Mock Version: 5.9 Mock Version: 5.9 Mock Version: 5.9 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/f42-build-55747816-6538638/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '57aa945ea58e44ec9d62d988bf7426d0', '-D', '/var/lib/mock/f42-build-55747816-6538638/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721347200 Wrote: /builddir/build/SRPMS/python-biopython-1.84-3.fc42.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -br --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/f42-build-55747816-6538638/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueraiseExc=FalseprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '1c62fa4d41304f76840d7c09aa11a8b8', '-D', '/var/lib/mock/f42-build-55747816-6538638/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -br --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721347200 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.RH2qbU + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + test -d /builddir/build/BUILD/python-biopython-1.84-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/python-biopython-1.84-build + /usr/bin/rm -rf /builddir/build/BUILD/python-biopython-1.84-build + /usr/bin/mkdir -p /builddir/build/BUILD/python-biopython-1.84-build + /usr/bin/mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.36wAqF + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + cd /builddir/build/BUILD/python-biopython-1.84-build + rm -rf biopython-1.84 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.84.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd biopython-1.84 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/python-biopython-1.84-replace_deprecated_function.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + RPM_EC=0 ++ jobs -p + exit 0 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.vUOvL2 + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + cd biopython-1.84 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + echo -n + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement not satisfied: setuptools >= 40.8 Exiting dependency generation pass: build backend + cat /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.84-3.fc42.buildreqs.nosrc.rpm Child return code was: 11 Dynamic buildrequires detected Going to install missing buildrequires. See root.log for details. ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -br --noprep --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/f42-build-55747816-6538638/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueraiseExc=FalseprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '5451f33df7ee49d8a2640bc0039b4132', '-D', '/var/lib/mock/f42-build-55747816-6538638/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -br --noprep --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721347200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.PgDfww + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + cd biopython-1.84 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + echo -n + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 74.1.3) running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Doc/_build' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' running dist_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Doc/_build' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/biopython-1.84.dist-info' Handling numpy from hook generated metadata: Requires-Dist (biopython) Requirement not satisfied: numpy + cat /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-buildrequires + rm -rfv biopython-1.84.dist-info/ removed 'biopython-1.84.dist-info/top_level.txt' removed 'biopython-1.84.dist-info/METADATA' removed 'biopython-1.84.dist-info/LICENSE' removed 'biopython-1.84.dist-info/LICENSE.rst' removed directory 'biopython-1.84.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.84-3.fc42.buildreqs.nosrc.rpm Child return code was: 11 Dynamic buildrequires detected Going to install missing buildrequires. See root.log for details. ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -br --noprep --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/f42-build-55747816-6538638/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueraiseExc=FalseprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '6df8449443b24e2dabf7708b3780a0c1', '-D', '/var/lib/mock/f42-build-55747816-6538638/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -br --noprep --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721347200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.cj9n7y + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + cd biopython-1.84 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + echo -n + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 74.1.3) running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Doc/_build' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' running dist_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Doc/_build' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/biopython-1.84.dist-info' Handling numpy from hook generated metadata: Requires-Dist (biopython) Requirement satisfied: numpy (installed: numpy 2.2.0) + cat /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-buildrequires + rm -rfv biopython-1.84.dist-info/ removed 'biopython-1.84.dist-info/top_level.txt' removed 'biopython-1.84.dist-info/METADATA' removed 'biopython-1.84.dist-info/LICENSE' removed 'biopython-1.84.dist-info/LICENSE.rst' removed directory 'biopython-1.84.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.84-3.fc42.buildreqs.nosrc.rpm Child return code was: 11 Dynamic buildrequires detected Going to install missing buildrequires. See root.log for details. ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -ba --noprep --noclean --target aarch64 /builddir/build/SPECS/python-biopython.spec'], chrootPath='/var/lib/mock/f42-build-55747816-6538638/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'unshare_net=TrueprintOutput=Falsenspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '403bd61cef814d95b002ecef9c1c5132', '-D', '/var/lib/mock/f42-build-55747816-6538638/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -ba --noprep --noclean --target aarch64 /builddir/build/SPECS/python-biopython.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1721347200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.L33Gk3 + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + cd biopython-1.84 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + echo -n + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 74.1.3) running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Doc/_build' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' running dist_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Doc/_build' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/biopython-1.84.dist-info' Handling numpy from hook generated metadata: Requires-Dist (biopython) Requirement satisfied: numpy (installed: numpy 2.2.0) + cat /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-buildrequires + rm -rfv biopython-1.84.dist-info/ removed 'biopython-1.84.dist-info/top_level.txt' removed 'biopython-1.84.dist-info/METADATA' removed 'biopython-1.84.dist-info/LICENSE' removed 'biopython-1.84.dist-info/LICENSE.rst' removed directory 'biopython-1.84.