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Dice.py
test_PDB_Dice ... ok
test_dice (test_PDB_Dice.DiceTests.test_dice)
Self test for PDB.Dice module. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.088 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Disordered.py
test_PDB_Disordered ... ok
test_copy_and_write_disordered (test_PDB_Disordered.TestDisordered.test_copy_and_write_disordered)
Extract, save, and parse again disordered atoms. ... ok
test_copy_disordered_atom (test_PDB_Disordered.TestDisordered.test_copy_disordered_atom)
Copies disordered atoms and all their children. ... ok
test_copy_entire_chain (test_PDB_Disordered.TestDisordered.test_copy_entire_chain)
Copy propagates throughout SMCRA object. ... ok
test_disordered_cog (test_PDB_Disordered.TestDisordered.test_disordered_cog)
Calculate DisorderedAtom center of geometry. ... ok
test_empty_disordered (test_PDB_Disordered.TestDisordered.test_empty_disordered)
Raise ValueError on center of mass calculation of empty DisorderedAtom. ... ok
test_remove_disordered_atom (test_PDB_Disordered.TestDisordered.test_remove_disordered_atom)
Remove altlocs from DisorderedAtom entities. ... ok
test_remove_disordered_residue (test_PDB_Disordered.TestDisordered.test_remove_disordered_residue)
Remove residues from DisorderedResidue entities. ... ok
test_structure_w_disordered_com (test_PDB_Disordered.TestDisordered.test_structure_w_disordered_com)
Calculate center of mass of structure including DisorderedAtoms. ... ok
test_transform_disordered (test_PDB_Disordered.TestDisordered.test_transform_disordered)
Transform propagates through disordered atoms. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.096 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Exposure.py
test_PDB_Exposure ... ok
test_ExposureCN (test_PDB_Exposure.Exposure.test_ExposureCN)
HSExposureCN. ... ok
test_HSExposureCA (test_PDB_Exposure.Exposure.test_HSExposureCA)
HSExposureCA. ... ok
test_HSExposureCB (test_PDB_Exposure.Exposure.test_HSExposureCB)
HSExposureCB. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.398 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_FragmentMapper.py
test_PDB_FragmentMapper ... ok
test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests.test_fragment_mapper)
Self test for FragmentMapper module. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.131 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_KDTree.py
test_PDB_KDTree ... ok
test_KDTree_exceptions (test_PDB_KDTree.KDTreeTest.test_KDTree_exceptions) ... ok
test_KDTree_neighbor_search_manual (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_manual)
Test all fixed radius neighbor search. ... ok
test_KDTree_neighbor_search_simple (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_simple)
Test all fixed radius neighbor search. ... ok
test_KDTree_point_search (test_PDB_KDTree.KDTreeTest.test_KDTree_point_search)
Test searching all points within a certain radius of center. ... ok
test_neighbor_search (test_PDB_KDTree.NeighborTest.test_neighbor_search)
NeighborSearch: Find nearby randomly generated coordinates. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.158 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIF2Dict.py
test_PDB_MMCIF2Dict ... ok
test_MMCIF2dict (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_MMCIF2dict) ... ok
test_inline_comments (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_inline_comments)
Comments may begin outside of column 1 if preceded by whitespace. ... ok
test_loop_keyword_case_insensitive (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_loop_keyword_case_insensitive)
Comments may begin outside of column 1. ... ok
test_quotefix (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_quotefix) ... ok
test_splitline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_splitline) ... ok
test_token_after_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_token_after_multiline)
Multi-line string followed by token on the same line. ... ok
test_truncated_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_truncated_multiline) ... ok
test_underscores (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_underscores) ... ok
test_verbatim_block (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_verbatim_block)
Verbatim blocks parsed correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.111 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFIO.py
test_PDB_MMCIFIO ... ok
test_mmcifio_multimodel (test_PDB_MMCIFIO.WriteTest.test_mmcifio_multimodel)
Write a multi-model, multi-chain mmCIF file. ... ok
test_mmcifio_select (test_PDB_MMCIFIO.WriteTest.test_mmcifio_select)
Write a selection of the structure using a Select subclass. ... ok
test_mmcifio_write_custom_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_custom_residue)
Write a chainless residue using PDBIO. ... ok
test_mmcifio_write_dict (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_dict)
Write an mmCIF dictionary out, read it in and compare them. ... ok
test_mmcifio_write_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue)
Write a single residue using MMCIFIO. ... ok
test_mmcifio_write_residue_w_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_w_chain)
Write a single residue (chain id == X) using MMCIFIO. ... ok
test_mmcifio_write_residue_wout_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_wout_chain)
Write a single orphan residue using MMCIFIO. ... ok
test_mmcifio_write_structure (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_structure)
Write a full structure using MMCIFIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.302 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFParser.py
test_PDB_MMCIFParser ... ok
test_conversion (test_PDB_MMCIFParser.CIFtoPDB.test_conversion)
Parse 1LCD.cif, write 1LCD.pdb, parse again and compare. ... ok
test_conversion_not_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_not_preserve_numbering)
Convert mmCIF to PDB and renumber atom serials. ... ok
test_conversion_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_preserve_numbering)
Convert mmCIF to PDB and preserve original serial numbering. ... ok
testModels (test_PDB_MMCIFParser.ParseReal.testModels)
Test file with multiple models. ... ok
test_filehandle (test_PDB_MMCIFParser.ParseReal.test_filehandle)
Test if the parser can handle file handle as well as filename. ... ok
test_header (test_PDB_MMCIFParser.ParseReal.test_header)
Test if the parser populates header data. ... ok
test_insertions (test_PDB_MMCIFParser.ParseReal.test_insertions)
Test file with residue insertion codes. ... ok
test_parsers (test_PDB_MMCIFParser.ParseReal.test_parsers)
Extract polypeptides from 1A80. ... ok
test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal.test_point_mutations_fast)
Test if FastMMCIFParser can parse point mutations correctly. ... ok
test_point_mutations_main (test_PDB_MMCIFParser.ParseReal.test_point_mutations_main)
Test if MMCIFParser parse point mutations correctly. ... ok
test_with_anisotrop (test_PDB_MMCIFParser.ParseReal.test_with_anisotrop) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.441 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_NACCESS.py
test_PDB_NACCESS ... ok
test_NACCESS (test_PDB_NACCESS.NACCESS_test.test_NACCESS)
Test calling NACCESS from Bio.PDB. ... skipped 'Install naccess if you want to use it from Biopython.'
test_NACCESS_asa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_asa_file)
Test parsing of pregenerated asa NACCESS file. ... ok
test_NACCESS_rsa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_rsa_file)
Test parsing of pregenerated rsa NACCESS file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.075 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBIO.py
test_PDB_PDBIO ... ok
test_model_numbering (test_PDB_PDBIO.WriteTest.test_model_numbering)
Preserve model serial numbers during I/O. ... ok
test_pdbio_missing_occupancy (test_PDB_PDBIO.WriteTest.test_pdbio_missing_occupancy)
Write PDB file with missing occupancy. ... ok
test_pdbio_pdb_format_limits (test_PDB_PDBIO.WriteTest.test_pdbio_pdb_format_limits)
Test raising error when structure cannot meet PDB format limits. ... ok
test_pdbio_select (test_PDB_PDBIO.WriteTest.test_pdbio_select)
Write a selection of the structure using a Select subclass. ... ok
test_pdbio_write_auto_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_auto_numbering)
Test writing PDB and do not preserve atom numbering. ... ok
test_pdbio_write_custom_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_custom_residue)
Write a chainless residue using PDBIO. ... ok
test_pdbio_write_preserve_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_preserve_numbering)
Test writing PDB and preserve atom numbering. ... ok
test_pdbio_write_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue)
Write a single residue using PDBIO. ... ok
test_pdbio_write_residue_w_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_w_chain)
Write a single residue (chain id == X) using PDBIO. ... ok
test_pdbio_write_residue_wout_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_wout_chain)
Write a single orphan residue using PDBIO. ... ok
test_pdbio_write_structure (test_PDB_PDBIO.WriteTest.test_pdbio_write_structure)
Write a full structure using PDBIO. ... ok
test_pdbio_write_truncated (test_PDB_PDBIO.WriteTest.test_pdbio_write_truncated)
Test parsing of truncated lines. ... ok
test_pdbio_write_unk_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_unk_element)
PDBIO raises PDBIOException when writing unrecognised atomic elements. ... ok
test_pdbio_write_x_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_x_element)
Write a structure with atomic element X with PDBIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.283 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBParser.py
test_PDB_PDBParser ... ok
test_1_flawedpdb_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_1_flawedpdb_permissive)
Parse a flawed PDB file in permissive mode: check warnings. ... ok
test_2_flawedpdb_strict (test_PDB_PDBParser.FlawedPDB_tests.test_2_flawedpdb_strict)
Parse a flawed PDB file in permissive mode: check errors. ... ok
test_3_bad_xyz_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_3_bad_xyz_permissive)
Parse an entry with bad x,y,z value with PERMISSIVE=True. ... ok
test_4_bad_xyz_strict (test_PDB_PDBParser.FlawedPDB_tests.test_4_bad_xyz_strict)
Parse an entry with bad x,y,z value with PERMISSIVE=False. ... ok
test_5_missing_occupancy_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_5_missing_occupancy_permissive)
Parse file with missing occupancy with PERMISSIVE=True. ... ok
test_6_missing_occupancy_strict (test_PDB_PDBParser.FlawedPDB_tests.test_6_missing_occupancy_strict)
Parse file with missing occupancy with PERMISSIVE=False. ... ok
test_structure_details (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_details)
Verify details of the parsed example PDB file. ... ok
test_structure_integrity (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_integrity)
Verify the structure of the parsed example PDB file. ... ok
test_1A8O_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_1A8O_strict)
Parse 1A8O.pdb file in strict mode. ... ok
test_SMCRA (test_PDB_PDBParser.ParseRealPDB_tests.test_SMCRA)
Walk down the structure hierarchy and test parser reliability. ... ok
test_duplicated_residue_permissive (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_permissive)
Catch exception on duplicated residue. ... ok
test_duplicated_residue_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_strict)
Throw exception on duplicated residue. ... ok
test_empty (test_PDB_PDBParser.ParseRealPDB_tests.test_empty)
Parse an empty file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.127 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_PSEA.py
test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path
----------------------------------------------------------------------
Ran 1 test in 0.073 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Polypeptide.py
test_PDB_Polypeptide ... ok
test_cappbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real)
Test CaPPBuilder on real PDB file. ... ok
test_cappbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real_nonstd)
Test CaPPBuilder on real PDB file allowing non-standard amino acids. ... ok
test_cappbuilder_tau (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_tau)
Test tau angles calculated with CaPPBuilder. ... ok
test_ppbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real)
Test PPBuilder on real PDB file. ... ok
test_ppbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real_nonstd)
Test PPBuilder on real PDB file allowing non-standard amino acids. ... ok
test_ppbuilder_torsion (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_torsion)
Test phi/psi angles calculated with PPBuilder. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.111 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_QCSuperimposer.py
test_PDB_QCSuperimposer ... ok
test_get_init_rms (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_get_init_rms)
Test initial RMS calculation. ... ok
test_get_transformed (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_get_transformed)
Test transformation of coordinates after QCP. ... ok
test_on_pdb (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_on_pdb)
Align a PDB to itself. ... ok
test_run (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_run)
Test QCP on dummy data. ... ok
test_set (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_set)
Test setting of initial parameters. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.105 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_ResidueDepth.py
test_PDB_ResidueDepth ... ok
setUpClass (test_PDB_ResidueDepth.MSMS_tests) ... skipped 'Install MSMS if you want to use it from Biopython.'
test_pdb_to_xyzr (test_PDB_ResidueDepth.ResidueDepth_tests.test_pdb_to_xyzr)
Test generation of xyzr (atomic radii) file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.103 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_SASA.py
test_PDB_SASA ... ok
test_custom_radii (test_PDB_SASA.TestShrakeRupley.test_custom_radii)
Run Shrake-Rupley with custom radii. ... ok
test_default_algorithm (test_PDB_SASA.TestShrakeRupley.test_default_algorithm)
Run Shrake-Rupley with default parameters. ... ok
test_fail_compute_entity_level (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_level)
Raise exception on input Atom entity. ... ok
test_fail_compute_entity_type (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_type)
Raise exception on unsupported entity type. ... ok
test_fail_compute_level_1 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_1)
Raise exception on invalid level parameter: X. ... ok
test_fail_compute_level_2 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_2)
Raise exception on invalid level parameter: S > C. ... ok
test_fail_empty_entity (test_PDB_SASA.TestShrakeRupley.test_fail_empty_entity)
Raise exception on invalid level parameter: S > C. ... ok
test_fail_n_points (test_PDB_SASA.TestShrakeRupley.test_fail_n_points)
Raise exception on bad n_points parameter. ... ok
test_fail_probe_radius (test_PDB_SASA.TestShrakeRupley.test_fail_probe_radius)
Raise exception on bad probe_radius parameter. ... ok
test_higher_resolution (test_PDB_SASA.TestShrakeRupley.test_higher_resolution)
Run Shrake-Rupley with 960 points per sphere. ... ok
test_level_C (test_PDB_SASA.TestShrakeRupley.test_level_C)
Run Shrake-Rupley with level C. ... ok
test_level_R (test_PDB_SASA.TestShrakeRupley.test_level_R)
Run Shrake-Rupley with level R. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.026 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_SMCRA.py
test_PDB_SMCRA ... ok
test_assign_unknown_element (test_PDB_SMCRA.Atom_Element.test_assign_unknown_element)
Unknown element is assigned 'X'. ... ok
test_atom_element_assignment (test_PDB_SMCRA.Atom_Element.test_atom_element_assignment)
Atom Element. ... ok
test_hydrogens (test_PDB_SMCRA.Atom_Element.test_hydrogens) ... ok
test_ions (test_PDB_SMCRA.Atom_Element.test_ions)
Element for magnesium is assigned correctly. ... ok
test_chain_cog (test_PDB_SMCRA.CenterOfMassTests.test_chain_cog)
Calculate center of geometry of individual chains. ... ok
test_com_empty_structure (test_PDB_SMCRA.CenterOfMassTests.test_com_empty_structure)
Center of mass of empty structure raises ValueError. ... ok
test_structure_cog (test_PDB_SMCRA.CenterOfMassTests.test_structure_cog)
Calculate Structure center of geometry. ... ok
test_structure_com (test_PDB_SMCRA.CenterOfMassTests.test_structure_com)
Calculate Structure center of mass. ... ok
test_change_chain_id (test_PDB_SMCRA.ChangingIdTests.test_change_chain_id)
Change the id of a model. ... ok
test_change_id_to_self (test_PDB_SMCRA.ChangingIdTests.test_change_id_to_self)
Changing the id to itself does nothing (does not raise). ... ok
test_change_model_id (test_PDB_SMCRA.ChangingIdTests.test_change_model_id)
Change the id of a model. ... ok
test_change_model_id_raises (test_PDB_SMCRA.ChangingIdTests.test_change_model_id_raises)
Cannot change id to a value already in use by another child. ... ok
test_change_residue_id (test_PDB_SMCRA.ChangingIdTests.test_change_residue_id)
Change the id of a residue. ... ok
test_full_id_is_updated_chain (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_chain)
Invalidate cached full_ids if an id is changed. ... ok
test_full_id_is_updated_residue (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_residue)
Invalidate cached full_ids if an id is changed. ... ok
test_atom_copy (test_PDB_SMCRA.CopyTests.test_atom_copy) ... ok
test_entity_copy (test_PDB_SMCRA.CopyTests.test_entity_copy)
Make a copy of a residue. ... ok
test_get_atoms (test_PDB_SMCRA.IterationTests.test_get_atoms)
Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok
test_get_chains (test_PDB_SMCRA.IterationTests.test_get_chains)
Yields chains from different models separately. ... ok
test_get_residues (test_PDB_SMCRA.IterationTests.test_get_residues)
Yields all residues from all models. ... ok
test_comparison_entities (test_PDB_SMCRA.SortingTests.test_comparison_entities)
Test comparing and sorting the several SMCRA objects. ... ok
test_residue_sort (test_PDB_SMCRA.SortingTests.test_residue_sort)
Test atoms are sorted correctly in residues. ... ok
test_transform (test_PDB_SMCRA.TransformTests.test_transform)
Transform entities (rotation and translation). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.391 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Selection.py
test_PDB_Selection ... ok
test_entities_not_homogenous (test_PDB_Selection.UnfoldEntitiesTests.test_entities_not_homogenous) ... ok
test_from_atom_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_atom_level)
Unfold from lowest level to all levels. ... ok
test_from_chain_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_chain_level)
Unfold from chain level to all levels. ... ok
test_from_model_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_model_level)
Unfold from model to all levels. ... ok
test_from_residue_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_residue_level)
Unfold from chain level to all levels. ... ok
test_from_structure_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_structure_level)
Unfold from highest level to all levels. ... ok
test_invalid_level (test_PDB_Selection.UnfoldEntitiesTests.test_invalid_level) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.089 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_StructureAlignment.py
C
test_PDB_StructureAlignment ... ok
test_StructAlign (test_PDB_StructureAlignment.StructureAlignTests.test_StructAlign)
Tests on module to align two proteins according to a FASTA alignment file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.318 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_Superimposer.py
C
test_PDB_Superimposer ... ok
test_Superimposer (test_PDB_Superimposer.SuperimposerTests.test_Superimposer)
Test on module that superimpose two protein structures. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.103 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_internal_coords.py
C
test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.102 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_parse_pdb_header.py
C
test_PDB_parse_pdb_header ... ok
test_1 (test_PDB_parse_pdb_header.ParseReal.test_1)
Parse the header of a known PDB file (1A8O). ... ok
test_2 (test_PDB_parse_pdb_header.ParseReal.test_2)
Parse the header of another PDB file (2BEG). ... ok
test_parse_header_line (test_PDB_parse_pdb_header.ParseReal.test_parse_header_line)
Unit test for parsing and converting fields in HEADER record. ... ok
test_parse_no_title (test_PDB_parse_pdb_header.ParseReal.test_parse_no_title)
Unit test for sensible result with no TITLE line. ... ok
test_parse_pdb_with_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_465)
Tests that parse_pdb_header now can identify some REMARK 465 entries. ... ok
test_parse_pdb_with_remark_99 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_99)
Tests that parse_pdb_header can identify REMARK 99 ASTRAL entries. ... ok
test_parse_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_remark_465)
A UNIT-test for the private function _parse_remark_465. ... ok
test_parse_title_line (test_PDB_parse_pdb_header.ParseReal.test_parse_title_line)
Unit test for correct parsing of multiline title records. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.123 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PDB_vectors.py
test_PDB_vectors ... ok
test_Vector (test_PDB_vectors.VectorTests.test_Vector)
Test Vector object. ... ok
test_Vector_angles (test_PDB_vectors.VectorTests.test_Vector_angles)
Test Vector angles. ... ok
test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
Confirm can generate coordinate space transform for 3 points. ... ok
test_division (test_PDB_vectors.VectorTests.test_division)
Confirm division works. ... ok
test_get_spherical_coordinates (test_PDB_vectors.VectorTests.test_get_spherical_coordinates)
Test spherical coordinates. ... ok
test_m2rotaxis_0 (test_PDB_vectors.VectorTests.test_m2rotaxis_0)
Test 0 deg rotation. Axis must be [1, 0, 0] as per Vector docs. ... ok
test_m2rotaxis_180 (test_PDB_vectors.VectorTests.test_m2rotaxis_180)
Test 180 deg rotation. ... ok
test_m2rotaxis_90 (test_PDB_vectors.VectorTests.test_m2rotaxis_90)
Test 90 deg rotation. ... ok
test_multi_coord_space (test_PDB_vectors.VectorTests.test_multi_coord_space)
Confirm multi_coord_space computes forward, reverse transforms. ... ok
test_normalization (test_PDB_vectors.VectorTests.test_normalization)
Test Vector normalization. ... ok
test_refmat (test_PDB_vectors.VectorTests.test_refmat)
Test refmat can mirror one matrix to another. ... ok
test_rotmat_0 (test_PDB_vectors.VectorTests.test_rotmat_0)
Test rotmat when the rotation is 0 deg (singularity). ... ok
test_rotmat_180 (test_PDB_vectors.VectorTests.test_rotmat_180)
Test rotmat when the rotation is 180 deg (singularity). ... ok
test_rotmat_90 (test_PDB_vectors.VectorTests.test_rotmat_90)
Test regular 90 deg rotation. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.088 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PQR.py
test_PQR ... ok
test_bad_charge (test_PQR.ParseSimplePQR.test_bad_charge)
Test if missing or malformed charge case is handled correctly. ... ok
test_bad_radius (test_PQR.ParseSimplePQR.test_bad_radius)
Test if missing, malformed or negative radius case is handled correctly. ... ok
test_bad_xyz (test_PQR.ParseSimplePQR.test_bad_xyz)
Test if bad coordinates exception is raised. ... ok
test_single_input (test_PQR.ParseSimplePQR.test_single_input)
Test if a single ATOM entry correctly parsed. ... ok
test_pdbio_write_pqr_structure (test_PQR.WriteTest.test_pdbio_write_pqr_structure)
Write a full structure using PDBIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.110 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Pathway.py
test_Pathway ... ok
testAdditionalFunctions (test_Pathway.GraphTestCase.testAdditionalFunctions) ... ok
test_Edges (test_Pathway.GraphTestCase.test_Edges) ... ok
test_Equals (test_Pathway.GraphTestCase.test_Equals) ... ok
test_Nodes (test_Pathway.GraphTestCase.test_Nodes) ... ok
test_RemoveNode (test_Pathway.GraphTestCase.test_RemoveNode) ... ok
testAdditionalFunctions (test_Pathway.MultiGraphTestCase.testAdditionalFunctions) ... ok
test_Edges (test_Pathway.MultiGraphTestCase.test_Edges) ... ok
test_Equals (test_Pathway.MultiGraphTestCase.test_Equals) ... ok
test_Nodes (test_Pathway.MultiGraphTestCase.test_Nodes) ... ok
test_RemoveNode (test_Pathway.MultiGraphTestCase.test_RemoveNode) ... ok
test_eq (test_Pathway.ReactionTestCase.test_eq) ... ok
test_rev (test_Pathway.ReactionTestCase.test_rev) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.012 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Phd.py
test_Phd ... ok
test_check_SeqIO (test_Phd.PhdTest454.test_check_SeqIO)
Test phd_454 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestOne.test_check_SeqIO)
Test phd1 using parser via SeqIO. ... ok
test_check_record_parser (test_Phd.PhdTestOne.test_check_record_parser)
Test phd1 file in detail. ... ok
test_check_SeqIO (test_Phd.PhdTestSolexa.test_check_SeqIO)
Test phd2 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestTwo.test_check_SeqIO)
Test phd2 using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.090 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop.py
test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.016 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py
test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.017 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_nodepend.py
test_PopGen_GenePop_nodepend ... ok
test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_file_record_parser)
Basic operation of the File Record Parser. ... ok
test_remove_features (test_PopGen_GenePop_nodepend.FileParserTest.test_remove_features)
Testing the ability to remove population/loci via class methods. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_wrong_file_parser)
Testing the ability to deal with wrongly formatted files. ... ok
test_record_parser (test_PopGen_GenePop_nodepend.ParserTest.test_record_parser)
Basic operation of the Record Parser. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest.test_wrong_file_parser)
Testing the ability to deal with wrongly formatted files. ... ok
test_record_basic (test_PopGen_GenePop_nodepend.RecordTest.test_record_basic)
Basic test on Record. ... ok
test_utils (test_PopGen_GenePop_nodepend.UtilsTest.test_utils)
Basic operation of GenePop Utils. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.027 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Prank_tool.py