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.L0aekT + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 biopython-1.84 + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_wheel.py /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir Processing /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84 Preparing metadata (pyproject.toml): started Running command Preparing metadata (pyproject.toml) running dist_info creating /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-dnmnkapq/biopython.egg-info writing /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-dnmnkapq/biopython.egg-info/PKG-INFO writing dependency_links to /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-dnmnkapq/biopython.egg-info/dependency_links.txt writing requirements to /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-dnmnkapq/biopython.egg-info/requires.txt writing top-level names to /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-dnmnkapq/biopython.egg-info/top_level.txt writing manifest file '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-dnmnkapq/biopython.egg-info/SOURCES.txt' reading manifest file '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-dnmnkapq/biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Doc/_build' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-dnmnkapq/biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-dnmnkapq/biopython-1.84.dist-info' Preparing metadata (pyproject.toml): finished with status 'done' Building wheels for collected packages: biopython Building wheel for biopython (pyproject.toml): started Running command Building wheel for biopython (pyproject.toml) running bdist_wheel running build running build_py creating build creating build/lib.linux-aarch64-cpython-313 creating build/lib.linux-aarch64-cpython-313/Bio copying Bio/File.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/LogisticRegression.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/MarkovModel.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/MaxEntropy.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/NaiveBayes.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/Seq.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/SeqFeature.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/SeqRecord.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/_utils.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/bgzf.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/kNN.py -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/pairwise2.py -> build/lib.linux-aarch64-cpython-313/Bio creating build/lib.linux-aarch64-cpython-313/Bio/Affy copying Bio/Affy/CelFile.py -> build/lib.linux-aarch64-cpython-313/Bio/Affy copying Bio/Affy/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Affy creating build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/a2m.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/analysis.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/bed.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/bigbed.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/bigmaf.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/bigpsl.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/chain.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/clustal.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/emboss.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/exonerate.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/fasta.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/hhr.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/interfaces.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/maf.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/mauve.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/msf.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/nexus.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/phylip.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/psl.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/sam.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/stockholm.py -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/tabular.py -> build/lib.linux-aarch64-cpython-313/Bio/Align creating build/lib.linux-aarch64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/Applications creating build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices creating build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO copying Bio/AlignIO/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/AlignIO creating build/lib.linux-aarch64-cpython-313/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Alphabet creating build/lib.linux-aarch64-cpython-313/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Application creating build/lib.linux-aarch64-cpython-313/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-aarch64-cpython-313/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-aarch64-cpython-313/Bio/Blast copying Bio/Blast/NCBIXML.py -> build/lib.linux-aarch64-cpython-313/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Blast copying Bio/Blast/_parser.py -> build/lib.linux-aarch64-cpython-313/Bio/Blast copying Bio/Blast/_writers.py -> build/lib.linux-aarch64-cpython-313/Bio/Blast creating build/lib.linux-aarch64-cpython-313/Bio/CAPS copying Bio/CAPS/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/CAPS creating build/lib.linux-aarch64-cpython-313/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Cluster creating build/lib.linux-aarch64-cpython-313/Bio/codonalign copying Bio/codonalign/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/codonalign copying Bio/codonalign/codonalignment.py -> build/lib.linux-aarch64-cpython-313/Bio/codonalign copying Bio/codonalign/codonseq.py -> build/lib.linux-aarch64-cpython-313/Bio/codonalign creating build/lib.linux-aarch64-cpython-313/Bio/Compass copying Bio/Compass/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Compass creating build/lib.linux-aarch64-cpython-313/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-aarch64-cpython-313/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-aarch64-cpython-313/Bio/Data copying Bio/Data/PDBData.py -> build/lib.linux-aarch64-cpython-313/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Data creating build/lib.linux-aarch64-cpython-313/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-aarch64-cpython-313/Bio/Emboss copying Bio/Emboss/Primer3.py -> build/lib.linux-aarch64-cpython-313/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-aarch64-cpython-313/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Emboss creating build/lib.linux-aarch64-cpython-313/Bio/Entrez copying Bio/Entrez/Parser.py -> build/lib.linux-aarch64-cpython-313/Bio/Entrez copying Bio/Entrez/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Entrez creating build/lib.linux-aarch64-cpython-313/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> build/lib.linux-aarch64-cpython-313/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> build/lib.linux-aarch64-cpython-313/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> build/lib.linux-aarch64-cpython-313/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-aarch64-cpython-313/Bio/ExPASy