test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.088 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Probcons_tool.py
test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.088 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_ProtParam.py
test_ProtParam ... ok
test_aromaticity (test_ProtParam.ProtParamTest.test_aromaticity)
Calculate protein aromaticity. ... ok
test_charge_at_pH (test_ProtParam.ProtParamTest.test_charge_at_pH)
Test charge_at_pH function. ... ok
test_count_amino_acids (test_ProtParam.ProtParamTest.test_count_amino_acids)
Calculate amino acid counts. ... ok
test_flexibility (test_ProtParam.ProtParamTest.test_flexibility)
Calculate protein flexibility. ... ok
test_get_amino_acids_percent (test_ProtParam.ProtParamTest.test_get_amino_acids_percent)
Calculate amino acid percentages. ... ok
test_get_molecular_weight (test_ProtParam.ProtParamTest.test_get_molecular_weight)
Calculate protein molecular weight. ... ok
test_get_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_molecular_weight_identical)
Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight)
Calculate monoisotopic molecular weight. ... ok
test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight_identical)
Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
test_gravy (test_ProtParam.ProtParamTest.test_gravy)
Calculate gravy. Tests all pre-defined scales. ... ok
test_instability_index (test_ProtParam.ProtParamTest.test_instability_index)
Calculate protein instability index. ... ok
test_isoelectric_point (test_ProtParam.ProtParamTest.test_isoelectric_point)
Calculate the isoelectric point. ... ok
test_molar_extinction_coefficient (test_ProtParam.ProtParamTest.test_molar_extinction_coefficient)
Molar extinction coefficient. ... ok
test_protein_scale (test_ProtParam.ProtParamTest.test_protein_scale)
Calculate the Kite Doolittle scale. ... ok
test_secondary_structure_fraction (test_ProtParam.ProtParamTest.test_secondary_structure_fraction)
Calculate secondary structure fractions. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.074 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_RCSBFormats.py
test_RCSBFormats ... ok
test_compare_chains (test_RCSBFormats.CompareStructures.test_compare_chains)
Compare parsed chains. ... ok
test_compare_models (test_RCSBFormats.CompareStructures.test_compare_models)
Compared parsed models. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.582 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Restriction.py
test_Restriction ... ok
test_basic_isochizomers (test_Restriction.EnzymeComparison.test_basic_isochizomers)
Test to be sure isochizomer and neoschizomers are as expected. ... ok
test_comparisons (test_Restriction.EnzymeComparison.test_comparisons)
Test comparison operators between different enzymes. ... ok
test_change (test_Restriction.RestrictionBatchPrintTest.test_change)
Test that change() changes something. ... ok
test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map1)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map2)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map3)
Test that print_as('map'); print_that() correctly wraps round. ... ok
test_analysis_restrictions (test_Restriction.RestrictionBatches.test_analysis_restrictions)
Test Fancier restriction analysis. ... ok
test_batch_analysis (test_Restriction.RestrictionBatches.test_batch_analysis)
Sequence analysis with a restriction batch. ... ok
test_creating_batch (test_Restriction.RestrictionBatches.test_creating_batch)
Creating and modifying a restriction batch. ... ok
test_premade_batches (test_Restriction.RestrictionBatches.test_premade_batches)
Test content of premade batches CommOnly, NoComm, AllEnzymes. ... ok
test_search_premade_batches (test_Restriction.RestrictionBatches.test_search_premade_batches)
Test search with pre-made batches CommOnly, NoComm, AllEnzymes. ... ok
test_formatted_seq (test_Restriction.SequenceTesting.test_formatted_seq)
Test several methods of FormattedSeq. ... ok
test_non_iupac_letters (test_Restriction.SequenceTesting.test_non_iupac_letters)
Test if non-IUPAC letters raise a TypeError. ... ok
test_sequence_object (test_Restriction.SequenceTesting.test_sequence_object)
Test if sequence must be a Seq or MutableSeq object. ... ok
test_circular_sequences (test_Restriction.SimpleEnzyme.test_circular_sequences)
Deal with cutting circular sequences. ... ok
test_cutting_border_positions (test_Restriction.SimpleEnzyme.test_cutting_border_positions)
Check if cutting after first and penultimate position works. ... ok
test_ear_cutting (test_Restriction.SimpleEnzyme.test_ear_cutting)
Test basic cutting with EarI (ambiguous overhang). ... ok
test_eco_cutting (test_Restriction.SimpleEnzyme.test_eco_cutting)
Test basic cutting with EcoRI (5'overhang). ... ok
test_init (test_Restriction.SimpleEnzyme.test_init)
Check for error during __init__. ... ok
test_kpn_cutting (test_Restriction.SimpleEnzyme.test_kpn_cutting)
Test basic cutting with KpnI (3'overhang). ... ok
test_overlapping_cut_sites (test_Restriction.SimpleEnzyme.test_overlapping_cut_sites)
Check if overlapping recognition sites are properly handled. ... ok
test_recognition_site_on_both_strands (test_Restriction.SimpleEnzyme.test_recognition_site_on_both_strands)
Check if recognition sites on both strands are properly handled. ... ok
test_shortcuts (test_Restriction.SimpleEnzyme.test_shortcuts)
Check if '/' and '//' work as '.search' and '.catalyse'. ... ok
test_sma_cutting (test_Restriction.SimpleEnzyme.test_sma_cutting)
Test basic cutting with SmaI (blunt cutter). ... ok
test_sna_cutting (test_Restriction.SimpleEnzyme.test_sna_cutting)
Test basic cutting with SnaI (unknown). ... ok
test_print_that (test_Restriction.TestPrintOutputs.test_print_that)
Test print_that function. ... ok
test_str_method (test_Restriction.TestPrintOutputs.test_str_method)
Test __str__ and __repr__ outputs. ... ok
test_supplier (test_Restriction.TestPrintOutputs.test_supplier)
Test output of supplier list for different enzyme types. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.216 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Astral.py
test_SCOP_Astral ... ok
testConstructWithCustomFile (test_SCOP_Astral.AstralTests.testConstructWithCustomFile) ... ok
testGetDomainsClustered (test_SCOP_Astral.AstralTests.testGetDomainsClustered) ... ok
testGetDomainsFromFile (test_SCOP_Astral.AstralTests.testGetDomainsFromFile) ... ok
testGetSeq (test_SCOP_Astral.AstralTests.testGetSeq) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Cla.py
test_SCOP_Cla ... ok
testError (test_SCOP_Cla.ClaTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testIndex (test_SCOP_Cla.ClaTests.testIndex)
Test CLA file indexing. ... ok
testParse (test_SCOP_Cla.ClaTests.testParse)
Test if all records in a CLA file are being read. ... ok
testRecord (test_SCOP_Cla.ClaTests.testRecord)
Test one record in detail. ... ok
testStr (test_SCOP_Cla.ClaTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.077 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Des.py
test_SCOP_Des ... ok
testError (test_SCOP_Des.DesTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Des.DesTests.testParse)
Test if all records in a DES file are being read. ... ok
testRecord (test_SCOP_Des.DesTests.testRecord)
Test one record in detail. ... ok
testStr (test_SCOP_Des.DesTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Dom.py
test_SCOP_Dom ... ok
testError (test_SCOP_Dom.DomTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Dom.DomTests.testParse)
Test if all records in a DOM file are being read. ... ok
testRecord (test_SCOP_Dom.DomTests.testRecord)
Test one record in detail. ... ok
testStr (test_SCOP_Dom.DomTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Hie.py
test_SCOP_Hie ... ok
testError (test_SCOP_Hie.HieTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Hie.HieTests.testParse)
Test if all records in a HIE file are being read. ... ok
testStr (test_SCOP_Hie.HieTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Raf.py
test_SCOP_Raf ... ok
testParse (test_SCOP_Raf.RafTests.testParse)
Parse a RAF record. ... ok
testSeqMapAdd (test_SCOP_Raf.RafTests.testSeqMapAdd) ... ok
testSeqMapIndex (test_SCOP_Raf.RafTests.testSeqMapIndex) ... ok
testSeqMapSlice (test_SCOP_Raf.RafTests.testSeqMapSlice) ... ok
test_SeqMap_getAtoms_err (test_SCOP_Raf.RafTests.test_SeqMap_getAtoms_err) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.094 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Residues.py
test_SCOP_Residues ... ok
testAstralParse (test_SCOP_Residues.ResiduesTests.testAstralParse)
Test if we can parse residue subsets enclosed in brackets. ... ok
testJustPdbId (test_SCOP_Residues.ResiduesTests.testJustPdbId) ... ok
testParse (test_SCOP_Residues.ResiduesTests.testParse) ... ok
testParseError (test_SCOP_Residues.ResiduesTests.testParseError) ... ok
testPdbId (test_SCOP_Residues.ResiduesTests.testPdbId) ... ok
testStr (test_SCOP_Residues.ResiduesTests.testStr) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_Scop.py
test_SCOP_Scop ... ok
testConstructFromDirectory (test_SCOP_Scop.ScopTests.testConstructFromDirectory) ... ok
testGetAscendent (test_SCOP_Scop.ScopTests.testGetAscendent) ... ok
testParse (test_SCOP_Scop.ScopTests.testParse) ... ok
testParseDomain (test_SCOP_Scop.ScopTests.testParseDomain) ... ok
testSccsOrder (test_SCOP_Scop.ScopTests.testSccsOrder) ... ok
test_get_descendents (test_SCOP_Scop.ScopTests.test_get_descendents)
Test getDescendents method. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SCOP_online.py
test_SCOP_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SVDSuperimposer.py
test_SVDSuperimposer ... ok
test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest.test_get_init_rms) ... ok
test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest.test_oldTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.016 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl.py
test_SearchIO_blat_psl ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_001)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_002)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_003)
Test parsing blat output (psl_34_003.psl). ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_004)
Test parsing blat output (psl_34_004.psl). ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_005)
Test parsing blat output (psl_34_005.psl). ... ok
test_psl_35_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_001)
Test parsing blat output (psl_35_001.psl). ... ok
test_psl_35_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_002)
Test parsing blat output (psl_35_002.psl). ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_001)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_002)
Test parsing blat output (psl_34_001.psl). ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_003)
Test parsing blat output (psl_34_003.psl). ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_004)
Test parsing blat output (psl_34_004.psl). ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_005)
Test parsing blat output (psl_34_005.psl). ... ok
test_psl_35_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_001)
Test parsing blat output (psl_35_001.psl). ... ok
test_psl_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_002)
Test parsing blat output (psl_35_002.psl). ... ok
test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_001)
Test parsing blat output (pslx_34_001.pslx). ... ok
test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_002)
Test parsing blat output (pslx_34_002.pslx). ... ok
test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_003)
Test parsing blat output (pslx_34_003.pslx). ... ok
test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_004)
Test parsing blat output (pslx_34_004.pslx). ... ok
test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_005)
Test parsing blat output (pslx_34_005.pslx). ... ok
test_pslx_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_35_002)
Test parsing blat output (pslx_35_002.pslx). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.114 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl_index.py
test_SearchIO_blat_psl_index ... ok
test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_001)
Test blat-psl indexing, multiple queries. ... ok
test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_002)
Test blat-psl indexing, single query, no hits. ... ok
test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_003)
Test blat-psl indexing, single query, single hit. ... ok
test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_004)
Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok
test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_005)
Test blat-psl indexing, multiple queries, no header. ... ok
test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_006)
Test blat-pslx indexing, multiple queries. ... ok
test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_007)
Test blat-pslx indexing, single query, no hits. ... ok
test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_008)
Test blat-pslx indexing, single query, single hit. ... ok
test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_009)
Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok
test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_010)
Test blat-pslx indexing, multiple queries, no header. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.154 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate.py
test_SearchIO_exonerate ... ok
test_exn_22_o_vulgar_cigar (test_SearchIO_exonerate.ExonerateCigarCases.test_exn_22_o_vulgar_cigar)
Test parsing exonerate output (exn_22_o_vulgar_cigar.exn). ... ok
test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_c2c)
Compares vulgar-text coordinate parsing for the coding2coding model. ... ok
test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_g2g)
Compares vulgar-text coordinate parsing for the genome2genome model. ... ok
test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_p2d)
Compares vulgar-text coordinate parsing for the protein2dna model. ... ok
test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_affine_local)
Test parsing exonerate output (exn_22_m_affine_local.exn). ... ok
test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_cdna2genome)
Test parsing exonerate output (exn_22_m_cdna2genome.exn). ... ok
test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding)
Test parsing exonerate output (exn_22_m_coding2coding.exn). ... ok
test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding_fshifts)
Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn). ... ok
test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2genome)
Test parsing exonerate output (exn_22_m_coding2genome.exn). ... ok
test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_dna2protein)
Test parsing exonerate output (exn_22_m_dna2protein.exn). ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_est2genome)
Test parsing exonerate output (exn_22_m_est2genome.exn). ... ok
test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_genome2genome)
Test parsing exonerate output (exn_22_m_genome2genome.exn). ... ok
test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ner)
Test parsing exonerate output (exn_22_m_ner.exn). ... ok
test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2dna_fshifts)
Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn). ... ok
test_exn_22_m_protein2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2genome)
Test parsing exonerate output (exn_22_m_protein2genome.exn). ... ok
test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped)
Test parsing exonerate output (exn_22_m_ungapped.exn). ... ok
test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped_trans)
Test parsing exonerate output (exn_22_m_ungapped_trans.exn). ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_multiple)
Test parsing exonerate output (exn_22_q_multiple.exn). ... ok
test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_none)
Test parsing exonerate output (exn_22_q_none.exn). ... ok
test_exn_24_m_protein2genome_revcomp_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_m_protein2genome_revcomp_fshifts)
Test parsing exonerate output (exn_24_m_protein2genome_revcomp_fshifts.exn). ... ok
test_exn_24_protein2genome_met_intron (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_protein2genome_met_intron)
Test parsing exonerate output (exn_24_m_protein2genome_met_intron.exn). ... ok
test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar)
Test parsing exonerate output (exn_22_o_vulgar.exn). ... ok
test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar_fshifts)
Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.152 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_text_index.py
test_SearchIO_exonerate_text_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_m_est2genome)
Test exonerate-text indexing, single. ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_q_multiple)
Test exonerate-text indexing, single. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.088 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_vulgar_index.py
test_SearchIO_exonerate_vulgar_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_m_est2genome)
Test exonerate-vulgar indexing, single. ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_q_multiple)
Test exonerate-vulgar indexing, single. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.090 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10.py
test_SearchIO_fasta_m10 ... ok
test_output002 (test_SearchIO_fasta_m10.Fasta34Cases.test_output002)
Test parsing fasta34 output (output002.m10). ... ok
test_output003 (test_SearchIO_fasta_m10.Fasta34Cases.test_output003)
Test parsing fasta34 output (output003.m10). ... ok
test_output001 (test_SearchIO_fasta_m10.Fasta35Cases.test_output001)
Test parsing fasta35 output (output001.m10). ... ok
test_output004 (test_SearchIO_fasta_m10.Fasta35Cases.test_output004)
Test parsing fasta35 output (output004.m10). ... ok
test_output005 (test_SearchIO_fasta_m10.Fasta35Cases.test_output005)
Test parsing ssearch35 output (output005.m10). ... ok
test_output006 (test_SearchIO_fasta_m10.Fasta35Cases.test_output006)
Test parsing fasta35 output (output006.m10). ... ok
test_output007 (test_SearchIO_fasta_m10.Fasta36Cases.test_output007)
Test parsing fasta36 output (output007.m10). ... ok
test_output008 (test_SearchIO_fasta_m10.Fasta36Cases.test_output008)
Test parsing tfastx36 output (output008.m10). ... ok
test_output009 (test_SearchIO_fasta_m10.Fasta36Cases.test_output009)
Test parsing fasta36 output (output009.m10). ... ok
test_output010 (test_SearchIO_fasta_m10.Fasta36Cases.test_output010)
Test parsing fasta36 output (output010.m10). ... ok
test_output011 (test_SearchIO_fasta_m10.Fasta36Cases.test_output011)
Test parsing fasta36 output (output011.m10). ... ok
test_output012 (test_SearchIO_fasta_m10.Fasta36Cases.test_output012)
Test parsing fasta36 output (output012.m10). ... ok
test_output013 (test_SearchIO_fasta_m10.Fasta36Cases.test_output013)
Test parsing fasta36 output (output013.m10). ... ok
test_output014 (test_SearchIO_fasta_m10.Fasta36Cases.test_output014)
Test parsing fasta36 output (output014.m10). ... ok
test_output015 (test_SearchIO_fasta_m10.Fasta36Cases.test_output015)
Test parsing fasta36 output (output015.m10). ... ok
test_output016 (test_SearchIO_fasta_m10.Fasta36Cases.test_output016)
Test parsing fasta36 output (output016.m10). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.135 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10_index.py
test_SearchIO_fasta_m10_index ... ok
test_output_001 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_001)
Test fasta-m10 indexing, fasta35, multiple queries. ... ok
test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_002)
Test fasta-m10 indexing, fasta34, multiple queries. ... ok
test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_005)
Test fasta-m10 indexing, ssearch35, multiple queries. ... ok
test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_008)
Test fasta-m10 indexing, tfastx36, multiple queries. ... ok
test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_009)
Test fasta-m10 indexing, fasta36, multiple queries. ... ok
test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_010)
Test fasta-m10 indexing, fasta36, single query, no hits. ... ok
test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_011)
Test fasta-m10 indexing, fasta36, single query, hits with single hsp. ... ok
test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_012)
Test fasta-m10 indexing, fasta36, single query with multiple hsps. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.160 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hhsuite2_text.py
test_SearchIO_hhsuite2_text ... ok
test_2uvo (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo)
Parsing 2uvo. ... ok
test_2uvo_emptytable (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_emptytable)
Parsing 4uvo with empty results table. ... ok
test_2uvo_onlyheader (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_onlyheader)
Parsing 4uvo with only header present. ... ok
test_4p79 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4p79)
Parsing 4p79_hhsearch_server_NOssm.hhr file. ... ok
test_4y9h_nossm (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4y9h_nossm)
Parsing 4y9h_hhsearch_server_NOssm.hhr file. ... ok
test_9590198 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_9590198)
Parsing hhpred_9590198.hhr file. ... ok
test_allx (test_SearchIO_hhsuite2_text.HhsuiteCases.test_allx)
Parsing allx.hhr file. ... ok
test_q9bsu1 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_q9bsu1)
Parsing hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.129 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text.py
C
test_SearchIO_hmmer2_text ... ok
test_hmmpfam_21 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_21)
Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out). ... ok
test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_22)
Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out). ... ok
test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out). ... ok
test_hmmpfam_23_break_in_end_of_seq (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_break_in_end_of_seq)
Test parsing hmmpfam 2.3 file with a line break in the end of seq marker. ... ok
test_hmmpfam_23_missing_consensus (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_missing_consensus)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out). ... ok
test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_no_match)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out). ... ok
test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_24)
Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out). ... ok
test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_20)
Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out). ... ok
test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_22)
Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.159 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text_index.py
test_SearchIO_hmmer2_text_index ... ok
test_hmmertext_text_21_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_21_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.1. ... ok
test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.2. ... ok
test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmsearch_001)
Test hmmer2-text indexing, HMMER 2.2. ... ok
test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_23_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.3. ... ok
test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_24_hmmpfam_001)
Test hmmer2-text indexing, HMMER 2.4. ... ok
test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_first_hmmpfam)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_last_hmmpfam)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_middle_hmmpfam)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok
test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmpfam)
Test hmmer2-text raw string retrieval, single query, hmmpfam. ... ok
test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmsearch)
Test hmmer2-text raw string retrieval, single query, hmmsearch. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.124 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
C
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab.py
test_SearchIO_hmmer3_domtab ... ok
test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_30_hmmsearch_001)
Parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001). ... ok
test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_31b1_hmmsearch_001)
Parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001). ... ok
test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_001)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001). ... ok
test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_002)
Parsing hmmscan-domtab, hmmscan 3.0, single query, no hits (domtab_30_hmmscan_002). ... ok
test_domtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_003)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003). ... ok
test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_004)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004). ... ok
test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_31b1_hmmscan_001)
Parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.066 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab_index.py
C
test_SearchIO_hmmer3_domtab_index ... ok
test_hmmerdomtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_001)
Test hmmscan-domtab indexing, HMMER 3.0, multiple queries. ... ok
test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_002)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_003)
Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_004)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmsearch_001)
Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_first)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, first (domtab_30_hmmscan_001.out). ... ok
test_hmmerdomtab_30_multiple_last (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_last)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, last (domtab_30_hmmscan_001.out). ... ok
test_hmmerdomtab_30_multiple_middle (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_middle)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, middle (domtab_30_hmmscan_001.out). ... ok
test_hmmerdomtab_30_single (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_single)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.077 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab.py
C
test_SearchIO_hmmer3_tab ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_001)
Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001). ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_002)
Test parsing hmmer3-tab, hmmscan 3.0, single query, no hits (tab_30_hmmscan_002). ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_003)
Test parsing hmmer3-tab, hmmscan 3.0, single query, single hit, single hsp (tab_30_hmmscan_003). ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_004)
Test parsing hmmer3-tab, hmmscan 3.0, single query, multiple hits (tab_30_hmmscan_004). ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_31b1_hmmscan_001)
Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases.test_31b1_hmmsearch_001)
Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.063 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab_index.py
test_SearchIO_hmmer3_tab_index ... ok
test_hmmer3tab_30_hmmscan_001 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_001)
Test hmmer3-tab indexing, HMMER 3.0, multiple queries. ... ok
test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_002)
Test hmmer3-tab indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_003)
Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_004)
Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_first)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, first (tab_30_hmmscan_001.out). ... ok
test_hmmer3tab_30_multiple_last (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_last)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, last (tab_30_hmmscan_001.out). ... ok
test_hmmer3tab_30_multiple_middle (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_middle)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, middle (tab_30_hmmscan_001.out). ... ok
test_hmmer3tab_30_single (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_single)
Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.070 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text.py
test_SearchIO_hmmer3_text ... ok
test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_001)
Parsing hmmersearch 3.0 (text_30_hmmsearch_001). ... ok
test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_002)
Parsing hmmersearch 3.0 (text_30_hmmsearch_002). ... ok
test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_003)
Parsing hmmersearch 3.0 (text_30_hmmsearch_003). ... ok
test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_004)
Parsing hmmersearch 3.0 (text_30_hmmsearch_004). ... ok
test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_005)
Parsing hmmersearch 3.0 (text_30_hmmsearch_005). ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b1_hmmsearch_001)
Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001). ... ok
test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmscan_001)
Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001). ... ok
test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_001)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001). ... ok
test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_002)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002). ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_001)
Parsing hmmscan 3.0 (text_30_hmmscan_001). ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_002)
Parsing hmmscan 3.0 (text_30_hmmscan_002). ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_003)
Parsing hmmscan 3.0 (text_30_hmmscan_003). ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_004)
Parsing hmmscan 3.0 (text_30_hmmscan_004). ... ok
test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_005)
Parsing hmmscan 3.0 (text_30_hmmscan_005). ... ok
test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_006)
Parsing hmmscan 3.0 (text_30_hmmscan_006). ... ok
test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_007)
Parsing hmmscan 3.0 (text_30_hmmscan_007). ... ok
test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_008)
Parsing hmmscan 3.0 (text_30_hmmscan_008). ... ok
test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_009)
Parsing hmmscan 3.0 (text_30_hmmscan_009). ... ok
test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_010)
Parsing hmmscan 3.0 (text_30_hmmscan_010). ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_31b1_hmmscan_001)
Parsing hmmscan 3.1b1 (text_31b1_hmmscan_001). ... ok
test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases.test_31b2_phmmer_001)
Parsing phmmer 3.1b2 (text_31b2_phmmer_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.169 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text_index.py
test_SearchIO_hmmer3_text_index ... ok
test_hmmertext_text_30_hmmscan_001 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_001)
Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok
test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_002)
Test hmmer3-text indexing, HMMER 3.0, single query, no hits. ... ok
test_hmmertext_text_30_hmmscan_006 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_006)
Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits. ... ok
test_hmmertext_text_30_hmmscan_007 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_007)
Test hmmer3-text indexing, HMMER 3.0, single query, no alignments. ... ok
test_hmmertext_text_30_hmmscan_008 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_008)
Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width. ... ok
test_hmmertext_text_30_hmmsearch_005 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmsearch_005)
Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok
test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_first)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out). ... ok
test_hmmer3text_30_multiple_last (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_last)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out). ... ok
test_hmmer3text_30_multiple_middle (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_middle)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out). ... ok
test_hmmer3text_30_single (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_single)
Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.104 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_interproscan_xml.py
test_SearchIO_interproscan_xml ... ok
test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases.test_xml_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.058 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_legacy.py
test_SearchIO_legacy ... ok
test_TaggingConsumer (test_SearchIO_legacy.TestParserSupport.test_TaggingConsumer) ... ok
test_attempt_read_and_call (test_SearchIO_legacy.TestParserSupport.test_attempt_read_and_call) ... ok
test_is_blank_line (test_SearchIO_legacy.TestParserSupport.test_is_blank_line) ... ok
test_read_and_call (test_SearchIO_legacy.TestParserSupport.test_read_and_call) ... ok
test_safe_peekline (test_SearchIO_legacy.TestParserSupport.test_safe_peekline) ... ok
test_safe_readline (test_SearchIO_legacy.TestParserSupport.test_safe_readline) ... ok
test_one (test_SearchIO_legacy.UndoHandleTests.test_one)
First test. ... ok
test_read (test_SearchIO_legacy.UndoHandleTests.test_read)
Test read method. ... ok
test_undohandle_read_block (test_SearchIO_legacy.UndoHandleTests.test_undohandle_read_block)
Test reading in blocks. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.054 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_model.py
test_SearchIO_model ... ok
test_coords_setters_getters (test_SearchIO_model.HSPFragmentCases.test_coords_setters_getters)
Test HSPFragment query and hit coordinate-related setters and getters. ... ok
test_coords_setters_readonly (test_SearchIO_model.HSPFragmentCases.test_coords_setters_readonly)
Test HSPFragment query and hit coordinate-related read-only getters. ... ok
test_default_attrs (test_SearchIO_model.HSPFragmentCases.test_default_attrs)
Test HSPFragment attributes' default values. ... ok
test_frame_set_error (test_SearchIO_model.HSPFragmentCases.test_frame_set_error)
Test HSPFragment query and hit frame setters, invalid values. ... ok
test_frame_set_ok (test_SearchIO_model.HSPFragmentCases.test_frame_set_ok)
Test HSPFragment query and hit frame setters. ... ok
test_getitem (test_SearchIO_model.HSPFragmentCases.test_getitem)
Test HSPFragment.__getitem__. ... ok
test_getitem_alignment_annot (test_SearchIO_model.HSPFragmentCases.test_getitem_alignment_annot)
Test HSPFragment.__getitem__, with alignment annotation. ... ok
test_getitem_attrs (test_SearchIO_model.HSPFragmentCases.test_getitem_attrs)
Test HSPFragment.__getitem__, with attributes. ... ok
test_id_desc_set (test_SearchIO_model.HSPFragmentCases.test_id_desc_set)
Test HSPFragment query and hit id and description setters. ... ok
test_init_with_seqrecord (test_SearchIO_model.HSPFragmentCases.test_init_with_seqrecord)
Test HSPFragment.__init__, with SeqRecord. ... ok
test_init_wrong_seqtypes (test_SearchIO_model.HSPFragmentCases.test_init_wrong_seqtypes)
Test HSPFragment.__init__, wrong sequence argument types. ... ok
test_len (test_SearchIO_model.HSPFragmentCases.test_len)
Test HSPFragment.__len__. ... ok
test_molecule_type_no_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_no_seq)
Test HSPFragment molecule_type property, query and hit sequences not present. ... ok
test_molecule_type_with_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_with_seq)
Test HSPFragment molecule_type property, query or hit sequences present. ... ok
test_pickle (test_SearchIO_model.HSPFragmentCases.test_pickle)
Test pickling and unpickling of HSPFragment. ... ok
test_repr (test_SearchIO_model.HSPFragmentCases.test_repr)
Test HSPFragment.__repr__. ... ok
test_seq_unequal_hit_query_len (test_SearchIO_model.HSPFragmentCases.test_seq_unequal_hit_query_len)
Test HSPFragment sequence setter with unequal hit and query lengths. ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentCases.test_seqmodel)
Test HSPFragment sequence attribute types and default values. ... ok
test_strand_set_error (test_SearchIO_model.HSPFragmentCases.test_strand_set_error)
Test HSPFragment query and hit strand setters, invalid values. ... ok
test_strand_set_from_minus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_minus_frame)
Test HSPFragment query and hit strand getters, from minus frame. ... ok
test_strand_set_from_plus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_plus_frame)
Test HSPFragment query and hit strand getters, from plus frame. ... ok
test_strand_set_from_zero_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_zero_frame)
Test HSPFragment query and hit strand getters, from zero frame. ... ok
test_strand_set_ok (test_SearchIO_model.HSPFragmentCases.test_strand_set_ok)
Test HSPFragment query and hit strand setters. ... ok
test_getitem (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem)
Test HSPFragment.__getitem__, no alignments. ... ok
test_getitem_only_hit (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_hit)
Test HSPFragment.__getitem__, only hit. ... ok
test_getitem_only_query (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_query)
Test HSPFragment.__getitem__, only query. ... ok
test_init (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_init)
Test HSPFragment.__init__ attributes. ... ok
test_iter (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_iter)
Test HSP.__iter__, no alignments. ... ok
test_len (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_len)
Test HSPFragment.__len__, no alignments. ... ok
test_repr (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_repr)
Test HSPFragment.__repr__, no alignments. ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_seqmodel)
Test HSPFragment sequence attributes, no alignments. ... ok
test_contains (test_SearchIO_model.HSPMultipleFragmentCases.test_contains)
Test HSP.__contains__. ... ok
test_delitem (test_SearchIO_model.HSPMultipleFragmentCases.test_delitem)
Test HSP.__delitem__. ... ok
test_fragments (test_SearchIO_model.HSPMultipleFragmentCases.test_fragments)
Test HSP.fragments property. ... ok
test_getitem (test_SearchIO_model.HSPMultipleFragmentCases.test_getitem)
Test HSP.__getitem__. ... ok
test_id_desc_set (test_SearchIO_model.HSPMultipleFragmentCases.test_id_desc_set)
Test HSP query and hit id and description setters. ... ok
test_is_fragmented (test_SearchIO_model.HSPMultipleFragmentCases.test_is_fragmented)
Test HSP.is_fragmented property. ... ok
test_len (test_SearchIO_model.HSPMultipleFragmentCases.test_len)
Test HSP.__len__. ... ok
test_molecule_type (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type)
Test HSP.molecule_type getter. ... ok
test_molecule_type_set (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type_set)
Test HSP.molecule_type setter. ... ok
test_pickle (test_SearchIO_model.HSPMultipleFragmentCases.test_pickle)
Test pickling and unpickling of HSP. ... ok
test_range (test_SearchIO_model.HSPMultipleFragmentCases.test_range)
Test HSP range properties. ... ok
test_ranges (test_SearchIO_model.HSPMultipleFragmentCases.test_ranges)
Test HSP ranges properties. ... ok
test_seqs (test_SearchIO_model.HSPMultipleFragmentCases.test_seqs)
Test HSP sequence properties. ... ok
test_setitem_multiple (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_multiple)
Test HSP.__setitem__, multiple items. ... ok
test_setitem_single (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_single)
Test HSP.__setitem__, single item. ... ok
test_setters_readonly (test_SearchIO_model.HSPMultipleFragmentCases.test_setters_readonly)
Test HSP read-only properties. ... ok
test_span (test_SearchIO_model.HSPMultipleFragmentCases.test_span)
Test HSP span properties. ... ok
test_alignment (test_SearchIO_model.HSPSingleFragmentCases.test_alignment)
Test HSP.alignment property. ... ok
test_aln_span (test_SearchIO_model.HSPSingleFragmentCases.test_aln_span)
Test HSP.aln_span property. ... ok
test_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_fragment)
Test HSP.fragment property. ... ok
test_init_no_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_init_no_fragment)
Test HSP.__init__ without fragments. ... ok
test_is_fragmented (test_SearchIO_model.HSPSingleFragmentCases.test_is_fragmented)
Test HSP.is_fragmented property. ... ok
test_len (test_SearchIO_model.HSPSingleFragmentCases.test_len)
Test HSP.__len__. ... ok
test_range (test_SearchIO_model.HSPSingleFragmentCases.test_range)
Test HSP range properties. ... ok
test_seq (test_SearchIO_model.HSPSingleFragmentCases.test_seq)
Test HSP sequence properties. ... ok
test_setters_readonly (test_SearchIO_model.HSPSingleFragmentCases.test_setters_readonly)
Test HSP read-only properties. ... ok
test_span (test_SearchIO_model.HSPSingleFragmentCases.test_span)
Test HSP span properties. ... ok
test_append (test_SearchIO_model.HitCases.test_append)
Test Hit.append. ... ok
test_bool (test_SearchIO_model.HitCases.test_bool)
Test Hit.__bool__. ... ok
test_delitem (test_SearchIO_model.HitCases.test_delitem)
Test Hit.__delitem__. ... ok
test_desc_set (test_SearchIO_model.HitCases.test_desc_set)
Test Hit.description setter. ... ok
test_desc_set_no_seqrecord (test_SearchIO_model.HitCases.test_desc_set_no_seqrecord)
Test Hit.description setter, without HSP SeqRecords. ... ok
test_filter (test_SearchIO_model.HitCases.test_filter)
Test Hit.filter. ... ok
test_filter_no_filtered (test_SearchIO_model.HitCases.test_filter_no_filtered)
Test Hit.hit_filter, all hits filtered out. ... ok
test_filter_no_func (test_SearchIO_model.HitCases.test_filter_no_func)
Test Hit.filter, without arguments. ... ok
test_fragments (test_SearchIO_model.HitCases.test_fragments)
Test Hit.fragments. ... ok
test_getitem_multiple (test_SearchIO_model.HitCases.test_getitem_multiple)
Test Hit.__getitem__, multiple items. ... ok
test_getitem_single (test_SearchIO_model.HitCases.test_getitem_single)
Test Hit.__getitem__, single item. ... ok
test_hsp_map_no_func (test_SearchIO_model.HitCases.test_hsp_map_no_func)
Test Hit.map, without arguments. ... ok
test_hsps (test_SearchIO_model.HitCases.test_hsps)
Test Hit.hsps. ... ok
test_id_set (test_SearchIO_model.HitCases.test_id_set)
Test Hit.id setter. ... ok
test_index (test_SearchIO_model.HitCases.test_index)
Test Hit.index. ... ok
test_index_not_present (test_SearchIO_model.HitCases.test_index_not_present)
Test Hit.index, when index is not present. ... ok
test_init_hsps_only (test_SearchIO_model.HitCases.test_init_hsps_only)
Test Hit.__init__, with hsps only. ... ok
test_init_id_only (test_SearchIO_model.HitCases.test_init_id_only)
Test Hit.__init__, with ID only. ... ok
test_init_none (test_SearchIO_model.HitCases.test_init_none)
Test Hit.__init__, no arguments. ... ok
test_item_multiple (test_SearchIO_model.HitCases.test_item_multiple)
Test Hit.__setitem__, multiple items. ... ok
test_iter (test_SearchIO_model.HitCases.test_iter)
Test Hit.__iter__. ... ok
test_len (test_SearchIO_model.HitCases.test_len)
Test Hit.__len__. ... ok
test_map (test_SearchIO_model.HitCases.test_map)
Test Hit.hsp_map. ... ok
test_pickle (test_SearchIO_model.HitCases.test_pickle)
Test pickling and unpickling of Hit. ... ok
test_pop (test_SearchIO_model.HitCases.test_pop)
Test Hit.pop. ... ok
test_repr (test_SearchIO_model.HitCases.test_repr)
Test Hit.__repr__. ... ok
test_setitem_single (test_SearchIO_model.HitCases.test_setitem_single)
Test Hit.__setitem__, single item. ... ok
test_sort (test_SearchIO_model.HitCases.test_sort)
Test Hit.sort. ... ok
test_sort_not_in_place (test_SearchIO_model.HitCases.test_sort_not_in_place)
Test Hit.sort, not in place. ... ok
test_validate_hsp_ok (test_SearchIO_model.HitCases.test_validate_hsp_ok)
Test Hit._validate_hsp. ... ok
test_validate_hsp_wrong_hit_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_hit_id)
Test Hit._validate_hsp, wrong hit ID. ... ok
test_validate_hsp_wrong_query_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_query_id)
Test Hit._validate_hsp, wrong query ID. ... ok
test_validate_hsp_wrong_type (test_SearchIO_model.HitCases.test_validate_hsp_wrong_type)
Test Hit._validate_hsp, wrong type. ... ok
test_absorb_hit_does_not_exist (test_SearchIO_model.QueryResultCases.test_absorb_hit_does_not_exist)
Test QueryResult.absorb, hit does not exist. ... ok
test_absorb_hit_exists (test_SearchIO_model.QueryResultCases.test_absorb_hit_exists)
Test QueryResult.absorb, hit with the same ID exists. ... ok
test_append_alt_id_exists (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists)
Test QueryResult.append, when alt ID exists. ... ok
test_append_alt_id_exists_alt (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists_alt)
Test QueryResult.append, when alt ID exists as primary. ... ok
test_append_custom_hit_key_function_ok (test_SearchIO_model.QueryResultCases.test_append_custom_hit_key_function_ok)
Test QueryResult.append, with custom hit key function. ... ok
test_append_id_exists (test_SearchIO_model.QueryResultCases.test_append_id_exists)
Test QueryResult.append, when ID exists. ... ok
test_append_ok (test_SearchIO_model.QueryResultCases.test_append_ok)
Test QueryResult.append. ... ok
test_bool (test_SearchIO_model.QueryResultCases.test_bool)
Test QueryResult.__bool__. ... ok
test_contains (test_SearchIO_model.QueryResultCases.test_contains)
Test QueryResult.__contains__. ... ok
test_contains_alt (test_SearchIO_model.QueryResultCases.test_contains_alt)
Test QueryResult.__contains__, with alternative IDs. ... ok
test_delitem_alt_ok (test_SearchIO_model.QueryResultCases.test_delitem_alt_ok)
Test QueryResult.__delitem__, with alt ID. ... ok
test_delitem_int_ok (test_SearchIO_model.QueryResultCases.test_delitem_int_ok)
Test QueryResult.__delitem__. ... ok
test_delitem_slice_ok (test_SearchIO_model.QueryResultCases.test_delitem_slice_ok)
Test QueryResult.__delitem__, with slice. ... ok
test_delitem_string_ok (test_SearchIO_model.QueryResultCases.test_delitem_string_ok)
Test QueryResult.__getitem__, with string. ... ok
test_description_set (test_SearchIO_model.QueryResultCases.test_description_set)
Test QueryResult.description setter. ... ok
test_description_set_no_seqrecord (test_SearchIO_model.QueryResultCases.test_description_set_no_seqrecord)
Test QueryResult.description setter, without HSP SeqRecords. ... ok
test_fragments (test_SearchIO_model.QueryResultCases.test_fragments)
Test QueryResult.fragments. ... ok
test_getitem_alt_ok (test_SearchIO_model.QueryResultCases.test_getitem_alt_ok)
Test QueryResult.__getitem__, single item with alternative ID. ... ok
test_getitem_default_ok (test_SearchIO_model.QueryResultCases.test_getitem_default_ok)
Test QueryResult.__getitem__. ... ok
test_getitem_int_ok (test_SearchIO_model.QueryResultCases.test_getitem_int_ok)
Test QueryResult.__getitem__, with integer. ... ok
test_getitem_slice_ok (test_SearchIO_model.QueryResultCases.test_getitem_slice_ok)
Test QueryResult.__getitem__, with slice. ... ok
test_getitm_slice_alt_ok (test_SearchIO_model.QueryResultCases.test_getitm_slice_alt_ok)
Test QueryResult.__getitem__, with slice and alt IDs. ... ok
test_hit_filter (test_SearchIO_model.QueryResultCases.test_hit_filter)
Test QueryResult.hit_filter. ... ok
test_hit_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hit_filter_no_filtered)
Test QueryResult.hit_filter, all hits filtered out. ... ok
test_hit_filter_no_func (test_SearchIO_model.QueryResultCases.test_hit_filter_no_func)
Test QueryResult.hit_filter, without arguments. ... ok
test_hit_keys (test_SearchIO_model.QueryResultCases.test_hit_keys)
Test QueryResult.hit_keys. ... ok
test_hit_map (test_SearchIO_model.QueryResultCases.test_hit_map)
Test QueryResult.hit_map. ... ok
test_hit_map_no_func (test_SearchIO_model.QueryResultCases.test_hit_map_no_func)
Test QueryResult.hit_map, without arguments. ... ok
test_hits (test_SearchIO_model.QueryResultCases.test_hits)
Test QueryResult.hits. ... ok
test_hsp_filter (test_SearchIO_model.QueryResultCases.test_hsp_filter)
Test QueryResult.hsp_filter. ... ok
test_hsp_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_filtered)
Test QueryResult.hsp_filter, all hits filtered out. ... ok
test_hsp_filter_no_func (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_func)
Test QueryResult.hsp_filter, no arguments. ... ok
test_hsp_map (test_SearchIO_model.QueryResultCases.test_hsp_map)
Test QueryResult.hsp_map. ... ok
test_hsp_map_no_func (test_SearchIO_model.QueryResultCases.test_hsp_map_no_func)
Test QueryResult.hsp_map, without arguments. ... ok
test_hsps (test_SearchIO_model.QueryResultCases.test_hsps)
Test QueryResult.hsps. ... ok
test_id_set (test_SearchIO_model.QueryResultCases.test_id_set)
Test QueryResult.id setter. ... ok
test_index (test_SearchIO_model.QueryResultCases.test_index)
Test QueryResult.index. ... ok
test_index_alt (test_SearchIO_model.QueryResultCases.test_index_alt)
Test QueryResult.index, with alt ID. ... ok
test_index_not_present (test_SearchIO_model.QueryResultCases.test_index_not_present)
Test QueryResult.index, when index is not present. ... ok
test_init_hits_only (test_SearchIO_model.QueryResultCases.test_init_hits_only)
Test QueryResult.__init__, with hits only. ... ok
test_init_id_only (test_SearchIO_model.QueryResultCases.test_init_id_only)
Test QueryResult.__init__, with ID only. ... ok
test_init_none (test_SearchIO_model.QueryResultCases.test_init_none)
Test QueryResult.__init__, no arguments. ... ok
test_items (test_SearchIO_model.QueryResultCases.test_items)
Test QueryResult.items. ... ok
test_iter (test_SearchIO_model.QueryResultCases.test_iter)
Test QueryResult.__iter__. ... ok
test_len (test_SearchIO_model.QueryResultCases.test_len)
Test QueryResult.__len__. ... ok
test_order (test_SearchIO_model.QueryResultCases.test_order) ... ok
test_pickle (test_SearchIO_model.QueryResultCases.test_pickle)
Test pickling and unpickling of QueryResult. ... ok
test_pop_int_index_ok (test_SearchIO_model.QueryResultCases.test_pop_int_index_ok)
Test QueryResult.pop, with integer index. ... ok
test_pop_nonexistent_key (test_SearchIO_model.QueryResultCases.test_pop_nonexistent_key)
Test QueryResult.pop with default for nonexistent key. ... ok
test_pop_nonexistent_with_default (test_SearchIO_model.QueryResultCases.test_pop_nonexistent_with_default)
Test QueryResult.pop with default for nonexistent key. ... ok
test_pop_ok (test_SearchIO_model.QueryResultCases.test_pop_ok)
Test QueryResult.pop. ... ok
test_pop_string_alt_ok (test_SearchIO_model.QueryResultCases.test_pop_string_alt_ok)
Test QueryResult.pop, with alternative ID. ... ok
test_pop_string_index_ok (test_SearchIO_model.QueryResultCases.test_pop_string_index_ok)
Test QueryResult.pop, with string index. ... ok
test_repr (test_SearchIO_model.QueryResultCases.test_repr)
Test QueryResult.__repr__. ... ok
test_setitem_from_empty (test_SearchIO_model.QueryResultCases.test_setitem_from_empty)
Test QueryResult.__setitem__, from empty container. ... ok
test_setitem_ok (test_SearchIO_model.QueryResultCases.test_setitem_ok)
Test QueryResult.__setitem__. ... ok
test_setitem_ok_alt (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt)
Test QueryResult.__setitem__, checking alt hit IDs. ... ok
test_setitem_ok_alt_existing (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_existing)
Test QueryResult.__setitem__, existing key. ... ok
test_setitem_ok_alt_ok_promote (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_ok_promote)
Test QueryResult.__setitem__, previously alt ID. ... ok
test_setitem_wrong_key_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_key_type)
Test QueryResult.__setitem__, wrong key type. ... ok
test_setitem_wrong_query_id (test_SearchIO_model.QueryResultCases.test_setitem_wrong_query_id)
Test QueryResult.__setitem__, wrong query ID. ... ok
test_setitem_wrong_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_type)
Test QueryResult.__setitem__, wrong type. ... ok
test_sort_key_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_key_not_in_place_ok)
Test QueryResult.sort, with custom key, not in place. ... ok
test_sort_key_ok (test_SearchIO_model.QueryResultCases.test_sort_key_ok)
Test QueryResult.sort, with custom key. ... ok
test_sort_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_not_in_place_ok)
Test QueryResult.sort, not in place. ... ok
test_sort_ok (test_SearchIO_model.QueryResultCases.test_sort_ok)
Test QueryResult.sort. ... ok
test_sort_reverse_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_not_in_place_ok)
Test QueryResult.sort, reverse, not in place. ... ok
test_sort_reverse_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_ok)
Test QueryResult.sort, reverse. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.110 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SearchIO_write.py
test_SearchIO_write ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy/__init__.py:12: BiopythonDeprecationWarning: The 'Bio.SearchIO._legacy' module for parsing BLAST plain text output is deprecated and will be removed in a future release of Biopython. Consider generating your BLAST output for parsing as XML or tabular format instead.