copying Bio/ExPASy/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-aarch64-cpython-313/Bio/ExPASy creating build/lib.linux-aarch64-cpython-313/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-aarch64-cpython-313/Bio/GenBank copying Bio/GenBank/Scanner.py -> build/lib.linux-aarch64-cpython-313/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-aarch64-cpython-313/Bio/GenBank creating build/lib.linux-aarch64-cpython-313/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-aarch64-cpython-313/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Geo creating build/lib.linux-aarch64-cpython-313/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics creating build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram creating build/lib.linux-aarch64-cpython-313/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-aarch64-cpython-313/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-aarch64-cpython-313/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-aarch64-cpython-313/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-aarch64-cpython-313/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/HMM creating build/lib.linux-aarch64-cpython-313/Bio/KEGG copying Bio/KEGG/REST.py -> build/lib.linux-aarch64-cpython-313/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/KEGG creating build/lib.linux-aarch64-cpython-313/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/KEGG/Compound creating build/lib.linux-aarch64-cpython-313/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/KEGG/Enzyme creating build/lib.linux-aarch64-cpython-313/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/KEGG/Gene creating build/lib.linux-aarch64-cpython-313/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/KEGG/Map creating build/lib.linux-aarch64-cpython-313/Bio/PDB creating build/lib.linux-aarch64-cpython-313/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB/mmtf creating build/lib.linux-aarch64-cpython-313/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-aarch64-cpython-313/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-aarch64-cpython-313/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/KEGG/KGML creating build/lib.linux-aarch64-cpython-313/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Medline creating build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/alignace.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/clusterbuster.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/mast.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/matrix.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/meme.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/minimal.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/pfm.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/thresholds.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/transfac.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/motifs/xms.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs creating build/lib.linux-aarch64-cpython-313/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs/applications creating build/lib.linux-aarch64-cpython-313/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> build/lib.linux-aarch64-cpython-313/Bio/motifs/jaspar creating build/lib.linux-aarch64-cpython-313/Bio/Nexus copying Bio/Nexus/Nexus.py -> build/lib.linux-aarch64-cpython-313/Bio/Nexus copying Bio/Nexus/Nodes.py -> build/lib.linux-aarch64-cpython-313/Bio/Nexus copying Bio/Nexus/StandardData.py -> build/lib.linux-aarch64-cpython-313/Bio/Nexus copying Bio/Nexus/Trees.py -> build/lib.linux-aarch64-cpython-313/Bio/Nexus copying Bio/Nexus/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Nexus creating build/lib.linux-aarch64-cpython-313/Bio/NMR copying Bio/NMR/NOEtools.py -> build/lib.linux-aarch64-cpython-313/Bio/NMR copying Bio/NMR/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/NMR copying Bio/NMR/xpktools.py -> build/lib.linux-aarch64-cpython-313/Bio/NMR creating build/lib.linux-aarch64-cpython-313/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Pathway creating build/lib.linux-aarch64-cpython-313/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-aarch64-cpython-313/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-aarch64-cpython-313/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Pathway/Rep copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/DSSP.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/Dice.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/FragmentMapper.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/HSExposure.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/MMCIFParser.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/NACCESS.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/PDBList.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/PDBMLParser.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/PICIO.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/PSEA.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/ResidueDepth.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/SASA.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/SCADIO.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/StructureAlignment.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/Superimposer.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/alphafold_db.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/binary_cif.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/cealign.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/ic_data.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/ic_rebuild.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/internal_coords.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/mmcifio.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/qcprot.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/vectors.py -> build/lib.linux-aarch64-cpython-313/Bio/PDB creating build/lib.linux-aarch64-cpython-313/Bio/phenotype copying Bio/phenotype/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/phenotype copying Bio/phenotype/phen_micro.py -> build/lib.linux-aarch64-cpython-313/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> build/lib.linux-aarch64-cpython-313/Bio/phenotype creating build/lib.linux-aarch64-cpython-313/Bio/PopGen copying Bio/PopGen/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/PopGen creating build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop creating build/lib.linux-aarch64-cpython-313/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> build/lib.linux-aarch64-cpython-313/Bio/Restriction copying Bio/Restriction/Restriction.py -> build/lib.linux-aarch64-cpython-313/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-aarch64-cpython-313/Bio/Restriction copying Bio/Restriction/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Restriction creating build/lib.linux-aarch64-cpython-313/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-aarch64-cpython-313/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-aarch64-cpython-313/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-aarch64-cpython-313/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-aarch64-cpython-313/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-aarch64-cpython-313/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-aarch64-cpython-313/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SCOP creating build/lib.linux-aarch64-cpython-313/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO copying Bio/SearchIO/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO copying Bio/SearchIO/_index.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO copying Bio/SearchIO/_utils.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO creating build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model creating build/lib.linux-aarch64-cpython-313/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/BlastIO creating build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HHsuiteIO creating build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO creating build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO creating build/lib.linux-aarch64-cpython-313/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-aarch64-cpython-313/Bio/SearchIO/InterproscanIO creating build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/GfaIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying Bio/SeqIO/_index.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO creating build/lib.linux-aarch64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> build/lib.linux-aarch64-cpython-313/Bio/SeqUtils creating build/lib.linux-aarch64-cpython-313/Bio/Sequencing copying Bio/Sequencing/Ace.py -> build/lib.linux-aarch64-cpython-313/Bio/Sequencing copying Bio/Sequencing/Phd.py -> build/lib.linux-aarch64-cpython-313/Bio/Sequencing copying Bio/Sequencing/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Sequencing creating build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Applications creating build/lib.linux-aarch64-cpython-313/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SVDSuperimposer creating build/lib.linux-aarch64-cpython-313/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-aarch64-cpython-313/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/SwissProt creating build/lib.linux-aarch64-cpython-313/Bio/TogoWS copying Bio/TogoWS/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/TogoWS creating build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/BaseTree.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/CDAO.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/Consensus.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/NeXML.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/Newick.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/NewickIO.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/NexusIO.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/_io.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo copying Bio/Phylo/_utils.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo creating build/lib.linux-aarch64-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/Applications creating build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML creating build/lib.linux-aarch64-cpython-313/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/UniGene creating build/lib.linux-aarch64-cpython-313/Bio/UniProt copying Bio/UniProt/GOA.py -> build/lib.linux-aarch64-cpython-313/Bio/UniProt copying Bio/UniProt/__init__.py -> build/lib.linux-aarch64-cpython-313/Bio/UniProt creating build/lib.linux-aarch64-cpython-313/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-aarch64-cpython-313/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-aarch64-cpython-313/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-aarch64-cpython-313/BioSQL copying BioSQL/Loader.py -> build/lib.linux-aarch64-cpython-313/BioSQL copying BioSQL/__init__.py -> build/lib.linux-aarch64-cpython-313/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 'Doc/_build' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' /usr/lib/python3.13/site-packages/setuptools/command/build_py.py:218: _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/python3.13/site-packages/setuptools/command/build_py.py:218: _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/python3.13/site-packages/setuptools/command/build_py.py:218: _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-aarch64-cpython-313/Bio copying Bio/py.typed -> build/lib.linux-aarch64-cpython-313/Bio copying Bio/Align/_aligncore.c -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/_codonaligner.c -> build/lib.linux-aarch64-cpython-313/Bio/Align copying Bio/Align/_pairwisealigner.c -> build/lib.linux-aarch64-cpython-313/Bio/Align creating build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> build/lib.linux-aarch64-cpython-313/Bio/Cluster copying Bio/Cluster/cluster.h -> build/lib.linux-aarch64-cpython-313/Bio/Cluster copying Bio/Cluster/clustermodule.c -> build/lib.linux-aarch64-cpython-313/Bio/Cluster creating build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/epost.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_clinvar.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_gene.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs creating build/lib.linux-aarch64-cpython-313/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd -> build/lib.linux-aarch64-cpython-313/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> build/lib.linux-aarch64-cpython-313/Bio/motifs copying Bio/Nexus/cnexus.c -> build/lib.linux-aarch64-cpython-313/Bio/Nexus copying Bio/PDB/bcifhelpermodule.c -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/ccealignmodule.c -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/PDB/kdtrees.c -> build/lib.linux-aarch64-cpython-313/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-aarch64-cpython-313/Bio/SeqIO copying BioSQL/py.typed -> build/lib.linux-aarch64-cpython-313/BioSQL running build_ext building 'Bio.Align._codonaligner' extension creating build/temp.linux-aarch64-cpython-313 creating build/temp.linux-aarch64-cpython-313/Bio creating build/temp.linux-aarch64-cpython-313/Bio/Align gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Align/_codonaligner.c -o build/temp.linux-aarch64-cpython-313/Bio/Align/_codonaligner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/Align/_codonaligner.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/Align/_codonaligner.cpython-313-aarch64-linux-gnu.so building 'Bio.Align._pairwisealigner' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Align/_pairwisealigner.c -o build/temp.linux-aarch64-cpython-313/Bio/Align/_pairwisealigner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/Align/_pairwisealigner.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/Align/_pairwisealigner.cpython-313-aarch64-linux-gnu.so building 'Bio.Align._aligncore' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Align/_aligncore.c -o build/temp.linux-aarch64-cpython-313/Bio/Align/_aligncore.