  warnings.warn(
ok
test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttab)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt). ... ok
test_write_multiple_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt). ... ok
test_write_multiple_from_blasttabc_allfields (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc_allfields)
Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt). ... ok
test_write_single_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttab)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt). ... ok
test_write_single_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttabc)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt). ... ok
test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_multiple_from_blastxml)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml). ... ok
test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_single_from_blastxml)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml). ... ok
test_write_multiple_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpsl)
Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl). ... ok
test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpslx)
Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx). ... ok
test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl)
Test blat-psl writing from blat-psl, single query (psl_34_004.psl). ... ok
test_write_single_from_blatpsl_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl_protein_query)
Test blat-psl writing from blat-psl, single query (psl_35_002.psl). ... ok
test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx)
Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx). ... ok
test_write_single_from_blatpslx_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx_protein_query)
Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx). ... ok
test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_multiple_from_hmmscandomtab)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok
test_write_single_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmscandomtab)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
test_write_single_from_hmmsearchdomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmsearchdomtab)
Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
test_write_multiple_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_multiple_from_hmmertab)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok
test_write_single_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_single_from_hmmertab)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.287 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqFeature.py
test_SeqFeature ... ok
test_eq_identical (test_SeqFeature.TestCompoundLocation.test_eq_identical)
Test two identical locations are equal. ... ok
test_eq_not_identical (test_SeqFeature.TestCompoundLocation.test_eq_not_identical)
Test two different locations are not equal. ... ok
test_reference_in_compound_location_record (test_SeqFeature.TestExtract.test_reference_in_compound_location_record)
Test compound location with reference to another record. ... ok
test_reference_in_compound_location_sequence (test_SeqFeature.TestExtract.test_reference_in_compound_location_sequence)
Test compound location with reference to another sequence. ... ok
test_reference_in_location_record (test_SeqFeature.TestExtract.test_reference_in_location_record)
Test location with reference to another record. ... ok
test_reference_in_location_sequence (test_SeqFeature.TestExtract.test_reference_in_location_sequence)
Test location with reference to another sequence. ... ok
test_fuzzy (test_SeqFeature.TestLocations.test_fuzzy)
Test fuzzy representations. ... ok
test_pickle (test_SeqFeature.TestPositions.test_pickle)
Test pickle behaviour of position instances. ... ok
test_eq_identical (test_SeqFeature.TestReference.test_eq_identical)
Test two identical references eq() to True. ... ok
test_eq_identical (test_SeqFeature.TestSeqFeature.test_eq_identical) ... ok
test_translation_checks_cds (test_SeqFeature.TestSeqFeature.test_translation_checks_cds)
Test that a CDS feature is subject to respective checks. ... ok
test_eq_identical (test_SeqFeature.TestSimpleLocation.test_eq_identical)
Test two identical locations are equal. ... ok
test_eq_not_identical (test_SeqFeature.TestSimpleLocation.test_eq_not_identical)
Test two different locations are not equal. ... ok
test_offsets (test_SeqFeature.TestSimpleLocation.test_offsets)
Test adding and subtracting integer offsets. ... ok
test_start_before_end (test_SeqFeature.TestSimpleLocation.test_start_before_end) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO.py
test_SeqIO ... ok
test_abi1 (test_SeqIO.TestSeqIO.test_abi1) ... ok
test_abi2 (test_SeqIO.TestSeqIO.test_abi2) ... ok
test_abi3 (test_SeqIO.TestSeqIO.test_abi3) ... ok
test_ace1 (test_SeqIO.TestSeqIO.test_ace1) ... ok
test_ace2 (test_SeqIO.TestSeqIO.test_ace2) ... ok
test_ace3 (test_SeqIO.TestSeqIO.test_ace3) ... ok
test_cif_atom1 (test_SeqIO.TestSeqIO.test_cif_atom1) ... ok
test_cif_atom2 (test_SeqIO.TestSeqIO.test_cif_atom2) ... ok
test_cif_seqres1 (test_SeqIO.TestSeqIO.test_cif_seqres1) ... ok
test_cif_seqres2 (test_SeqIO.TestSeqIO.test_cif_seqres2) ... ok
test_clustal1 (test_SeqIO.TestSeqIO.test_clustal1) ... ok
test_clustal2 (test_SeqIO.TestSeqIO.test_clustal2) ... ok
test_clustal3 (test_SeqIO.TestSeqIO.test_clustal3) ... ok
test_clustal4 (test_SeqIO.TestSeqIO.test_clustal4) ... ok
test_clustal_to_nexus_with_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_with_mol_type)
Convert Clustal to NEXUS with molecule type. ... ok
test_clustal_to_nexus_without_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_without_mol_type)
Convert Clustal to NEXUS without molecule type. ... ok
test_embl1 (test_SeqIO.TestSeqIO.test_embl1) ... ok
test_embl10 (test_SeqIO.TestSeqIO.test_embl10) ... ok
test_embl11 (test_SeqIO.TestSeqIO.test_embl11) ... ok
test_embl12 (test_SeqIO.TestSeqIO.test_embl12) ... ok
test_embl13 (test_SeqIO.TestSeqIO.test_embl13)
Test parsing embl file with wrapped locations and unspecified type. ... ok
test_embl14 (test_SeqIO.TestSeqIO.test_embl14)
Test parsing file with features over-indented for EMBL. ... ok
test_embl2 (test_SeqIO.TestSeqIO.test_embl2) ... ok
test_embl3 (test_SeqIO.TestSeqIO.test_embl3) ... ok
test_embl4 (test_SeqIO.TestSeqIO.test_embl4) ... ok
test_embl5 (test_SeqIO.TestSeqIO.test_embl5) ... ok
test_embl6 (test_SeqIO.TestSeqIO.test_embl6) ... ok
test_embl7 (test_SeqIO.TestSeqIO.test_embl7) ... ok
test_embl8 (test_SeqIO.TestSeqIO.test_embl8) ... ok
test_embl9 (test_SeqIO.TestSeqIO.test_embl9) ... ok
test_emboss1 (test_SeqIO.TestSeqIO.test_emboss1) ... ok
test_emboss2 (test_SeqIO.TestSeqIO.test_emboss2) ... ok
test_emboss3 (test_SeqIO.TestSeqIO.test_emboss3) ... ok
test_empty_file (test_SeqIO.TestSeqIO.test_empty_file)
Check parsers can cope with an empty file. ... ok
test_fasta1 (test_SeqIO.TestSeqIO.test_fasta1) ... ok
test_fasta10 (test_SeqIO.TestSeqIO.test_fasta10) ... ok
test_fasta11 (test_SeqIO.TestSeqIO.test_fasta11) ... ok
test_fasta12 (test_SeqIO.TestSeqIO.test_fasta12) ... ok
test_fasta13 (test_SeqIO.TestSeqIO.test_fasta13) ... ok
test_fasta14 (test_SeqIO.TestSeqIO.test_fasta14) ... ok
test_fasta15 (test_SeqIO.TestSeqIO.test_fasta15) ... ok
test_fasta16 (test_SeqIO.TestSeqIO.test_fasta16) ... ok
test_fasta17 (test_SeqIO.TestSeqIO.test_fasta17) ... ok
test_fasta18 (test_SeqIO.TestSeqIO.test_fasta18) ... ok
test_fasta19 (test_SeqIO.TestSeqIO.test_fasta19) ... ok
test_fasta2 (test_SeqIO.TestSeqIO.test_fasta2) ... ok
test_fasta20 (test_SeqIO.TestSeqIO.test_fasta20) ... ok
test_fasta21 (test_SeqIO.TestSeqIO.test_fasta21) ... ok
test_fasta22 (test_SeqIO.TestSeqIO.test_fasta22) ... ok
test_fasta23 (test_SeqIO.TestSeqIO.test_fasta23) ... ok
test_fasta24 (test_SeqIO.TestSeqIO.test_fasta24) ... ok
test_fasta3 (test_SeqIO.TestSeqIO.test_fasta3) ... ok
test_fasta4 (test_SeqIO.TestSeqIO.test_fasta4) ... ok
test_fasta5 (test_SeqIO.TestSeqIO.test_fasta5) ... ok
test_fasta6 (test_SeqIO.TestSeqIO.test_fasta6) ... ok
test_fasta7 (test_SeqIO.TestSeqIO.test_fasta7) ... ok
test_fasta8 (test_SeqIO.TestSeqIO.test_fasta8) ... ok
test_fasta9 (test_SeqIO.TestSeqIO.test_fasta9) ... ok
test_fasta_2line1 (test_SeqIO.TestSeqIO.test_fasta_2line1) ... ok
test_fasta_to_seqxml_with_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_with_mol_type)
Convert FASTA to SeqXML with molecule type. ... ok
test_fasta_to_seqxml_without_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_without_mol_type)
Convert FASTA to SeqXML without molecule type. ... ok
test_fastq1 (test_SeqIO.TestSeqIO.test_fastq1) ... ok
test_fastq2 (test_SeqIO.TestSeqIO.test_fastq2) ... ok
test_fastq3 (test_SeqIO.TestSeqIO.test_fastq3) ... ok
test_fastq4 (test_SeqIO.TestSeqIO.test_fastq4) ... ok
test_fastq5 (test_SeqIO.TestSeqIO.test_fastq5) ... ok
test_fastq_illumina1 (test_SeqIO.TestSeqIO.test_fastq_illumina1) ... ok
test_fastq_solexa1 (test_SeqIO.TestSeqIO.test_fastq_solexa1) ... ok
test_fastq_solexa2 (test_SeqIO.TestSeqIO.test_fastq_solexa2) ... ok
test_genbank1 (test_SeqIO.TestSeqIO.test_genbank1) ... ok
test_genbank10 (test_SeqIO.TestSeqIO.test_genbank10) ... ok
test_genbank11 (test_SeqIO.TestSeqIO.test_genbank11) ... ok
test_genbank12 (test_SeqIO.TestSeqIO.test_genbank12) ... ok
test_genbank13 (test_SeqIO.TestSeqIO.test_genbank13) ... ok
test_genbank14 (test_SeqIO.TestSeqIO.test_genbank14) ... ok
test_genbank15 (test_SeqIO.TestSeqIO.test_genbank15) ... ok
test_genbank16 (test_SeqIO.TestSeqIO.test_genbank16)
Test parsing Genbank file from Vector NTI with an odd LOCUS line. ... ok
test_genbank17 (test_SeqIO.TestSeqIO.test_genbank17) ... ok
test_genbank18 (test_SeqIO.TestSeqIO.test_genbank18) ... ok
test_genbank19 (test_SeqIO.TestSeqIO.test_genbank19) ... ok
test_genbank2 (test_SeqIO.TestSeqIO.test_genbank2) ... ok
test_genbank20 (test_SeqIO.TestSeqIO.test_genbank20)
Test parsing GenPept file with nasty bond locations. ... ok
test_genbank21 (test_SeqIO.TestSeqIO.test_genbank21) ... ok
test_genbank22 (test_SeqIO.TestSeqIO.test_genbank22)
Test that genbank format write doesn't destroy db_source in annotations. ... ok
test_genbank23 (test_SeqIO.TestSeqIO.test_genbank23)
Test that peptide genbank files can be written with long names. ... ok
test_genbank3 (test_SeqIO.TestSeqIO.test_genbank3) ... ok
test_genbank4 (test_SeqIO.TestSeqIO.test_genbank4) ... ok
test_genbank5 (test_SeqIO.TestSeqIO.test_genbank5) ... ok
test_genbank6 (test_SeqIO.TestSeqIO.test_genbank6) ... ok
test_genbank7 (test_SeqIO.TestSeqIO.test_genbank7) ... ok
test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8) ... ok
test_genbank9 (test_SeqIO.TestSeqIO.test_genbank9) ... ok
test_ig1 (test_SeqIO.TestSeqIO.test_ig1) ... ok
test_ig2 (test_SeqIO.TestSeqIO.test_ig2) ... ok
test_ig3 (test_SeqIO.TestSeqIO.test_ig3)
Test parsing a MASE alignment with sequence O_ANT70 being shorter. ... ok
test_imgt1 (test_SeqIO.TestSeqIO.test_imgt1)
Test parsing file with features over-indented for EMBL. ... ok
test_imgt2 (test_SeqIO.TestSeqIO.test_imgt2) ... ok
test_nexus1 (test_SeqIO.TestSeqIO.test_nexus1) ... ok
test_pdb_atom1 (test_SeqIO.TestSeqIO.test_pdb_atom1) ... ok
test_pdb_atom2 (test_SeqIO.TestSeqIO.test_pdb_atom2) ... ok
test_pdb_atom3 (test_SeqIO.TestSeqIO.test_pdb_atom3) ... ok
test_pdb_seqres1 (test_SeqIO.TestSeqIO.test_pdb_seqres1) ... ok
test_pdb_seqres2 (test_SeqIO.TestSeqIO.test_pdb_seqres2) ... ok
test_pdb_seqres3 (test_SeqIO.TestSeqIO.test_pdb_seqres3) ... ok
test_phd1 (test_SeqIO.TestSeqIO.test_phd1) ... ok
test_phd2 (test_SeqIO.TestSeqIO.test_phd2) ... ok
test_phd3 (test_SeqIO.TestSeqIO.test_phd3) ... ok
test_phd4 (test_SeqIO.TestSeqIO.test_phd4) ... ok
test_phylip1 (test_SeqIO.TestSeqIO.test_phylip1) ... ok
test_phylip2 (test_SeqIO.TestSeqIO.test_phylip2) ... ok
test_phylip3 (test_SeqIO.TestSeqIO.test_phylip3) ... ok
test_phylip4 (test_SeqIO.TestSeqIO.test_phylip4) ... ok
test_phylip5 (test_SeqIO.TestSeqIO.test_phylip5) ... ok
test_phylip6 (test_SeqIO.TestSeqIO.test_phylip6) ... ok
test_phylip7 (test_SeqIO.TestSeqIO.test_phylip7) ... ok
test_pir1 (test_SeqIO.TestSeqIO.test_pir1) ... ok
test_pir2 (test_SeqIO.TestSeqIO.test_pir2) ... ok
test_pir3 (test_SeqIO.TestSeqIO.test_pir3) ... ok
test_pir4 (test_SeqIO.TestSeqIO.test_pir4) ... ok
test_pir5 (test_SeqIO.TestSeqIO.test_pir5) ... ok
test_qual1 (test_SeqIO.TestSeqIO.test_qual1) ... ok
test_seqxml1 (test_SeqIO.TestSeqIO.test_seqxml1) ... ok
test_seqxml2 (test_SeqIO.TestSeqIO.test_seqxml2) ... ok
test_seqxml3 (test_SeqIO.TestSeqIO.test_seqxml3) ... ok
test_sff1 (test_SeqIO.TestSeqIO.test_sff1) ... ok
test_snapgene1 (test_SeqIO.TestSeqIO.test_snapgene1) ... ok
test_stockholm1 (test_SeqIO.TestSeqIO.test_stockholm1) ... ok
test_stockholm2 (test_SeqIO.TestSeqIO.test_stockholm2) ... ok
test_swiss1 (test_SeqIO.TestSeqIO.test_swiss1) ... ok
test_swiss11 (test_SeqIO.TestSeqIO.test_swiss11) ... ok
test_swiss12 (test_SeqIO.TestSeqIO.test_swiss12) ... ok
test_swiss13 (test_SeqIO.TestSeqIO.test_swiss13) ... ok
test_swiss14 (test_SeqIO.TestSeqIO.test_swiss14) ... ok
test_swiss15 (test_SeqIO.TestSeqIO.test_swiss15) ... ok
test_swiss16 (test_SeqIO.TestSeqIO.test_swiss16) ... ok
test_swiss17 (test_SeqIO.TestSeqIO.test_swiss17) ... ok
test_swiss18 (test_SeqIO.TestSeqIO.test_swiss18) ... ok
test_swiss19 (test_SeqIO.TestSeqIO.test_swiss19) ... ok
test_swiss2 (test_SeqIO.TestSeqIO.test_swiss2) ... ok
test_swiss20 (test_SeqIO.TestSeqIO.test_swiss20) ... ok
test_swiss3 (test_SeqIO.TestSeqIO.test_swiss3) ... ok
test_swiss4 (test_SeqIO.TestSeqIO.test_swiss4) ... ok
test_swiss5 (test_SeqIO.TestSeqIO.test_swiss5) ... ok
test_swiss6 (test_SeqIO.TestSeqIO.test_swiss6) ... ok
test_swiss7 (test_SeqIO.TestSeqIO.test_swiss7) ... ok
test_swiss8 (test_SeqIO.TestSeqIO.test_swiss8) ... ok
test_swiss9 (test_SeqIO.TestSeqIO.test_swiss9) ... ok
test_tab1 (test_SeqIO.TestSeqIO.test_tab1) ... ok
test_uniprot_xml1 (test_SeqIO.TestSeqIO.test_uniprot_xml1) ... ok
test_uniprot_xml2 (test_SeqIO.TestSeqIO.test_uniprot_xml2) ... ok
test_uniprot_xml3 (test_SeqIO.TestSeqIO.test_uniprot_xml3) ... ok
test_uniprot_xml4 (test_SeqIO.TestSeqIO.test_uniprot_xml4) ... ok
test_uniprot_xml5 (test_SeqIO.TestSeqIO.test_uniprot_xml5) ... ok
test_xdna1 (test_SeqIO.TestSeqIO.test_xdna1) ... ok
test_gzip_fasta (test_SeqIO.TestZipped.test_gzip_fasta)
Testing FASTA with gzip. ... ok
test_gzip_fastq (test_SeqIO.TestZipped.test_gzip_fastq)
Testing FASTQ with gzip. ... ok
test_gzip_genbank (test_SeqIO.TestZipped.test_gzip_genbank)
Testing GenBank with gzip. ... ok
----------------------------------------------------------------------
Ran 1 test in 20.273 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_AbiIO.py
C
test_SeqIO_AbiIO ... ok
test_file_type (test_SeqIO_AbiIO.TestAbi.test_file_type)
Test if filetype is ABIF. ... ok
test_no_smpl1 (test_SeqIO_AbiIO.TestAbi.test_no_smpl1)
Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok
test_raw (test_SeqIO_AbiIO.TestAbi.test_raw)
Test access to raw ABIF tags. ... ok
test_seqrecord (test_SeqIO_AbiIO.TestAbi.test_seqrecord)
Test if the extracted seqrecords data are equal to expected values. ... ok
test_trim (test_SeqIO_AbiIO.TestAbi.test_trim)
Test if trim works. ... ok
test_file_type (test_SeqIO_AbiIO.TestAbiFake.test_file_type)
Test if error is raised if filetype is not ABIF. ... ok
test_nonascii_tag (test_SeqIO_AbiIO.TestAbiNonAscii.test_nonascii_tag)
Test that we can handle non-ascii tags. ... ok
test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode.test_file_mode)
Test if exception is raised if file is not opened in 'rb' mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.332 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_FastaIO.py
C
test_SeqIO_FastaIO ... ok
test_edgecases_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_FastaTwoLineParser)
Test FastaTwoLineParser edge-cases. ... ok
test_edgecases_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_SimpleFastaParser)
Test SimpleFastaParser edge-cases. ... ok
test_exceptions_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_exceptions_FastaTwoLineParser)
Test FastaTwoLineParser exceptions. ... ok
test_regular_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_FastaTwoLineParser)
Test regular FastaTwoLineParser cases. ... ok
test_regular_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_SimpleFastaParser)
Test regular SimpleFastaParser cases. ... ok
test_multi_dna_files (test_SeqIO_FastaIO.TitleFunctions.test_multi_dna_files)
Test Fasta files containing multiple nucleotide sequences. ... ok
test_multi_protein_files (test_SeqIO_FastaIO.TitleFunctions.test_multi_protein_files)
Test Fasta files containing multiple protein sequences. ... ok
test_no_name (test_SeqIO_FastaIO.TitleFunctions.test_no_name)
Test FASTA record with no identifier. ... ok
test_single_nucleic_files (test_SeqIO_FastaIO.TitleFunctions.test_single_nucleic_files)
Test Fasta files containing a single nucleotide sequence. ... ok
test_single_proteino_files (test_SeqIO_FastaIO.TitleFunctions.test_single_proteino_files)
Test Fasta files containing a single protein sequence. ... ok
test_fails (test_SeqIO_FastaIO.Wrapping.test_fails)
Test case which should fail. ... ok
test_passes (test_SeqIO_FastaIO.Wrapping.test_passes)
Test case which should pass. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.092 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Gck.py
C
test_SeqIO_Gck ... ok
test_conflicting_lengths (test_SeqIO_Gck.TestGckWithArtificialData.test_conflicting_lengths)
Read a file with incorrect length. ... ok
test_read (test_SeqIO_Gck.TestGckWithArtificialData.test_read)
Read an artificial sample file. ... ok
test_read (test_SeqIO_Gck.TestGckWithImproperHeader.test_read)
Read a file with an incomplete header. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Insdc.py
C
test_SeqIO_Insdc ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)?
  warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: unassigned DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
ok
test_conversion (test_SeqIO_Insdc.ConvertTestsInsdc.test_conversion)
Test format conversion by SeqIO.write/SeqIO.parse and SeqIO.convert. ... ok
test_annotation1 (test_SeqIO_Insdc.TestEmbl.test_annotation1)
Check parsing of annotation from EMBL files (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmbl.test_annotation2)
Check parsing of annotation from EMBL files (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmbl.test_annotation3)
Check parsing of annotation from EMBL files (3). ... ok
test_annotation4 (test_SeqIO_Insdc.TestEmbl.test_annotation4)
Check parsing of annotation from EMBL files (4). ... ok
test_writing_empty_qualifiers (test_SeqIO_Insdc.TestEmbl.test_writing_empty_qualifiers) ... ok
test_annotation1 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation1)
Check writing-and-parsing EMBL file (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation2)
Check writing-and-parsing EMBL file (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation3)
Check writing-and-parsing EMBL file (3). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.125 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_NibIO.py
test_SeqIO_NibIO ... ok
test_read_even (test_SeqIO_NibIO.TestNibReaderWriter.test_read_even) ... ok
test_read_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_read_odd) ... ok
test_write_even (test_SeqIO_NibIO.TestNibReaderWriter.test_write_even) ... ok
test_write_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_write_odd) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.086 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_PdbIO.py
test_SeqIO_PdbIO ... ok
test_atom_parse (test_SeqIO_PdbIO.TestCifAtom.test_atom_parse)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestCifAtom.test_atom_read)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom.test_atom_read_noheader)
Read a single-chain CIF without a header by ATOM entries. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_missing)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_parse)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_read)
Read a single-chain structure by sequence entries. ... ok
test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_noheader)
Parse a PDB with no HEADER line. ... ok
test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom.test_atom_parse)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read_noheader)
Read a single-chain PDB without a header by ATOM entries. ... ok
test_atom_with_insertion (test_SeqIO_PdbIO.TestPdbAtom.test_atom_with_insertion)
Read a PDB with residue insertion code. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_missing)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_parse)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_read)
Read a single-chain structure by sequence entries. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.825 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_QualityIO.py
C
test_SeqIO_QualityIO ... ok
test_illumina_to_sanger (test_SeqIO_QualityIO.MappingTests.test_illumina_to_sanger)
Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62). ... ok
test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests.test_phred_quality_from_solexa)
Mapping check for function phred_quality_from_solexa. ... ok
test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests.test_sanger_to_illumina)
Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62). ... ok
test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests.test_sanger_to_solexa)
Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62). ... ok
test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests.test_solexa_quality_from_phred)
Mapping check for function solexa_quality_from_phred. ... ok
test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests.test_solexa_to_sanger)
Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62). ... ok
test_fasta_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_fasta_as_fastq) ... ok
test_sff_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_sff_as_fastq) ... ok
test_reject_high_and_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_and_low) ... ok
test_reject_high_but_not_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_but_not_low) ... ok
test_fasta (test_SeqIO_QualityIO.TestQual.test_fasta)
Check FASTQ parsing matches FASTA parsing. ... ok
test_fasta_out (test_SeqIO_QualityIO.TestQual.test_fasta_out)
Check FASTQ to FASTA output. ... ok
test_paired (test_SeqIO_QualityIO.TestQual.test_paired)
Check FASTQ parsing matches FASTA+QUAL parsing. ... ok
test_qual (test_SeqIO_QualityIO.TestQual.test_qual)
Check FASTQ parsing matches QUAL parsing. ... ok
test_qual_negative (test_SeqIO_QualityIO.TestQual.test_qual_negative)
Check QUAL negative scores mapped to PHRED zero. ... ok
test_qual_out (test_SeqIO_QualityIO.TestQual.test_qual_out)
Check FASTQ to QUAL output. ... ok
test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_1000)
Read and write back simple example with mixed case 1000bp read. ... ok
test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_2000)
Read and write back simple example with upper case 2000bp read. ... ok
test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_dna)
Read and write back simple example with ambiguous DNA. ... ok
test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_rna)
Read and write back simple example with ambiguous RNA. ... ok
test_reference_conversion (test_SeqIO_QualityIO.TestReferenceFastqConversions.test_reference_conversion) ... ok
test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_end)
Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL. ... ok
test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_start)
Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL. ... ok
test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_in_middle)
Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL. ... ok
test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_end)
Test converting E3MFGYR02_index_in_middle into FASTA+QUAL. ... ok
test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_start)
Test converting E3MFGYR02_index_at_start into FASTA+QUAL. ... ok
test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions.test_no_manifest)
Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL. ... ok
test_original (test_SeqIO_QualityIO.TestReferenceSffConversions.test_original)
Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL. ... ok
test_negative_clip (test_SeqIO_QualityIO.TestSFF.test_negative_clip) ... ok
test_overlapping_clip (test_SeqIO_QualityIO.TestSFF.test_overlapping_clip) ... ok
test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02)
Write and read back E3MFGYR02_random_10_reads.sff. ... ok
test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_end)
Write and read back E3MFGYR02_alt_index_at_end.sff. ... ok
test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_start)
Write and read back E3MFGYR02_alt_index_at_start.sff. ... ok
test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_in_middle)
Write and read back E3MFGYR02_alt_index_in_middle.sff. ... ok
test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_at_start)
Write and read back E3MFGYR02_index_at_start.sff. ... ok
test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_in_middle)
Write and read back E3MFGYR02_index_in_middle.sff. ... ok
test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_no_manifest)
Write and read back E3MFGYR02_no_manifest.sff. ... ok
test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_trimmed)
Write and read back E3MFGYR02_random_10_reads.sff (trimmed). ... ok
test_example_fasta (test_SeqIO_QualityIO.TestWriteRead.test_example_fasta)
Write and read back example.fasta. ... ok
test_example_fastq (test_SeqIO_QualityIO.TestWriteRead.test_example_fastq)
Write and read back example.fastq. ... ok
test_example_qual (test_SeqIO_QualityIO.TestWriteRead.test_example_qual)
Write and read back example.qual. ... ok
test_generated (test_SeqIO_QualityIO.TestWriteRead.test_generated)
Write and read back odd SeqRecord objects. ... ok
test_greek_sff (test_SeqIO_QualityIO.TestWriteRead.test_greek_sff)
Write and read back greek.sff. ... ok
test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead.test_illumina_faked)
Write and read back illumina_faked.fastq. ... ok
test_paired_sff (test_SeqIO_QualityIO.TestWriteRead.test_paired_sff)
Write and read back paired.sff. ... ok
test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead.test_sanger_93)
Write and read back sanger_93.fastq. ... ok
test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead.test_sanger_faked)
Write and read back sanger_faked.fastq. ... ok
test_solexa_example (test_SeqIO_QualityIO.TestWriteRead.test_solexa_example)
Write and read back solexa_example.fastq. ... ok
test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead.test_solexa_faked)
Write and read back solexa_faked.fastq. ... ok
test_tricky (test_SeqIO_QualityIO.TestWriteRead.test_tricky)
Write and read back tricky.fastq. ... ok
test_conversion (test_SeqIO_QualityIO.TestsConverter.test_conversion) ... ok
test_failure_detection (test_SeqIO_QualityIO.TestsConverter.test_failure_detection) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.608 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SeqXML.py
test_SeqIO_SeqXML ... ok
test_duplicated_dbxref (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_dbxref)
Read multiple cross references to a single source. ... ok
test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_property)
Read property with multiple values. ... ok
test_empty_description (test_SeqIO_SeqXML.TestDetailedRead.test_empty_description)
Check empty description. ... ok
test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead.test_full_characters_set_read)
Read full characters set for each type. ... ok
test_global_species (test_SeqIO_SeqXML.TestDetailedRead.test_global_species)
Check global species. ... ok
test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead.test_local_source_definition)
Check local source. ... ok
test_local_species (test_SeqIO_SeqXML.TestDetailedRead.test_local_species)
Check local species. ... ok
test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead.test_read_minimal_required)
Check minimal record. ... ok
test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_special_characters_desc)
Read special XML characters in description. ... ok
test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_unicode_characters_desc)
Test special unicode characters in the description. ... ok
test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_dna)
Read and write DNA. ... ok
test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_globalSpecies)
Read and write global species. ... ok
test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_protein)
Read and write protein. ... ok
test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_rna)
Read and write RNA. ... ok
test_write_species (test_SeqIO_SeqXML.TestReadAndWrite.test_write_species)
Test writing species from annotation tags. ... ok
test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles.test_for_errors)
Handling of corrupt files. ... ok
test_check_dna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_dna_header)
Check if the header information is parsed. ... ok
test_check_global_species_example_header (test_SeqIO_SeqXML.TestReadHeader.test_check_global_species_example_header)
Check if the header information is parsed. ... ok
test_check_protein_header (test_SeqIO_SeqXML.TestReadHeader.test_check_protein_header)
Check if the header information is parsed. ... ok
test_check_rna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_rna_header)
Check if the header information is parsed. ... ok
test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead.test_check_SeqIO)
Files readable using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.104 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SnapGene.py
test_SeqIO_SnapGene ... ok
test_extra_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_extra_dna)
Read a file with supernumerary DNA packet. ... ok
test_invalid_cookie (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_invalid_cookie)
Read a file with missing or invalid cookie packet. ... ok
test_missing_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_missing_dna)
Read a file without a DNA packet. ... ok
test_truncated_packet (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_truncated_packet)
Read a file with incomplete packet. ... ok
test_read (test_SeqIO_SnapGene.TestSnapGene.test_read)
Read sample files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.095 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_TwoBitIO.py
test_SeqIO_TwoBitIO ... ok
test_bigendian (test_SeqIO_TwoBitIO.Parsing.test_bigendian) ... ok
test_littleendian (test_SeqIO_TwoBitIO.Parsing.test_littleendian) ... ok
test_sequence_long (test_SeqIO_TwoBitIO.Parsing.test_sequence_long) ... ok
test_add (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_add) ... ok
test_bytes (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_bytes) ... ok
test_contains (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_contains) ... ok
test_count (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_count) ... ok
test_defined (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_defined) ... ok
test_endswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_endswith) ... ok
test_find (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_find) ... ok
test_getitem (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_getitem) ... ok
test_hash (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_hash) ... ok
test_index (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_index) ... ok
test_islower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_islower) ... ok
test_isupper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_isupper) ... ok
test_lower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lower) ... ok
test_lstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lstrip) ... ok
test_mul (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_mul) ... ok
test_radd (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_radd) ... ok
test_replace (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_replace) ... ok
test_repr (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_repr) ... ok
test_rfind (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rfind) ... ok
test_rindex (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rindex) ... ok
test_rsplit (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rsplit) ... ok
test_rstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rstrip) ... ok
test_split (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_split) ... ok
test_startswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_startswith) ... ok
test_str (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_str) ... ok
test_strip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_strip) ... ok
test_translate (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_translate) ... ok
test_upper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_upper) ... ok
test_eq (test_SeqIO_TwoBitIO.TestComparisons.test_eq) ... ok
test_ge (test_SeqIO_TwoBitIO.TestComparisons.test_ge) ... ok
test_gt (test_SeqIO_TwoBitIO.TestComparisons.test_gt) ... ok
test_le (test_SeqIO_TwoBitIO.TestComparisons.test_le) ... ok
test_lt (test_SeqIO_TwoBitIO.TestComparisons.test_lt) ... ok
test_ne (test_SeqIO_TwoBitIO.TestComparisons.test_ne) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.074 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Xdna.py
test_SeqIO_Xdna ... ok
test_corrupted_length (test_SeqIO_Xdna.TestInvalidXdna.test_corrupted_length)
Read a file with incorrect length. ... ok
test_invalid_sequence_type (test_SeqIO_Xdna.TestInvalidXdna.test_invalid_sequence_type)
Read a file with an unknown sequence type. ... ok
test_missing_features (test_SeqIO_Xdna.TestInvalidXdna.test_missing_features)
Read a file with an incorrect number of features. ... ok
test_unsupported_version (test_SeqIO_Xdna.TestInvalidXdna.test_unsupported_version)
Read a file with unexpected version number. ... ok
test_read (test_SeqIO_Xdna.TestXdna.test_read)
Read sample files. ... ok
test_warnings_on_data_loss (test_SeqIO_Xdna.TestXdnaWriter.test_warnings_on_data_loss)
Emit warnings when dropping data on write. ... ok
test_write_sequence_type (test_SeqIO_Xdna.TestXdnaWriter.test_write_sequence_type)
Write correct sequence type. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_features.py
test_SeqIO_features ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: unassigned DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA
  warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning)
/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line
  warnings.warn(
ok
test_after (test_SeqIO_features.FeatureWriting.test_after)
Features: write/read simple after locations. ... ok
test_before (test_SeqIO_features.FeatureWriting.test_before)
Features: write/read simple before locations. ... ok
test_between (test_SeqIO_features.FeatureWriting.test_between)
GenBank/EMBL write/read simple between locations. ... ok
test_exact (test_SeqIO_features.FeatureWriting.test_exact)
GenBank/EMBL write/read simple exact locations. ... ok
test_fuzzy_join (test_SeqIO_features.FeatureWriting.test_fuzzy_join)
Features: write/read fuzzy join locations. ... ok
test_join (test_SeqIO_features.FeatureWriting.test_join)
GenBank/EMBL write/read simple join locations. ... ok
test_oneof (test_SeqIO_features.FeatureWriting.test_oneof)
Features: write/read simple one-of locations. ... ok
test_unknown (test_SeqIO_features.FeatureWriting.test_unknown)
GenBank/EMBL write/read with unknown end points. ... ok
test_within (test_SeqIO_features.FeatureWriting.test_within)
Features: write/read simple within locations. ... ok
test_mixed_strand (test_SeqIO_features.GenBankLocations.test_mixed_strand) ... ok
test_rev_comp_styles (test_SeqIO_features.GenBankLocations.test_rev_comp_styles) ... ok
test_CDS (test_SeqIO_features.NC_000932.test_CDS)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_CDS (test_SeqIO_features.NC_005816.test_CDS)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_Features (test_SeqIO_features.NC_005816.test_Features)
Checking GenBank features sequences vs FASTA ffn file. ... ok
test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816.test_GenBank_vs_EMBL) ... ok
test_Genome (test_SeqIO_features.NC_005816.test_Genome)
Checking GenBank sequence vs FASTA fna file. ... ok
test_Translations (test_SeqIO_features.NC_005816.test_Translations)
Checking translation of FASTA features (faa vs ffn). ... ok
test_qualifiers (test_SeqIO_features.SeqFeatureCreation.test_qualifiers)
Pass in qualifiers to SeqFeatures. ... ok
test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_join)
Feature on DNA (join, mixed strand). ... ok
test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_multi_join)
Feature on DNA (multi-join, mixed strand). ... ok
test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_between)
Feature on protein (between location, zero length). ... ok
test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join)
Feature on protein (join). ... ok
test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join_fuzzy)
Feature on protein (fuzzy join). ... ok
test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_multi_join)
Feature on protein (multi-join). ... ok
test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_oneof)
Feature on protein (one-of positions). ... ok
test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_simple)
Feature on protein (simple). ... ok
test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna)
Feature on DNA (simple, default strand). ... ok
test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join)
Feature on DNA (join, strand +1). ... ok
test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_after)
Feature on DNA (join, strand -1, after position). ... ok
test_simple_dna_join_before (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_before)
Feature on DNA (join, strand -1, before position). ... ok
test_simple_dna_join_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_strand_minus)
Feature on DNA (join, strand -1). ... ok
test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand0)
Feature on DNA (simple, strand 0). ... ok
test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand1)
Feature on DNA (simple, strand +1). ... ok
test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_minus)
Feature on DNA (simple, strand -1). ... ok
test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_none)
Feature on DNA (simple, strand None). ... ok
test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_rna)
Feature on RNA (simple, default strand). ... ok
test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_single_letter_dna)
Feature on DNA (single letter, default strand). ... ok
test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna)
Feature on DNA (between location, zero length, default strand). ... ok
test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna_end)
Feature on DNA (between location at end, zero length, default strand). ... ok
test_AAA03323 (test_SeqIO_features.TestWriteRead.test_AAA03323)
Write and read back AAA03323.embl. ... ok
test_AE017046 (test_SeqIO_features.TestWriteRead.test_AE017046)
Write and read back AE017046.embl. ... ok
test_DD231055_edited (test_SeqIO_features.TestWriteRead.test_DD231055_edited)
Write and read back DD231055_edited.embl. ... ok
test_Human_contigs (test_SeqIO_features.TestWriteRead.test_Human_contigs)
Write and read back Human_contigs.embl. ... ok
test_NC_000932 (test_SeqIO_features.TestWriteRead.test_NC_000932)
Write and read back NC_000932.gb. ... ok
test_NC_005816 (test_SeqIO_features.TestWriteRead.test_NC_005816)
Write and read back NC_005816.gb. ... ok
test_NT_019265 (test_SeqIO_features.TestWriteRead.test_NT_019265)
Write and read back NT_019265.gb. ... ok
test_SC10H5 (test_SeqIO_features.TestWriteRead.test_SC10H5)
Write and read back SC10H5.embl. ... ok
test_TRBG361 (test_SeqIO_features.TestWriteRead.test_TRBG361)
Write and read back TRBG361.embl. ... ok
test_U87107 (test_SeqIO_features.TestWriteRead.test_U87107)
Write and read back U87107.embl. ... ok
test_arab1 (test_SeqIO_features.TestWriteRead.test_arab1)
Write and read back arab1.gb. ... ok
test_blank_seq (test_SeqIO_features.TestWriteRead.test_blank_seq)
Write and read back blank_seq.gb. ... ok
test_cor6 (test_SeqIO_features.TestWriteRead.test_cor6)
Write and read back cor6_6.gb. ... ok
test_dbsource_wrap (test_SeqIO_features.TestWriteRead.test_dbsource_wrap)
Write and read back dbsource_wrap.gb. ... ok
test_extra_keywords (test_SeqIO_features.TestWriteRead.test_extra_keywords)
Write and read back extra_keywords.gb. ... ok
test_gbvrl1_start (test_SeqIO_features.TestWriteRead.test_gbvrl1_start)
Write and read back gbvrl1_start.seq. ... ok
test_noref (test_SeqIO_features.TestWriteRead.test_noref)
Write and read back noref.gb. ... ok
test_one_of (test_SeqIO_features.TestWriteRead.test_one_of)
Write and read back of_one.gb. ... ok
test_origin_line (test_SeqIO_features.TestWriteRead.test_origin_line)
Write and read back origin_line.gb. ... ok
test_pri1 (test_SeqIO_features.TestWriteRead.test_pri1)
Write and read back pri1.gb. ... ok
test_protein_refseq (test_SeqIO_features.TestWriteRead.test_protein_refseq)
Write and read back protein_refseq.gb. ... ok
test_protein_refseq2 (test_SeqIO_features.TestWriteRead.test_protein_refseq2)