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/Align/_aligncore.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/Align/_aligncore.cpython-313-aarch64-linux-gnu.so building 'Bio.cpairwise2' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/cpairwise2module.c -o build/temp.linux-aarch64-cpython-313/Bio/cpairwise2module.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/cpairwise2.cpython-313-aarch64-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-aarch64-cpython-313/Bio/Nexus gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Nexus/cnexus.c -o build/temp.linux-aarch64-cpython-313/Bio/Nexus/cnexus.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/Nexus/cnexus.cpython-313-aarch64-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-aarch64-cpython-313/Bio/motifs gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/motifs/_pwm.c -o build/temp.linux-aarch64-cpython-313/Bio/motifs/_pwm.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/motifs/_pwm.cpython-313-aarch64-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-aarch64-cpython-313/Bio/Cluster gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Cluster/cluster.c -o build/temp.linux-aarch64-cpython-313/Bio/Cluster/cluster.o gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Cluster/clustermodule.c -o build/temp.linux-aarch64-cpython-313/Bio/Cluster/clustermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/Cluster/cluster.o build/temp.linux-aarch64-cpython-313/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/Cluster/_cluster.cpython-313-aarch64-linux-gnu.so building 'Bio.PDB.ccealign' extension creating build/temp.linux-aarch64-cpython-313/Bio/PDB gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-aarch64-cpython-313/Bio/PDB/ccealignmodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/PDB/ccealign.cpython-313-aarch64-linux-gnu.so building 'Bio.PDB.kdtrees' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/PDB/kdtrees.c -o build/temp.linux-aarch64-cpython-313/Bio/PDB/kdtrees.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/PDB/kdtrees.cpython-313-aarch64-linux-gnu.so building 'Bio.PDB._bcif_helper' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/PDB/bcifhelpermodule.c -o build/temp.linux-aarch64-cpython-313/Bio/PDB/bcifhelpermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/PDB/bcifhelpermodule.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/PDB/_bcif_helper.cpython-313-aarch64-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-aarch64-cpython-313/Bio/SeqIO gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-aarch64-cpython-313/Bio/SeqIO/_twoBitIO.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-313/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-313/Bio/SeqIO/_twoBitIO.cpython-313-aarch64-linux-gnu.so installing to build/bdist.linux-aarch64/wheel running install running install_lib creating build/bdist.linux-aarch64 creating build/bdist.linux-aarch64/wheel creating build/bdist.linux-aarch64/wheel/Bio copying build/lib.linux-aarch64-cpython-313/Bio/File.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/LogisticRegression.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/MarkovModel.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/MaxEntropy.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/NaiveBayes.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/Seq.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/SeqFeature.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/SeqRecord.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/_utils.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/bgzf.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/kNN.py -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/pairwise2.py -> build/bdist.linux-aarch64/wheel/./Bio creating build/bdist.linux-aarch64/wheel/Bio/Affy copying build/lib.linux-aarch64-cpython-313/Bio/Affy/CelFile.py -> build/bdist.linux-aarch64/wheel/./Bio/Affy copying build/lib.linux-aarch64-cpython-313/Bio/Affy/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Affy creating build/bdist.linux-aarch64/wheel/Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/AlignInfo.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/a2m.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/analysis.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/bed.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/bigbed.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/bigmaf.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/bigpsl.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/chain.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/clustal.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/emboss.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/exonerate.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/fasta.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/hhr.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/interfaces.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/maf.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/mauve.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/msf.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/nexus.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/phylip.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/psl.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/sam.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/stockholm.py -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/tabular.py -> build/bdist.linux-aarch64/wheel/./Bio/Align creating build/bdist.linux-aarch64/wheel/Bio/Align/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Align/Applications/_ClustalOmega.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Align/Applications/_Clustalw.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Align/Applications/_Dialign.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Align/Applications/_MSAProbs.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Align/Applications/_Mafft.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Align/Applications/_Muscle.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Align/Applications/_Prank.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Align/Applications/_Probcons.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Align/Applications/_TCoffee.