Write and read back protein_refseq2.gb. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.650 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_index.py
test_SeqIO_index ... ok
test_alpha_fails (test_SeqIO_index.IndexDictTests.test_alpha_fails)
Reject alphabet argument in Bio.SeqIO.index(). ... ok
test_alpha_fails_db (test_SeqIO_index.IndexDictTests.test_alpha_fails_db)
Reject alphabet argument in Bio.SeqIO.index_db(). ... ok
test_duplicates_index (test_SeqIO_index.IndexDictTests.test_duplicates_index)
Index file with duplicate identifiers with Bio.SeqIO.index(). ... ok
test_duplicates_index_db (test_SeqIO_index.IndexDictTests.test_duplicates_index_db)
Index file with duplicate identifiers with Bio.SeqIO.index_db(). ... ok
test_duplicates_to_dict (test_SeqIO_index.IndexDictTests.test_duplicates_to_dict)
Index file with duplicate identifiers with Bio.SeqIO.to_dict(). ... ok
test_key_checks (test_SeqIO_index.IndexDictTests.test_key_checks) ... ok
test_raw_checks (test_SeqIO_index.IndexDictTests.test_raw_checks) ... ok
test_simple_checks (test_SeqIO_index.IndexDictTests.test_simple_checks) ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingManyFiles.test_order_index_db)
Check index_db preserves order in multiple indexed files. ... ok
test_order_index (test_SeqIO_index.IndexOrderingSingleFile.test_order_index)
Check index preserves order in indexed file. ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingSingleFile.test_order_index_db)
Check index_db preserves ordering indexed file. ... ok
test_order_to_dict (test_SeqIO_index.IndexOrderingSingleFile.test_order_to_dict)
Check to_dict preserves order in indexed file. ... ok
test_child_folder_rel (test_SeqIO_index.NewIndexTest.test_child_folder_rel)
Check relative links to child folder. ... ok
test_same_folder (test_SeqIO_index.NewIndexTest.test_same_folder)
Check relative links in same folder. ... ok
test_some_abs (test_SeqIO_index.NewIndexTest.test_some_abs)
Check absolute filenames in index. ... ok
test_old (test_SeqIO_index.OldIndexTest.test_old)
Load existing index with no options (from parent directory). ... ok
test_old_check_same_thread (test_SeqIO_index.OldIndexTest.test_old_check_same_thread)
Setting check_same_thread to False doesn't raise an exception. ... ok
test_old_contents (test_SeqIO_index.OldIndexTest.test_old_contents)
Check actual filenames in existing indexes. ... ok
test_old_files (test_SeqIO_index.OldIndexTest.test_old_files)
Load existing index with correct files (from parent directory). ... ok
test_old_files_same_dir (test_SeqIO_index.OldIndexTest.test_old_files_same_dir)
Load existing index with correct files (from same directory). ... ok
test_old_files_wrong (test_SeqIO_index.OldIndexTest.test_old_files_wrong)
Load existing index with wrong files. ... ok
test_old_files_wrong2 (test_SeqIO_index.OldIndexTest.test_old_files_wrong2)
Load existing index with wrong number of files. ... ok
test_old_format (test_SeqIO_index.OldIndexTest.test_old_format)
Load existing index with correct format. ... ok
test_old_format_wrong (test_SeqIO_index.OldIndexTest.test_old_format_wrong)
Load existing index with wrong format. ... ok
test_old_rel (test_SeqIO_index.OldIndexTest.test_old_rel)
Load existing index (with relative paths) with no options (from parent directory). ... ok
test_old_same_dir (test_SeqIO_index.OldIndexTest.test_old_same_dir)
Load existing index with no options (from same directory). ... ok
test_old_same_dir_rel (test_SeqIO_index.OldIndexTest.test_old_same_dir_rel)
Load existing index (with relative paths) with no options (from same directory). ... ok
----------------------------------------------------------------------
Ran 1 test in 9.532 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_online.py
test_SeqIO_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqIO_write.py
test_SeqIO_write ... ok
test_alignment_formats (test_SeqIO_write.WriterTests.test_alignment_formats) ... ok
test_bad_handle (test_SeqIO_write.WriterTests.test_bad_handle) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.122 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqRecord.py
test_SeqRecord ... ok
test_annotations (test_SeqRecord.SeqRecordCreation.test_annotations)
Pass in annotations to SeqRecords. ... ok
test_letter_annotations (test_SeqRecord.SeqRecordCreation.test_letter_annotations)
Pass in letter annotations to SeqRecords. ... ok
test_replacing_seq (test_SeqRecord.SeqRecordCreation.test_replacing_seq)
Replacing .seq if .letter_annotation present. ... ok
test_valid_annotations (test_SeqRecord.SeqRecordCreation.test_valid_annotations) ... ok
test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation.test_valid_dbxrefs) ... ok
test_valid_description (test_SeqRecord.SeqRecordCreation.test_valid_description) ... ok
test_valid_features (test_SeqRecord.SeqRecordCreation.test_valid_features) ... ok
test_valid_id (test_SeqRecord.SeqRecordCreation.test_valid_id) ... ok
test_valid_name (test_SeqRecord.SeqRecordCreation.test_valid_name) ... ok
test_add_seq (test_SeqRecord.SeqRecordMethods.test_add_seq)
Simple addition of Seq or string. ... ok
test_add_seq_left (test_SeqRecord.SeqRecordMethods.test_add_seq_left)
Simple left addition of Seq or string. ... ok
test_add_seqrecord (test_SeqRecord.SeqRecordMethods.test_add_seqrecord)
Simple left addition of SeqRecord from genbank file. ... ok
test_add_simple (test_SeqRecord.SeqRecordMethods.test_add_simple)
Simple addition. ... ok
test_bytes (test_SeqRecord.SeqRecordMethods.test_bytes) ... ok
test_contains (test_SeqRecord.SeqRecordMethods.test_contains) ... ok
test_count (test_SeqRecord.SeqRecordMethods.test_count) ... ok
test_format (test_SeqRecord.SeqRecordMethods.test_format) ... ok
test_format_spaces (test_SeqRecord.SeqRecordMethods.test_format_spaces) ... ok
test_format_str (test_SeqRecord.SeqRecordMethods.test_format_str) ... ok
test_format_str_binary (test_SeqRecord.SeqRecordMethods.test_format_str_binary) ... ok
test_islower (test_SeqRecord.SeqRecordMethods.test_islower) ... ok
test_isupper (test_SeqRecord.SeqRecordMethods.test_isupper) ... ok
test_iter (test_SeqRecord.SeqRecordMethods.test_iter) ... ok
test_lower (test_SeqRecord.SeqRecordMethods.test_lower) ... ok
test_repr (test_SeqRecord.SeqRecordMethods.test_repr) ... ok
test_slice_add_shift (test_SeqRecord.SeqRecordMethods.test_slice_add_shift)
Simple slice and add to shift. ... ok
test_slice_add_simple (test_SeqRecord.SeqRecordMethods.test_slice_add_simple)
Simple slice and add. ... ok
test_slice_simple (test_SeqRecord.SeqRecordMethods.test_slice_simple)
Simple slice. ... ok
test_slice_variants (test_SeqRecord.SeqRecordMethods.test_slice_variants)
Simple slices using different start/end values. ... ok
test_slice_zero (test_SeqRecord.SeqRecordMethods.test_slice_zero)
Zero slice. ... ok
test_slicing (test_SeqRecord.SeqRecordMethods.test_slicing) ... ok
test_str (test_SeqRecord.SeqRecordMethods.test_str) ... ok
test_upper (test_SeqRecord.SeqRecordMethods.test_upper) ... ok
test_eq_exception (test_SeqRecord.SeqRecordMethodsMore.test_eq_exception) ... ok
test_ge_exception (test_SeqRecord.SeqRecordMethodsMore.test_ge_exception) ... ok
test_gt_exception (test_SeqRecord.SeqRecordMethodsMore.test_gt_exception) ... ok
test_hash_exception (test_SeqRecord.SeqRecordMethodsMore.test_hash_exception) ... ok
test_le_exception (test_SeqRecord.SeqRecordMethodsMore.test_le_exception) ... ok
test_lt_exception (test_SeqRecord.SeqRecordMethodsMore.test_lt_exception) ... ok
test_ne_exception (test_SeqRecord.SeqRecordMethodsMore.test_ne_exception) ... ok
test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_mutable_seq) ... ok
test_reverse_complement_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_seq) ... ok
test_translate (test_SeqRecord.SeqRecordMethodsMore.test_translate) ... ok
test_defaults (test_SeqRecord.TestTranslation.test_defaults) ... ok
test_new_annot (test_SeqRecord.TestTranslation.test_new_annot) ... ok
test_preserve (test_SeqRecord.TestTranslation.test_preserve) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.158 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SeqUtils.py
test_SeqUtils ... ok
test_GC_skew (test_SeqUtils.SeqUtilsTests.test_GC_skew) ... ok
test_checksum1 (test_SeqUtils.SeqUtilsTests.test_checksum1) ... ok
test_checksum2 (test_SeqUtils.SeqUtilsTests.test_checksum2) ... ok
test_checksum3 (test_SeqUtils.SeqUtilsTests.test_checksum3) ... ok
test_codon_adaptation_index (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index) ... ok
test_codon_adaptation_index_calculation (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_calculation)
Test Codon Adaptation Index (CAI) calculation for an mRNA. ... ok
test_codon_adaptation_index_initialization (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_initialization)
Test Codon Adaptation Index (CAI) initialization from sequences. ... ok
test_codon_usage_custom_old (test_SeqUtils.SeqUtilsTests.test_codon_usage_custom_old)
Test Codon Adaptation Index (CAI) using FASTA file for background. ... ok
test_codon_usage_ecoli (test_SeqUtils.SeqUtilsTests.test_codon_usage_ecoli)
Test Codon Adaptation Index (CAI) using default E. coli data. ... ok
test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests.test_crc_checksum_collision) ... ok
test_gc_fraction (test_SeqUtils.SeqUtilsTests.test_gc_fraction)
Tests gc_fraction function. ... ok
test_lcc_mult (test_SeqUtils.SeqUtilsTests.test_lcc_mult) ... ok
test_lcc_simp (test_SeqUtils.SeqUtilsTests.test_lcc_simp) ... ok
test_seq1_seq3 (test_SeqUtils.SeqUtilsTests.test_seq1_seq3) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.218 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Seq_objs.py
test_Seq_objs ... ok
test_eq (test_Seq_objs.ComparisonTests.test_eq) ... ok
test_ge (test_Seq_objs.ComparisonTests.test_ge) ... ok
test_gt (test_Seq_objs.ComparisonTests.test_gt) ... ok
test_le (test_Seq_objs.ComparisonTests.test_le) ... ok
test_lt (test_Seq_objs.ComparisonTests.test_lt) ... ok
test_ne (test_Seq_objs.ComparisonTests.test_ne) ... ok
test_unknown_seq (test_Seq_objs.FileBasedTests.test_unknown_seq)
Test if feature extraction works properly for unknown sequences. ... ok
test_addition (test_Seq_objs.PartialSequenceTests.test_addition) ... ok
test_complement (test_Seq_objs.PartialSequenceTests.test_complement) ... ok
test_getitem (test_Seq_objs.PartialSequenceTests.test_getitem) ... ok
test_init (test_Seq_objs.PartialSequenceTests.test_init) ... ok
test_lower_upper (test_Seq_objs.PartialSequenceTests.test_lower_upper) ... ok
test_multiplication (test_Seq_objs.PartialSequenceTests.test_multiplication) ... ok
test_replace (test_Seq_objs.PartialSequenceTests.test_replace) ... ok
test_repr (test_Seq_objs.PartialSequenceTests.test_repr) ... ok
test_transcribe (test_Seq_objs.PartialSequenceTests.test_transcribe) ... ok
test_MutableSeq_extend (test_Seq_objs.StringMethodTests.test_MutableSeq_extend)
Check extending a MutableSeq object. ... ok
test_MutableSeq_init_error (test_Seq_objs.StringMethodTests.test_MutableSeq_init_error)
Check MutableSeq __init__ raises the appropriate exceptions. ... ok
test_MutableSeq_setitem (test_Seq_objs.StringMethodTests.test_MutableSeq_setitem)
Check setting sequence contents of a MutableSeq object. ... ok
test_Seq_init_error (test_Seq_objs.StringMethodTests.test_Seq_init_error)
Check Seq __init__ raises the appropriate exceptions. ... ok
test_count_overlap (test_Seq_objs.StringMethodTests.test_count_overlap)
Check count_overlap exception matches python string count method. ... ok
test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_GG)
Check our count_overlap method using GG with variable ends and starts. ... ok
test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_NN)
Check our count_overlap method using NN with variable ends and starts. ... ok
test_equality (test_Seq_objs.StringMethodTests.test_equality)
Test equality when mixing types. ... ok
test_join_MutableSeq (test_Seq_objs.StringMethodTests.test_join_MutableSeq)
Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok
test_join_MutableSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_MutableSeq_TypeError_iter)
Checks that a TypeError is thrown for all non-iterable types. ... ok
test_join_MutableSeq_mixed (test_Seq_objs.StringMethodTests.test_join_MutableSeq_mixed)
Check MutableSeq objects can be joined. ... ok
test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests.test_join_MutableSeq_with_file)
Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok
test_join_Seq (test_Seq_objs.StringMethodTests.test_join_Seq)
Checks if Seq join correctly concatenates sequence with the spacer. ... ok
test_join_Seq_TypeError (test_Seq_objs.StringMethodTests.test_join_Seq_TypeError)
Checks that a TypeError is thrown for all non-iterable types. ... ok
test_join_Seq_with_file (test_Seq_objs.StringMethodTests.test_join_Seq_with_file)
Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok
test_str_comparison (test_Seq_objs.StringMethodTests.test_str_comparison) ... ok
test_str_count (test_Seq_objs.StringMethodTests.test_str_count)
Check matches the python string count method. ... ok
test_str_count_overlap_GG (test_Seq_objs.StringMethodTests.test_str_count_overlap_GG)
Check our count_overlap method using GG. ... ok
test_str_count_overlap_NN (test_Seq_objs.StringMethodTests.test_str_count_overlap_NN)
Check our count_overlap method using NN. ... ok
test_str_encode (test_Seq_objs.StringMethodTests.test_str_encode)
Check matches the python string encode method. ... ok
test_str_endswith (test_Seq_objs.StringMethodTests.test_str_endswith)
Check matches the python string endswith method. ... ok
test_str_find (test_Seq_objs.StringMethodTests.test_str_find)
Check matches the python string find method. ... ok
test_str_getitem (test_Seq_objs.StringMethodTests.test_str_getitem)
Check slicing and indexing works like a string. ... ok
test_str_hash (test_Seq_objs.StringMethodTests.test_str_hash) ... ok
test_str_index (test_Seq_objs.StringMethodTests.test_str_index)
Check matches the python string index method. ... ok
test_str_islower (test_Seq_objs.StringMethodTests.test_str_islower)
Check matches the python string islower method. ... ok
test_str_isupper (test_Seq_objs.StringMethodTests.test_str_isupper)
Check matches the python string isupper method. ... ok
test_str_length (test_Seq_objs.StringMethodTests.test_str_length)
Check matches the python string __len__ method. ... ok
test_str_lower (test_Seq_objs.StringMethodTests.test_str_lower)
Check matches the python string lower method. ... ok
test_str_lstrip (test_Seq_objs.StringMethodTests.test_str_lstrip)
Check matches the python string lstrip method. ... ok
test_str_replace (test_Seq_objs.StringMethodTests.test_str_replace)
Check matches the python string replace method. ... ok
test_str_rfind (test_Seq_objs.StringMethodTests.test_str_rfind)
Check matches the python string rfind method. ... ok
test_str_rindex (test_Seq_objs.StringMethodTests.test_str_rindex)
Check matches the python string rindex method. ... ok
test_str_rsplit (test_Seq_objs.StringMethodTests.test_str_rsplit)
Check matches the python string rsplit method. ... ok
test_str_rstrip (test_Seq_objs.StringMethodTests.test_str_rstrip)
Check matches the python string rstrip method. ... ok
test_str_split (test_Seq_objs.StringMethodTests.test_str_split)
Check matches the python string split method. ... ok
test_str_startswith (test_Seq_objs.StringMethodTests.test_str_startswith)
Check matches the python string startswith method. ... ok
test_str_strip (test_Seq_objs.StringMethodTests.test_str_strip)
Check matches the python string strip method. ... ok
test_str_upper (test_Seq_objs.StringMethodTests.test_str_upper)
Check matches the python string upper method. ... ok
test_the_back_transcription (test_Seq_objs.StringMethodTests.test_the_back_transcription)
Check obj.back_transcribe() method. ... ok
test_the_complement (test_Seq_objs.StringMethodTests.test_the_complement)
Check obj.complement() method. ... ok
test_the_reverse_complement (test_Seq_objs.StringMethodTests.test_the_reverse_complement)
Check obj.reverse_complement() method. ... ok
test_the_transcription (test_Seq_objs.StringMethodTests.test_the_transcription)
Check obj.transcribe() method. ... ok
test_the_translate (test_Seq_objs.StringMethodTests.test_the_translate)
Check obj.translate() method. ... ok
test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_ambig_codons)
Check obj.translate() method with ambiguous codons. ... ok
test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_invalid_codons)
Check obj.translate() method with invalid codons. ... ok
test_the_translation_of_stops (test_Seq_objs.StringMethodTests.test_the_translation_of_stops)
Check obj.translate() method with stop codons. ... ok
test_tomutable (test_Seq_objs.StringMethodTests.test_tomutable)
Check creating a MutableSeq object. ... ok
test_toseq (test_Seq_objs.StringMethodTests.test_toseq)
Check creating a Seq object. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.154 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SffIO.py
test_SffIO ... ok
test_alt_index_at_end (test_SffIO.TestAlternativeIndexes.test_alt_index_at_end) ... ok
test_alt_index_at_start (test_SffIO.TestAlternativeIndexes.test_alt_index_at_start) ... ok
test_alt_index_in_middle (test_SffIO.TestAlternativeIndexes.test_alt_index_in_middle) ... ok
test_index_at_start (test_SffIO.TestAlternativeIndexes.test_index_at_start) ... ok
test_index_in_middle (test_SffIO.TestAlternativeIndexes.test_index_in_middle) ... ok
test_trim (test_SffIO.TestAlternativeIndexes.test_trim) ... ok
test_index1 (test_SffIO.TestConcatenated.test_index1) ... ok
test_index2 (test_SffIO.TestConcatenated.test_index2) ... ok
test_parse1 (test_SffIO.TestConcatenated.test_parse1) ... ok
test_parse2 (test_SffIO.TestConcatenated.test_parse2) ... ok
test_parses_gzipped_stream (test_SffIO.TestConcatenated.test_parses_gzipped_stream) ... ok
test_30bytes (test_SffIO.TestErrors.test_30bytes) ... ok
test_31bytes (test_SffIO.TestErrors.test_31bytes) ... ok
test_31bytes_bad_flowgram (test_SffIO.TestErrors.test_31bytes_bad_flowgram) ... ok
test_31bytes_bad_ver (test_SffIO.TestErrors.test_31bytes_bad_ver) ... ok
test_31bytes_index_header (test_SffIO.TestErrors.test_31bytes_index_header) ... ok
test_bad_index_eof (test_SffIO.TestErrors.test_bad_index_eof) ... ok
test_bad_index_length (test_SffIO.TestErrors.test_bad_index_length) ... ok
test_bad_index_offset (test_SffIO.TestErrors.test_bad_index_offset) ... ok
test_empty (test_SffIO.TestErrors.test_empty) ... ok
test_index_lengths (test_SffIO.TestErrors.test_index_lengths) ... ok
test_index_mft_data_size (test_SffIO.TestErrors.test_index_mft_data_size) ... ok
test_index_mft_version (test_SffIO.TestErrors.test_index_mft_version) ... ok
test_index_name_no_null (test_SffIO.TestErrors.test_index_name_no_null) ... ok
test_no_index (test_SffIO.TestErrors.test_no_index) ... ok
test_no_manifest_xml (test_SffIO.TestErrors.test_no_manifest_xml) ... ok
test_premature_end_of_index (test_SffIO.TestErrors.test_premature_end_of_index) ... ok
test_unknown_index (test_SffIO.TestErrors.test_unknown_index) ... ok
test_both_ways (test_SffIO.TestIndex.test_both_ways) ... ok
test_manifest (test_SffIO.TestIndex.test_manifest) ... ok
test_index (test_SffIO.TestSelf.test_index) ... ok
test_read (test_SffIO.TestSelf.test_read) ... ok
test_read_wrong (test_SffIO.TestSelf.test_read_wrong) ... ok
test_write (test_SffIO.TestSelf.test_write) ... ok
test_coords (test_SffIO.TestUAN.test_coords) ... ok
test_region (test_SffIO.TestUAN.test_region) ... ok
test_time (test_SffIO.TestUAN.test_time) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.102 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_SwissProt.py
test_SwissProt ... ok
test_O23729 (test_SwissProt.TestSwissProt.test_O23729)
Parsing SwissProt file O23729.txt. ... ok
test_O95832 (test_SwissProt.TestSwissProt.test_O95832)
Parsing SwissProt file O95832.txt. ... ok
test_P04439 (test_SwissProt.TestSwissProt.test_P04439)
Parsing SwissProt file P04439.txt. ... ok
test_P0A186 (test_SwissProt.TestSwissProt.test_P0A186)
Parsing SwissProt file P0A186.txt. ... ok
test_P0CK95 (test_SwissProt.TestSwissProt.test_P0CK95)
Parsing SwissProt file P0CK95.txt. ... ok
test_P16235 (test_SwissProt.TestSwissProt.test_P16235)
Parsing SwissProt file P16235.txt. ... ok
test_P39896 (test_SwissProt.TestSwissProt.test_P39896)
Parsing SwissProt file P39896.txt. ... ok
test_P60137 (test_SwissProt.TestSwissProt.test_P60137)
Parsing SwissProt file P60137.txt. ... ok
test_P60904 (test_SwissProt.TestSwissProt.test_P60904)
Parsing SwissProt file P60904.txt. ... ok
test_P62258 (test_SwissProt.TestSwissProt.test_P62258)
Parsing SwissProt file P62258. ... ok
test_P68308 (test_SwissProt.TestSwissProt.test_P68308)
Parsing SwissProt file P68308.txt. ... ok
test_Q13454 (test_SwissProt.TestSwissProt.test_Q13454)
Parsing SwissProt file Q13454.txt. ... ok
test_Q13639 (test_SwissProt.TestSwissProt.test_Q13639)
Parsing SwissProt file Q13639. ... ok
test_Q7Z739 (test_SwissProt.TestSwissProt.test_Q7Z739)
Parsing SwissProt file Q7Z739.txt, which has new qualifiers for ligands from Uniprot version 2022_03. ... ok
test_ft_line (test_SwissProt.TestSwissProt.test_ft_line)
Parsing SwissProt file O23729, which has a new-style FT line. ... ok
test_sp012 (test_SwissProt.TestSwissProt.test_sp012)
Parsing SwissProt file sp012. ... ok
test_sp013 (test_SwissProt.TestSwissProt.test_sp013)
Parsing SwissProt file sp013. ... ok
test_sp015 (test_SwissProt.TestSwissProt.test_sp015)
Parsing SwissProt file sp015. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.232 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TCoffee_tool.py
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.089 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TogoWS.py
C
test_TogoWS ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.086 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_TreeConstruction.py
C
test_TreeConstruction ... ok
test_known_matrices (test_TreeConstruction.DistanceCalculatorTest.test_known_matrices) ... ok
test_known_matrices_msa (test_TreeConstruction.DistanceCalculatorTest.test_known_matrices_msa) ... ok
test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest.test_nonmatching_seqs) ... ok
test_nonmatching_seqs_msa (test_TreeConstruction.DistanceCalculatorTest.test_nonmatching_seqs_msa) ... ok
test_bad_construction (test_TreeConstruction.DistanceMatrixTest.test_bad_construction) ... ok
test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest.test_bad_manipulation) ... ok
test_format_phylip (test_TreeConstruction.DistanceMatrixTest.test_format_phylip) ... ok
test_good_construction (test_TreeConstruction.DistanceMatrixTest.test_good_construction) ... ok
test_good_manipulation (test_TreeConstruction.DistanceMatrixTest.test_good_manipulation) ... ok
test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest.test_built_tree) ... ok
test_built_tree_msa (test_TreeConstruction.DistanceTreeConstructorTest.test_built_tree_msa) ... ok
test_nj (test_TreeConstruction.DistanceTreeConstructorTest.test_nj) ... ok
test_nj_msa (test_TreeConstruction.DistanceTreeConstructorTest.test_nj_msa) ... ok
test_upgma (test_TreeConstruction.DistanceTreeConstructorTest.test_upgma) ... ok
test_upgma_msa (test_TreeConstruction.DistanceTreeConstructorTest.test_upgma_msa) ... ok
test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest.test_get_neighbors) ... ok
test_get_score (test_TreeConstruction.ParsimonyScorerTest.test_get_score) ... ok
test_get_score_msa (test_TreeConstruction.ParsimonyScorerTest.test_get_score_msa) ... ok
test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest.test_build_tree) ... ok
test_build_tree_msa (test_TreeConstruction.ParsimonyTreeConstructorTest.test_build_tree_msa) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.710 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_UniGene.py