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Align/Applications/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/Applications creating build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices creating build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/BENNER22 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/BENNER6 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/BENNER74 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/BLASTN -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/BLASTP -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM45 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM50 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM62 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM80 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM90 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/DAYHOFF -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/FENG -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/GENETIC -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/GONNET1992 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/HOXD70 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/JOHNSON -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/JONES -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/LEVIN -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/MCLACHLAN -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/MDM78 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/MEGABLAST -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/NUC.4.4 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/PAM250 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/PAM30 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/PAM70 -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/RAO -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/RISLER -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/SCHNEIDER -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/STR -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/substitution_matrices/data/TRANS -> build/bdist.linux-aarch64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-aarch64-cpython-313/Bio/Align/_aligncore.c -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/_codonaligner.c -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/_pairwisealigner.c -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/_codonaligner.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/_pairwisealigner.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio/Align copying build/lib.linux-aarch64-cpython-313/Bio/Align/_aligncore.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio/Align creating build/bdist.linux-aarch64/wheel/Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/ClustalIO.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/EmbossIO.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/FastaIO.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/Interfaces.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/MafIO.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/MauveIO.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/MsfIO.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/NexusIO.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/PhylipIO.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/StockholmIO.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO copying build/lib.linux-aarch64-cpython-313/Bio/AlignIO/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/AlignIO creating build/bdist.linux-aarch64/wheel/Bio/Alphabet copying build/lib.linux-aarch64-cpython-313/Bio/Alphabet/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Alphabet creating build/bdist.linux-aarch64/wheel/Bio/Application copying build/lib.linux-aarch64-cpython-313/Bio/Application/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Application creating build/bdist.linux-aarch64/wheel/Bio/Blast copying build/lib.linux-aarch64-cpython-313/Bio/Blast/Applications.py -> build/bdist.linux-aarch64/wheel/./Bio/Blast copying build/lib.linux-aarch64-cpython-313/Bio/Blast/NCBIWWW.py -> build/bdist.linux-aarch64/wheel/./Bio/Blast copying build/lib.linux-aarch64-cpython-313/Bio/Blast/NCBIXML.py -> build/bdist.linux-aarch64/wheel/./Bio/Blast copying build/lib.linux-aarch64-cpython-313/Bio/Blast/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Blast copying build/lib.linux-aarch64-cpython-313/Bio/Blast/_parser.py -> build/bdist.linux-aarch64/wheel/./Bio/Blast copying build/lib.linux-aarch64-cpython-313/Bio/Blast/_writers.py -> build/bdist.linux-aarch64/wheel/./Bio/Blast creating build/bdist.linux-aarch64/wheel/Bio/CAPS copying build/lib.linux-aarch64-cpython-313/Bio/CAPS/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/CAPS creating build/bdist.linux-aarch64/wheel/Bio/Cluster copying build/lib.linux-aarch64-cpython-313/Bio/Cluster/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Cluster copying build/lib.linux-aarch64-cpython-313/Bio/Cluster/cluster.c -> build/bdist.linux-aarch64/wheel/./Bio/Cluster copying build/lib.linux-aarch64-cpython-313/Bio/Cluster/cluster.h -> build/bdist.linux-aarch64/wheel/./Bio/Cluster copying build/lib.linux-aarch64-cpython-313/Bio/Cluster/clustermodule.c -> build/bdist.linux-aarch64/wheel/./Bio/Cluster copying build/lib.linux-aarch64-cpython-313/Bio/Cluster/_cluster.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio/Cluster creating build/bdist.linux-aarch64/wheel/Bio/codonalign copying build/lib.linux-aarch64-cpython-313/Bio/codonalign/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/codonalign copying build/lib.linux-aarch64-cpython-313/Bio/codonalign/codonalignment.py -> build/bdist.linux-aarch64/wheel/./Bio/codonalign copying build/lib.linux-aarch64-cpython-313/Bio/codonalign/codonseq.py -> build/bdist.linux-aarch64/wheel/./Bio/codonalign creating build/bdist.linux-aarch64/wheel/Bio/Compass copying build/lib.linux-aarch64-cpython-313/Bio/Compass/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Compass creating build/bdist.linux-aarch64/wheel/Bio/Data copying build/lib.linux-aarch64-cpython-313/Bio/Data/CodonTable.py -> build/bdist.linux-aarch64/wheel/./Bio/Data copying build/lib.linux-aarch64-cpython-313/Bio/Data/IUPACData.py -> build/bdist.linux-aarch64/wheel/./Bio/Data copying build/lib.linux-aarch64-cpython-313/Bio/Data/PDBData.py -> build/bdist.linux-aarch64/wheel/./Bio/Data copying build/lib.linux-aarch64-cpython-313/Bio/Data/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Data creating build/bdist.linux-aarch64/wheel/Bio/Emboss copying build/lib.linux-aarch64-cpython-313/Bio/Emboss/Applications.py -> build/bdist.linux-aarch64/wheel/./Bio/Emboss copying build/lib.linux-aarch64-cpython-313/Bio/Emboss/Primer3.py -> build/bdist.linux-aarch64/wheel/./Bio/Emboss copying build/lib.linux-aarch64-cpython-313/Bio/Emboss/PrimerSearch.py -> build/bdist.linux-aarch64/wheel/./Bio/Emboss copying build/lib.linux-aarch64-cpython-313/Bio/Emboss/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Emboss creating build/bdist.linux-aarch64/wheel/Bio/Entrez copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/Parser.py -> build/bdist.linux-aarch64/wheel/./Bio/Entrez copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Entrez creating build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/EMBL_General.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/GenBank_General.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/HomoloGene.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-common1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-display1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-format1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-link1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-list1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-math1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-para1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-references1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-section1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/MMDB.