C
test_UniGene ... ok
test_parse (test_UniGene.TestUniGene.test_parse) ... ok
test_read (test_UniGene.TestUniGene.test_read) ... ok
test_read_value_error (test_UniGene.TestUniGene.test_read_value_error) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.036 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_UniProt_GOA.py
test_UniProt_GOA ... ok
test_gaf_iterator (test_UniProt_GOA.GoaTests.test_gaf_iterator)
Test GOA GAF file iterator. ... ok
test_gpa_iterator (test_UniProt_GOA.GoaTests.test_gpa_iterator)
Test GOA GPA file iterator. ... ok
test_gpi_iterator (test_UniProt_GOA.GoaTests.test_gpi_iterator)
Test GOA GPI file iterator, gpi-version: 1.1. ... ok
test_gpi_iterator_one_two (test_UniProt_GOA.GoaTests.test_gpi_iterator_one_two)
Test GOA GPI file iterator, gpi-version: 1.2. ... ok
test_selection_writing (test_UniProt_GOA.GoaTests.test_selection_writing)
Test record_has, and writerec. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.029 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
C
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Uniprot.py
test_Uniprot ... ok
test_F2CXE6 (test_Uniprot.TestUniprot.test_F2CXE6)
Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok
test_H2CNN8 (test_Uniprot.TestUniprot.test_H2CNN8)
Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok
test_P60904 (test_Uniprot.TestUniprot.test_P60904)
Parsing SwissProt file P60904.txt. ... ok
test_P84001 (test_Uniprot.TestUniprot.test_P84001)
Parse mass spec structured comment with unknown loc. ... ok
test_Q13639 (test_Uniprot.TestUniprot.test_Q13639)
Compare SwissProt text and uniprot XML versions of Q13639. ... ok
test_multi_ex (test_Uniprot.TestUniprot.test_multi_ex)
Compare SwissProt text and uniprot XML versions of several examples. ... ok
test_multi_ex_index (test_Uniprot.TestUniprot.test_multi_ex_index)
Index SwissProt text and uniprot XML versions of several examples. ... ok
test_sp016 (test_Uniprot.TestUniprot.test_sp016)
Parsing SwissProt file sp016. ... ok
test_submittedName_allowed (test_Uniprot.TestUniprot.test_submittedName_allowed)
Checks if parser supports new XML Element (submittedName). ... ok
test_uni001 (test_Uniprot.TestUniprot.test_uni001)
Parsing Uniprot file uni001. ... ok
test_uni003 (test_Uniprot.TestUniprot.test_uni003)
Parsing Uniprot file uni003. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.225 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_Wise.py
test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
----------------------------------------------------------------------
Ran 1 test in 0.018 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_XXmotif_tool.py
test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.079 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_align.py
test_align ... ok
test_basic_alignment (test_align.TestBasics.test_basic_alignment)
Basic tests on a simple alignment of three sequences. ... ok
test_empty_alignment (test_align.TestBasics.test_empty_alignment)
Very simple tests on an empty alignment. ... ok
test_format_conversion (test_align.TestReading.test_format_conversion)
Parse the alignment file and get an alignment object. ... ok
test_read_clustal1 (test_align.TestReading.test_read_clustal1)
Parse an alignment file and get an alignment object. ... ok
test_read_clustal2 (test_align.TestReading.test_read_clustal2)
Parse an alignment file and get an alignment object. ... ok
test_read_fasta (test_align.TestReading.test_read_fasta) ... ok
test_read_write_clustal (test_align.TestReading.test_read_write_clustal)
Test the base alignment stuff. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.097 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_align_substitution_matrices.py
test_align_substitution_matrices ... ok
test_basics_matrix (test_align_substitution_matrices.TestBasics.test_basics_matrix)
Test basic matrix operations. ... ok
test_basics_vector (test_align_substitution_matrices.TestBasics.test_basics_vector)
Test basic vector operations. ... ok
test_nucleotide_freq (test_align_substitution_matrices.TestBasics.test_nucleotide_freq)
Test nucleotide frequency calculations. ... ok
test_pickling (test_align_substitution_matrices.TestBasics.test_pickling)
Test pickling a substitution matrix. ... ok
test_protein_freq (test_align_substitution_matrices.TestBasics.test_protein_freq)
Test amino acid frequency calculations. ... ok
test_read_write (test_align_substitution_matrices.TestBasics.test_read_write)
Test reading and writing substitution matrices. ... ok
test_loading (test_align_substitution_matrices.TestLoading.test_loading)
Confirm that all provided substitution matrices can be loaded. ... ok
test1_observed_frequencies (test_align_substitution_matrices.TestScoringMatrices.test1_observed_frequencies)
Test calculating substitution frequencies. ... ok
test2_observed_probabilities (test_align_substitution_matrices.TestScoringMatrices.test2_observed_probabilities)
Test calculating substitution probabilities. ... ok
test3_observed_symmetric_probabilities (test_align_substitution_matrices.TestScoringMatrices.test3_observed_symmetric_probabilities)
Test symmetrizing substitution probabilities. ... ok
test4_aminoacid_probabilities (test_align_substitution_matrices.TestScoringMatrices.test4_aminoacid_probabilities)
Test calculating expected amino acid probabilities. ... ok
test5_expected_probabilities (test_align_substitution_matrices.TestScoringMatrices.test5_expected_probabilities)
Test calculating expected amino acid substitution probabilities. ... ok
test6_scores (test_align_substitution_matrices.TestScoringMatrices.test6_scores)
Test calculating amino acid substitution log-ratios. ... ok
test_ident (test_align_substitution_matrices.TestScoringMatrices.test_ident)
Test calculating the +6/-1 matrix as an approximation of BLOSUM62. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.426 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_cellosaurus.py
test_cellosaurus ... ok
test__str__ (test_cellosaurus.TestCellosaurus.test__str__)
Test string function. ... ok
test_parse (test_cellosaurus.TestCellosaurus.test_parse)
Test parsing function. ... ok
test_read (test_cellosaurus.TestCellosaurus.test_read)
Test read function. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_codonalign.py
test_codonalign ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython.
  warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/Seq.py:2779: BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be translated as amino acid.
  warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA)
  warnings.warn(
/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA)
  warnings.warn(
ok
test_TypeError (test_codonalign.TestAddition.test_TypeError)
Check that TypeError is thrown for non CodonAlignment/MultipleSequenceAlignment objects. ... ok
test_ValueError (test_codonalign.TestAddition.test_ValueError)
Check that ValueError is thrown for Alignments of different lengths. ... ok
test_addition_CodonAlignment (test_codonalign.TestAddition.test_addition_CodonAlignment)
Check addition of CodonAlignment and CodonAlignment. ... ok
test_addition_MultipleSeqAlignment (test_codonalign.TestAddition.test_addition_MultipleSeqAlignment)
Check addition of CodonAlignment and MultipleSeqAlignment. ... ok
test_IO (test_codonalign.TestBuildAndIO.test_IO) ... ok
test_align (test_codonalign.TestCodonAlignment.test_align) ... ok
test_seq (test_codonalign.TestCodonSeq.test_seq) ... ok
test_mk (test_codonalign.Test_MK.test_mk) ... ok
test_build (test_codonalign.Test_build.test_build) ... ok
test_dn_ds (test_codonalign.Test_dn_ds.test_dn_ds) ... ok
test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) ... ok
----------------------------------------------------------------------
Ran 1 test in 5.879 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_geo.py
test_geo ... ok
test_GSE16 (test_geo.TestGeo.test_GSE16) ... ok
test_GSM645 (test_geo.TestGeo.test_GSM645) ... ok
test_GSM691 (test_geo.TestGeo.test_GSM691) ... ok
test_GSM700 (test_geo.TestGeo.test_GSM700) ... ok
test_GSM804 (test_geo.TestGeo.test_GSM804) ... ok
test_record_str (test_geo.TestGeo.test_record_str) ... ok
test_soft_ex_affy (test_geo.TestGeo.test_soft_ex_affy) ... ok
test_soft_ex_affy_chp (test_geo.TestGeo.test_soft_ex_affy_chp) ... ok
test_soft_ex_dual (test_geo.TestGeo.test_soft_ex_dual) ... ok
test_soft_ex_family (test_geo.TestGeo.test_soft_ex_family) ... ok
test_soft_ex_platform (test_geo.TestGeo.test_soft_ex_platform) ... ok
test_soft_ex_series (test_geo.TestGeo.test_soft_ex_series) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.071 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_kNN.py
test_kNN ... ok
test_calculate_model (test_kNN.TestKNN.test_calculate_model) ... ok
test_calculate_probability (test_kNN.TestKNN.test_calculate_probability) ... ok
test_classify (test_kNN.TestKNN.test_classify) ... ok
test_leave_one_out (test_kNN.TestKNN.test_leave_one_out) ... ok
test_model_accuracy (test_kNN.TestKNN.test_model_accuracy) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.015 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_mmtf.py
test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.070 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_mmtf_online.py
test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
----------------------------------------------------------------------
Ran 1 test in 0.066 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_motifs.py
test_motifs ... ok
test_calculate_pseudocounts (test_motifs.MotifTestPWM.test_calculate_pseudocounts) ... ok
test_getitem (test_motifs.MotifTestPWM.test_getitem) ... ok
test_simple (test_motifs.MotifTestPWM.test_simple)
Test if Bio.motifs PWM scoring works. ... ok
test_with_bad_char (test_motifs.MotifTestPWM.test_with_bad_char)
Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok
test_with_mixed_case (test_motifs.MotifTestPWM.test_with_mixed_case)
Test if Bio.motifs PWM scoring works with mixed case. ... ok
test_TFoutput (test_motifs.MotifTestsBasic.test_TFoutput)
Ensure that we can write proper TransFac output files. ... ok
test_alignace_parsing (test_motifs.MotifTestsBasic.test_alignace_parsing)
Test if Bio.motifs can parse AlignAce output files. ... ok
test_clusterbuster_parsing_and_output (test_motifs.MotifTestsBasic.test_clusterbuster_parsing_and_output)
Test if Bio.motifs can parse and output Cluster Buster PFM files. ... ok
test_format (test_motifs.MotifTestsBasic.test_format) ... ok
test_pfm_four_columns_parsing (test_motifs.MotifTestsBasic.test_pfm_four_columns_parsing)
Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 columns). ... ok
test_pfm_four_rows_parsing (test_motifs.MotifTestsBasic.test_pfm_four_rows_parsing)
Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 rows). ... ok
test_pfm_parsing (test_motifs.MotifTestsBasic.test_pfm_parsing)
Test if Bio.motifs can parse JASPAR-style pfm files. ... ok
test_reverse_complement (test_motifs.MotifTestsBasic.test_reverse_complement)
Test if motifs can be reverse-complemented. ... ok
test_sites_parsing (test_motifs.MotifTestsBasic.test_sites_parsing)
Test if Bio.motifs can parse JASPAR-style sites files. ... ok
test_xms_parsing (test_motifs.MotifTestsBasic.test_xms_parsing)
Test if Bio.motifs can parse and output xms PFM files. ... ok
test_mast_parser_1 (test_motifs.TestMAST.test_mast_parser_1)
Parse motifs/mast.crp0.de.oops.txt.xml file. ... ok
test_mast_parser_2 (test_motifs.TestMAST.test_mast_parser_2)
Parse motifs/mast.adh.de.oops.html.xml file. ... ok
test_mast_parser_3 (test_motifs.TestMAST.test_mast_parser_3)
Parse motifs/mast.Klf1-200.cd.oops.xml.xml file. ... ok
test_meme_parser_1 (test_motifs.TestMEME.test_meme_parser_1)
Parse motifs/meme.INO_up800.classic.oops.xml file. ... ok
test_meme_parser_2 (test_motifs.TestMEME.test_meme_parser_2)
Parsing motifs/meme.adh.classic.oops.xml file. ... ok
test_meme_parser_3 (test_motifs.TestMEME.test_meme_parser_3)
Parse motifs/meme.farntrans5.classic.anr.xml file. ... ok
test_meme_parser_rna (test_motifs.TestMEME.test_meme_parser_rna)
Test if Bio.motifs can parse MEME output files using RNA. ... ok
test_minimal_meme_parser (test_motifs.TestMEME.test_minimal_meme_parser)
Parse motifs/minimal_test.meme file. ... ok
test_permissive_transfac_parser (test_motifs.TestTransfac.test_permissive_transfac_parser)
Parse the TRANSFAC-like file motifs/MA0056.1.transfac. ... ok
test_transfac_parser (test_motifs.TestTransfac.test_transfac_parser)
Parse motifs/transfac.dat file. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.125 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_motifs_online.py
test_motifs_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.051 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2.py
test_pairwise2 ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
  warnings.warn(
ok
test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok
test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments)
``_clean_alignments`` removes redundant and wrong alignments. ... ok
test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix)
``print_matrix`` prints nested lists as nice matrices. ... ok
test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments)
One possible start position in local alignment is not a match. ... ok
test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name)
Test for wrong function names. ... ok
test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters)
Test for number of parameters. ... ok
test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names)
Test for unknown parameter in parameter names. ... ok
test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings)
Test for warnings. ... ok
test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1)
Test 1. ... ok
test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2)
Test 2. ... ok
test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple)
Test globalxx. ... ok
test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2)
Do the same test with sequence order reversed. ... ok
test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input)
Do a global alignment with sequences supplied as lists. ... ok
test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only)
Test one_alignment_only parameter. ... ok
test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords)
Test equality of calls with and without keywords. ... ok
test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62)
Test localds with blosum62. ... ok
test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result)
Return no alignment. ... ok
test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric)
Test if alignment is independent on direction of sequence. ... ok
test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms)
Two different local alignments. ... ok
test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1)
Test localxx. ... ok
test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2)
Test localxx with ``full_sequences=True``. ... ok
test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic)
Test the generic method with local alignments. ... ok
test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1)
Test 1. ... ok
test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2)
Test 2. ... ok
test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3)
Test 3. ... ok
test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1)
Test sequence with only one match. ... ok
test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2)
Test sequences with two possible match positions. ... ok
test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3)
Like test 1, but global alignment. ... ok
test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1)
Test 1. ... ok
test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2)
Test 2. ... ok
test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3)
Test 3. ... ok
test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4)
Test 4. ... ok
test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps)
Turn off end-gap penalties. ... ok
test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2)
Do the same, but use the generic method (with the same result). ... ok
test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps)
Test alignment where end-gaps are differently penalized. ... ok
test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening)
Add gap-extend penalty to gap-opening penalty. ... ok
test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1)
Test 1. ... ok
test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2)
Test 2. ... ok
test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension)
Test separate gap-extension penalties and list input. ... ok
test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1)
Open a gap in second sequence only. ... ok
test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2)
Force a bad alignment. ... ok
test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global)
Test ``score_only`` in a global alignment. ... ok
test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local)
Test ``score_only`` in a local alignment. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.110 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise2_no_C.py
test_pairwise2_no_C ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
  warnings.warn(
ok
test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok
test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments)
``_clean_alignments`` removes redundant and wrong alignments. ... ok
test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix)
``print_matrix`` prints nested lists as nice matrices. ... ok
test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments)
One possible start position in local alignment is not a match. ... ok
test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name)
Test for wrong function names. ... ok
test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters)
Test for number of parameters. ... ok
test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names)
Test for unknown parameter in parameter names. ... ok
test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings)
Test for warnings. ... ok
test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1)
Test 1. ... ok
test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2)
Test 2. ... ok
test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple)
Test globalxx. ... ok
test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2)
Do the same test with sequence order reversed. ... ok
test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input)
Do a global alignment with sequences supplied as lists. ... ok
test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only)
Test one_alignment_only parameter. ... ok
test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords)
Test equality of calls with and without keywords. ... ok
test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62)
Test localds with blosum62. ... ok
test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result)
Return no alignment. ... ok
test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric)
Test if alignment is independent on direction of sequence. ... ok
test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms)
Two different local alignments. ... ok
test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1)
Test localxx. ... ok
test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2)
Test localxx with ``full_sequences=True``. ... ok
test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic)
Test the generic method with local alignments. ... ok
test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1)
Test 1. ... ok
test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2)
Test 2. ... ok
test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3)
Test 3. ... ok
test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1)
Test sequence with only one match. ... ok
test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2)
Test sequences with two possible match positions. ... ok
test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3)
Like test 1, but global alignment. ... ok
test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1)
Test 1. ... ok
test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2)
Test 2. ... ok
test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3)
Test 3. ... ok
test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4)
Test 4. ... ok
test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps)
Turn off end-gap penalties. ... ok
test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2)
Do the same, but use the generic method (with the same result). ... ok
test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps)
Test alignment where end-gaps are differently penalized. ... ok
test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening)
Add gap-extend penalty to gap-opening penalty. ... ok
test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1)
Test 1. ... ok
test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2)
Test 2. ... ok
test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension)
Test separate gap-extension penalties and list input. ... ok
test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1)
Open a gap in second sequence only. ... ok
test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2)
Force a bad alignment. ... ok
test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global)
Test ``score_only`` in a global alignment. ... ok
test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local)
Test ``score_only`` in a local alignment. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.106 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_pairwise_alignment_map.py
test_pairwise_alignment_map ... ok
test1 (test_pairwise_alignment_map.TestComplex.test1) ... ok
test2 (test_pairwise_alignment_map.TestComplex.test2) ... ok
test_internal (test_pairwise_alignment_map.TestSimple.test_internal) ... ok
test_left_overhang (test_pairwise_alignment_map.TestSimple.test_left_overhang) ... ok
test_reverse_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_sequence) ... ok
test_reverse_transcript (test_pairwise_alignment_map.TestSimple.test_reverse_transcript) ... ok
test_reverse_transcript_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_transcript_sequence) ... ok
test_right_overhang (test_pairwise_alignment_map.TestSimple.test_right_overhang) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype.py
test_phenotype ... ok
test_CsvIterator (test_phenotype.TestPhenoMicro.test_CsvIterator)
Test basic functionalities of CsvIterator file parser. ... ok
test_JsonIterator (test_phenotype.TestPhenoMicro.test_JsonIterator)
Test basic functionalities of JsonIterator file parser. ... ok
test_PlateRecord (test_phenotype.TestPhenoMicro.test_PlateRecord)
Test basic functionalities of PlateRecord objects. ... ok
test_PlateRecord_errors (test_phenotype.TestPhenoMicro.test_PlateRecord_errors)
Test bad arguments with PlateRecord objects. ... ok
test_WellRecord (test_phenotype.TestPhenoMicro.test_WellRecord)
Test basic functionalities of WellRecord objects. ... ok
test_bad_fit_args (test_phenotype.TestPhenoMicro.test_bad_fit_args)
Test error handling of the fit method. ... ok
test_phenotype_IO (test_phenotype.TestPhenoMicro.test_phenotype_IO)
Test basic functionalities of phenotype IO methods. ... ok
test_phenotype_IO_errors (test_phenotype.TestPhenoMicro.test_phenotype_IO_errors)
Test bad arguments to phenotype IO methods. ... ok
----------------------------------------------------------------------
Ran 1 test in 7.517 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phenotype_fit.py
test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality.
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_phyml_tool.py
test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.117 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prodoc.py
test_prodoc ... ok
test_parse_pdoc (test_prodoc.TestProdocParse.test_parse_pdoc)
Parsing an excerpt of prosite.doc. ... ok
test_read_pdoc00100 (test_prodoc.TestProdocRead.test_read_pdoc00100)
Reading Prodoc record PDOC00100. ... ok
test_read_pdoc00113 (test_prodoc.TestProdocRead.test_read_pdoc00113)
Reading Prodoc record PDOC00113. ... ok
test_read_pdoc00144 (test_prodoc.TestProdocRead.test_read_pdoc00144)
Reading Prodoc record PDOC00144. ... ok
test_read_pdoc00149 (test_prodoc.TestProdocRead.test_read_pdoc00149)
Reading Prodoc record PDOC00149. ... ok
test_read_pdoc00340 (test_prodoc.TestProdocRead.test_read_pdoc00340)
Reading Prodoc record PDOC00340. ... ok
test_read_pdoc00424 (test_prodoc.TestProdocRead.test_read_pdoc00424)
Reading Prodoc record PDOC00424. ... ok
test_read_pdoc00472 (test_prodoc.TestProdocRead.test_read_pdoc00472)
Reading Prodoc record PDOC00472. ... ok
test_read_pdoc00640 (test_prodoc.TestProdocRead.test_read_pdoc00640)
Reading Prodoc record PDOC00640. ... ok
test_read_pdoc00787 (test_prodoc.TestProdocRead.test_read_pdoc00787)
Reading Prodoc record PDOC00787. ... ok
test_read_pdoc0933 (test_prodoc.TestProdocRead.test_read_pdoc0933)
Reading Prodoc record PDOC00933. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.018 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_prosite.py
test_prosite ... ok
test_read1 (test_prosite.TestPrositeRead.test_read1)
Parsing Prosite record ps00107.txt. ... ok
test_read2 (test_prosite.TestPrositeRead.test_read2)
Parsing Prosite record ps00159.txt. ... ok
test_read3 (test_prosite.TestPrositeRead.test_read3)
Parsing Prosite record ps00165.txt. ... ok
test_read4 (test_prosite.TestPrositeRead.test_read4)
Parsing Prosite record ps00432.txt. ... ok
test_read5 (test_prosite.TestPrositeRead.test_read5)
Parsing Prosite record ps00488.txt. ... ok
test_read6 (test_prosite.TestPrositeRead.test_read6)
Parsing Prosite record ps00546.txt. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.085 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_raxml_tool.py
test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.114 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_samtools_tool.py
test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program
        if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.018 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_seq.py
C
test_seq ... ok
test_ambiguous_values (test_seq.TestAmbiguousComplements.test_ambiguous_values)
Test that other tests do not introduce characters to our values. ... ok
test_mutable_seq (test_seq.TestAttributes.test_mutable_seq) ... ok
test_seq (test_seq.TestAttributes.test_seq) ... ok
test_complement_ambiguous_dna_values (test_seq.TestComplement.test_complement_ambiguous_dna_values) ... ok
test_complement_ambiguous_rna_values (test_seq.TestComplement.test_complement_ambiguous_rna_values) ... ok
test_complement_incompatible_letters (test_seq.TestComplement.test_complement_incompatible_letters) ... ok
test_complement_of_dna (test_seq.TestComplement.test_complement_of_dna) ... ok
test_complement_of_mixed_dna_rna (test_seq.TestComplement.test_complement_of_mixed_dna_rna) ... ok
test_complement_of_rna (test_seq.TestComplement.test_complement_of_rna) ... ok
test_immutable (test_seq.TestComplement.test_immutable) ... ok
test_reverse_complements (test_seq.TestDoubleReverseComplement.test_reverse_complements)
Test double reverse complement preserves the sequence. ... ok
test_add_method (test_seq.TestMutableSeq.test_add_method)
Test adding wrong type to MutableSeq. ... ok
test_appending (test_seq.TestMutableSeq.test_appending) ... ok
test_as_string (test_seq.TestMutableSeq.test_as_string) ... ok
test_complement (test_seq.TestMutableSeq.test_complement) ... ok
test_complement_dna_string (test_seq.TestMutableSeq.test_complement_dna_string) ... ok
test_complement_mixed_aphabets (test_seq.TestMutableSeq.test_complement_mixed_aphabets) ... ok
test_complement_old (test_seq.TestMutableSeq.test_complement_old) ... ok
test_complement_rna (test_seq.TestMutableSeq.test_complement_rna) ... ok
test_complement_rna_string (test_seq.TestMutableSeq.test_complement_rna_string) ... ok
test_contains_method (test_seq.TestMutableSeq.test_contains_method) ... ok
test_converting_to_immutable (test_seq.TestMutableSeq.test_converting_to_immutable) ... ok
test_count (test_seq.TestMutableSeq.test_count) ... ok
test_delete_stride_slice (test_seq.TestMutableSeq.test_delete_stride_slice) ... ok
test_deleting_item (test_seq.TestMutableSeq.test_deleting_item) ... ok
test_deleting_slice (test_seq.TestMutableSeq.test_deleting_slice) ... ok
test_endswith (test_seq.TestMutableSeq.test_endswith) ... ok
test_equal_comparison (test_seq.TestMutableSeq.test_equal_comparison)
Test __eq__ comparison method. ... ok
test_extend_method (test_seq.TestMutableSeq.test_extend_method) ... ok
test_extend_with_mutable_seq (test_seq.TestMutableSeq.test_extend_with_mutable_seq) ... ok
test_extract_third_nucleotide (test_seq.TestMutableSeq.test_extract_third_nucleotide)
Test extracting every third nucleotide (slicing with stride 3). ... ok
test_first_nucleotide (test_seq.TestMutableSeq.test_first_nucleotide) ... ok
test_greater_than_comparison (test_seq.TestMutableSeq.test_greater_than_comparison)
Test __gt__ comparison method. ... ok
test_greater_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_comparison_of_incompatible_types) ... ok
test_greater_than_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_comparison_with_str) ... ok
test_greater_than_or_equal_comparison (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison)
Test __ge__ comparison method. ... ok
test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_of_incompatible_types) ... ok
test_greater_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_with_str) ... ok
test_index (test_seq.TestMutableSeq.test_index) ... ok
test_inserting (test_seq.TestMutableSeq.test_inserting) ... ok
test_length (test_seq.TestMutableSeq.test_length) ... ok
test_less_than_comparison (test_seq.TestMutableSeq.test_less_than_comparison)
Test __lt__ comparison method. ... ok
test_less_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_comparison_of_incompatible_types) ... ok
test_less_than_comparison_with_str (test_seq.TestMutableSeq.test_less_than_comparison_with_str) ... ok
test_less_than_or_equal_comparison (test_seq.TestMutableSeq.test_less_than_or_equal_comparison)
Test __le__ comparison method. ... ok
test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_of_incompatible_types) ... ok
test_less_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_with_str) ... ok
test_mutableseq_construction (test_seq.TestMutableSeq.test_mutableseq_construction)
Test MutableSeq object initialization. ... ok
test_not_equal_comparison (test_seq.TestMutableSeq.test_not_equal_comparison)
Test __ne__ comparison method. ... ok
test_popping_last_item (test_seq.TestMutableSeq.test_popping_last_item) ... ok
test_radd_method_wrong_type (test_seq.TestMutableSeq.test_radd_method_wrong_type) ... ok
test_remove_items (test_seq.TestMutableSeq.test_remove_items) ... ok
test_repr (test_seq.TestMutableSeq.test_repr) ... ok
test_reverse (test_seq.TestMutableSeq.test_reverse)
Test using reverse method. ... ok
test_reverse_complement (test_seq.TestMutableSeq.test_reverse_complement) ... ok
test_reverse_complement_old (test_seq.TestMutableSeq.test_reverse_complement_old) ... ok
test_reverse_complement_rna (test_seq.TestMutableSeq.test_reverse_complement_rna) ... ok
test_reverse_with_stride (test_seq.TestMutableSeq.test_reverse_with_stride)
Test reverse using -1 stride. ... ok
test_set_wobble_codon_to_n (test_seq.TestMutableSeq.test_set_wobble_codon_to_n)
Test setting wobble codon to N (set slice with stride 3). ... ok
test_setting_item (test_seq.TestMutableSeq.test_setting_item) ... ok
test_setting_slices (test_seq.TestMutableSeq.test_setting_slices) ... ok
test_startswith (test_seq.TestMutableSeq.test_startswith) ... ok
test_transcribe (test_seq.TestMutableSeq.test_transcribe) ... ok
test_truncated_repr (test_seq.TestMutableSeq.test_truncated_repr) ... ok
test_immutable (test_seq.TestReverseComplement.test_immutable) ... ok
test_reverse_complement (test_seq.TestReverseComplement.test_reverse_complement) ... ok
test_reverse_complement_of_dna (test_seq.TestReverseComplement.test_reverse_complement_of_dna) ... ok
test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement.test_reverse_complement_of_mixed_dna_rna) ... ok
test_reverse_complement_of_rna (test_seq.TestReverseComplement.test_reverse_complement_of_rna) ... ok
test_as_string (test_seq.TestSeq.test_as_string)
Test converting Seq to string. ... ok
test_cast_to_list (test_seq.TestSeq.test_cast_to_list) ... ok
test_concatenation_of_seq (test_seq.TestSeq.test_concatenation_of_seq) ... ok
test_extract_third_nucleotide (test_seq.TestSeq.test_extract_third_nucleotide)
Test extracting every third nucleotide (slicing with stride 3). ... ok
test_first_nucleotide (test_seq.TestSeq.test_first_nucleotide)
Test getting first nucleotide of Seq. ... ok
test_last_nucleotide (test_seq.TestSeq.test_last_nucleotide)
Test getting last nucleotide of Seq. ... ok
test_length (test_seq.TestSeq.test_length)
Test len method on Seq object. ... ok
test_replace (test_seq.TestSeq.test_replace) ... ok
test_repr (test_seq.TestSeq.test_repr)
Test representation of Seq object. ... ok
test_reverse (test_seq.TestSeq.test_reverse)
Test reverse using -1 stride. ... ok
test_seq_construction (test_seq.TestSeq.test_seq_construction)
Test Seq object initialization. ... ok
test_slicing (test_seq.TestSeq.test_slicing)
Test slicing of Seq. ... ok
test_truncated_repr (test_seq.TestSeq.test_truncated_repr) ... ok
test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides) ... ok
test_adding_generic_nucleotide_with_other_nucleotides_inplace (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides_inplace) ... ok
test_adding_protein_with_nucleotides (test_seq.TestSeqAddition.test_adding_protein_with_nucleotides) ... ok
test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides) ... ok
test_addition_dna_rna_with_generic_nucleotides_inplace (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides_inplace) ... ok
test_addition_dna_with_dna (test_seq.TestSeqAddition.test_addition_dna_with_dna) ... ok
test_addition_dna_with_dna_inplace (test_seq.TestSeqAddition.test_addition_dna_with_dna_inplace) ... ok
test_addition_dna_with_rna (test_seq.TestSeqAddition.test_addition_dna_with_rna) ... ok
test_addition_proteins (test_seq.TestSeqAddition.test_addition_proteins) ... ok
test_addition_proteins_inplace (test_seq.TestSeqAddition.test_addition_proteins_inplace) ... ok
test_addition_rna_with_rna (test_seq.TestSeqAddition.test_addition_rna_with_rna) ... ok
test_addition_rna_with_rna_inplace (test_seq.TestSeqAddition.test_addition_rna_with_rna_inplace) ... ok
test_defined (test_seq.TestSeqDefined.test_defined) ... ok
test_undefined (test_seq.TestSeqDefined.test_undefined) ... ok
test_zero_length (test_seq.TestSeqDefined.test_zero_length) ... ok
test_imul_method (test_seq.TestSeqMultiplication.test_imul_method)
Test imul method; relies on addition and mull methods. ... ok
test_imul_method_exceptions (test_seq.TestSeqMultiplication.test_imul_method_exceptions)
Test imul method exceptions. ... ok
test_mul_method (test_seq.TestSeqMultiplication.test_mul_method)
Test mul method; relies on addition method. ... ok
test_mul_method_exceptions (test_seq.TestSeqMultiplication.test_mul_method_exceptions)
Test mul method exceptions. ... ok
test_rmul_method (test_seq.TestSeqMultiplication.test_rmul_method)
Test rmul method; relies on addition method. ... ok
test_rmul_method_exceptions (test_seq.TestSeqMultiplication.test_rmul_method_exceptions)
Test rmul method exceptions. ... ok
test_add_method_using_wrong_object (test_seq.TestSeqStringMethods.test_add_method_using_wrong_object) ... ok
test_append_nucleotides (test_seq.TestSeqStringMethods.test_append_nucleotides) ... ok
test_append_proteins (test_seq.TestSeqStringMethods.test_append_proteins) ... ok
test_contains_method (test_seq.TestSeqStringMethods.test_contains_method) ... ok
test_counting_characters (test_seq.TestSeqStringMethods.test_counting_characters) ... ok
test_endswith (test_seq.TestSeqStringMethods.test_endswith) ... ok
test_finding_characters (test_seq.TestSeqStringMethods.test_finding_characters) ... ok
test_greater_than_comparison (test_seq.TestSeqStringMethods.test_greater_than_comparison)
Test __gt__ comparison method. ... ok
test_greater_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_comparison_of_incompatible_types)
Test incompatible types __gt__ comparison method. ... ok
test_greater_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison)
Test __ge__ comparison method. ... ok
test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison_of_incompatible_types)
Test incompatible types __ge__ comparison method. ... ok
test_hash (test_seq.TestSeqStringMethods.test_hash) ... ok
test_less_than_comparison (test_seq.TestSeqStringMethods.test_less_than_comparison)
Test __lt__ comparison method. ... ok
test_less_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_comparison_of_incompatible_types)
Test incompatible types __lt__ comparison method. ... ok
test_less_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison)
Test __le__ comparison method. ... ok
test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison_of_incompatible_types)
Test incompatible types __le__ comparison method. ... ok
test_mutableseq_upper_lower (test_seq.TestSeqStringMethods.test_mutableseq_upper_lower) ... ok
test_not_equal_comparsion (test_seq.TestSeqStringMethods.test_not_equal_comparsion)
Test __ne__ comparison method. ... ok
test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods.test_radd_method_using_wrong_object) ... ok
test_splits (test_seq.TestSeqStringMethods.test_splits) ... ok
test_startswith (test_seq.TestSeqStringMethods.test_startswith) ... ok
test_string_methods (test_seq.TestSeqStringMethods.test_string_methods) ... ok
test_stripping_characters (test_seq.TestSeqStringMethods.test_stripping_characters) ... ok
test_stops (test_seq.TestStopCodons.test_stops) ... ok
test_translation_of_stops (test_seq.TestStopCodons.test_translation_of_stops) ... ok
test_back_transcribe_rna_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_into_dna) ... ok
test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_string_into_dna) ... ok
test_seq_object_back_transcription_method (test_seq.TestTranscription.test_seq_object_back_transcription_method) ... ok
test_seq_object_transcription_method (test_seq.TestTranscription.test_seq_object_transcription_method) ... ok
test_transcription_dna_into_rna (test_seq.TestTranscription.test_transcription_dna_into_rna) ... ok
test_transcription_dna_string_into_rna (test_seq.TestTranscription.test_transcription_dna_string_into_rna) ... ok
test_gapped_seq_no_gap_char_given (test_seq.TestTranslating.test_gapped_seq_no_gap_char_given) ... ok
test_gapped_seq_with_gap_char_given (test_seq.TestTranslating.test_gapped_seq_with_gap_char_given) ... ok
test_translation (test_seq.TestTranslating.test_translation) ... ok
test_translation_extra_stop_codon (test_seq.TestTranslating.test_translation_extra_stop_codon) ... ok
test_translation_incomplete_codon (test_seq.TestTranslating.test_translation_incomplete_codon) ... ok
test_translation_of_asparagine (test_seq.TestTranslating.test_translation_of_asparagine) ... ok
test_translation_of_gapped_string_no_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_no_gap_char_given) ... ok
test_translation_of_gapped_string_with_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_with_gap_char_given) ... ok
test_translation_of_glutamine (test_seq.TestTranslating.test_translation_of_glutamine) ... ok
test_translation_of_invalid_codon (test_seq.TestTranslating.test_translation_of_invalid_codon) ... ok
test_translation_of_leucine (test_seq.TestTranslating.test_translation_of_leucine) ... ok
test_translation_of_string (test_seq.TestTranslating.test_translation_of_string) ... ok
test_translation_on_proteins (test_seq.TestTranslating.test_translation_on_proteins)
Check translation fails on a protein. ... ok
test_translation_to_stop (test_seq.TestTranslating.test_translation_to_stop) ... ok
test_translation_using_cds (test_seq.TestTranslating.test_translation_using_cds) ... ok
test_translation_using_tables_with_ambiguous_stop_codons (test_seq.TestTranslating.test_translation_using_tables_with_ambiguous_stop_codons)
Check for error and warning messages. ... ok
test_translation_with_bad_table_argument (test_seq.TestTranslating.test_translation_with_bad_table_argument) ... ok
test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating.test_translation_with_codon_table_as_table_argument) ... ok
test_translation_wrong_type (test_seq.TestTranslating.test_translation_wrong_type)
Test translation table cannot be CodonTable. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.091 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
C
+ for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat`
+ echo C
+ export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/lib64/python3.12/site-packages
+ /usr/bin/python3 run_tests.py --offline -v test_translate.py
test_translate ... ok
test_ambiguous (test_translate.TestTranscriptionTranslation.test_ambiguous) ... ok
test_dna_rna_translation (test_translate.TestTranscriptionTranslation.test_dna_rna_translation) ... ok
test_transcription (test_translate.TestTranscriptionTranslation.test_transcription) ... ok
test_translation (test_translate.TestTranscriptionTranslation.test_translation) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.053 seconds
Skipping any tests requiring internet access
Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)]
Operating system: posix linux
~/build/BUILD/python-biopython-1.81
+ popd
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: python3-biopython-1.81-4.fc39.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.6gJvOZ
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.81
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/doc/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/doc/python3-biopython
+ cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/Scripts /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/doc/python3-biopython
+ cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/CONTRIB.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/doc/python3-biopython
+ cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/DEPRECATED.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/doc/python3-biopython
+ cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/NEWS.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/doc/python3-biopython
+ cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/README.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/doc/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.BgPdxh
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.81
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/licenses/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/licenses/python3-biopython
+ cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/licenses/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython = 1.81-4.fc39 python3-biopython = 1.81-4.fc39 python3-biopython(x86-64) = 1.81-4.fc39 python3.12-biopython = 1.81-4.fc39 python3.12dist(biopython) = 1.81 python3dist(biopython) = 1.81
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) python(abi) = 3.12 python3.12dist(numpy) rtld(GNU_HASH)
Processing files: python-biopython-doc-1.81-4.fc39.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.D6NWMy
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.81
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/doc/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/doc/python-biopython-doc
+ cp -pr /builddir/build/BUILD/python-biopython-1.81/biopython-1.81/Doc /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/doc/python-biopython-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.NKTuGb
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.81
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/licenses/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/licenses/python-biopython-doc
+ cp -pr /builddir/build/BUILD/python-biopython-1.81/biopython-1.81/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64/usr/share/licenses/python-biopython-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython-doc = 1.81-4.fc39
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-biopython-debugsource-1.81-4.fc39.x86_64
Provides: python-biopython-debugsource = 1.81-4.fc39 python-biopython-debugsource(x86-64) = 1.81-4.fc39
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python3-biopython-debuginfo-1.81-4.fc39.x86_64
Provides: debuginfo(build-id) = 1cfbba362a3da52c29685ff4b8c7f8baa888f52a debuginfo(build-id) = 445d627c5e75922dc76cf6502dba4a6120e2defa debuginfo(build-id) = 4d7f22c35ead76a3b89258519083157a04b855ae debuginfo(build-id) = 5d7bee95a091186bff0fd48e0de163f3e69c7203 debuginfo(build-id) = 72859ab1b3bc2c6cd5d7d761fc1cf26c418afd46 debuginfo(build-id) = 9fd66fc6816954535ee62af83be99ecf6fbc7b7a debuginfo(build-id) = af2766f6a9b141c886e3d318870f51f1b60510b2 debuginfo(build-id) = ca2402fbac873e164cc9ebbc468016fb78427fcf debuginfo(build-id) = de70f2e0b426049e5b9ae4bed5b2d2be26085d4b python-biopython-debuginfo = 1.81-4.fc39 python3-biopython-debuginfo = 1.81-4.fc39 python3-biopython-debuginfo(x86-64) = 1.81-4.fc39 python3.12-biopython-debuginfo = 1.81-4.fc39
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: python-biopython-debugsource(x86-64) = 1.81-4.fc39
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64
Wrote: /builddir/build/RPMS/python-biopython-doc-1.81-4.fc39.noarch.rpm
Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.81-4.fc39.x86_64.rpm
Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.81-4.fc39.x86_64.rpm
Wrote: /builddir/build/RPMS/python3-biopython-1.81-4.fc39.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.OVIwU2
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.81
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.fHhrP7
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/python-biopython-1.81-SPECPARTS
+ rm -rf python-biopython-1.81 python-biopython-1.81.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0