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/MMDB.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/MMDB_Features.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Access.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_General.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Project.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NCBI_all.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NSE.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/NSE.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/OMSSA.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/PDB_General.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/PIR_General.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/PRF_General.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/SP_General.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/SP_General.mod.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/archivearticle.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/archivecustom-classes.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/archivecustom-models.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/archivecustom-modules.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/articlemeta.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/backmatter.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/chars.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/common.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/default-classes.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/default-mixes.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/display.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/eInfo_020511.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/eLink_090910.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/eLink_101123.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/ePost_020511.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/eSearch_020511.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/eSpell.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/eSummary_041029.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/egquery.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/einfo.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/elink.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/elink_020122.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/epost.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/esearch.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/esummary-v1.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/esummary_clinvar.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/esummary_gene.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/format.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/htmltable.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isoamsa.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isoamsb.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isoamsc.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isoamsn.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isoamso.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isoamsr.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isobox.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isocyr1.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isocyr2.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isodia.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isogrk1.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isogrk2.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isogrk3.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isogrk4.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isolat1.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isolat2.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isomfrk.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isomopf.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isomscr.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isonum.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isopub.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/isotech.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/journalmeta.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/link.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/list.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/math.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/mathml2.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/mathml3-qname1.mod -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/mathml3.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/mathmlsetup.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/mmlalias.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/mmlextra.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/modules.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/notat.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/para.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/phrase.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pmc-1.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_020114.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_080101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_090101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_100101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_100301.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_110101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_120101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_130101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_130501.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_140101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_150101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_180101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_180601.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/pubmed_190101.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/references.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/section.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/taxon.dtd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/xhtml-table-1.mod -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/DTDs/xmlspecchars.ent -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/DTDs creating build/bdist.linux-aarch64/wheel/Bio/Entrez/XSDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/XSDs/IPGReportSet.xsd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/XSDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/XSDs copying build/lib.linux-aarch64-cpython-313/Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd -> build/bdist.linux-aarch64/wheel/./Bio/Entrez/XSDs creating build/bdist.linux-aarch64/wheel/Bio/ExPASy copying build/lib.linux-aarch64-cpython-313/Bio/ExPASy/Enzyme.py -> build/bdist.linux-aarch64/wheel/./Bio/ExPASy copying build/lib.linux-aarch64-cpython-313/Bio/ExPASy/Prodoc.py -> build/bdist.linux-aarch64/wheel/./Bio/ExPASy copying build/lib.linux-aarch64-cpython-313/Bio/ExPASy/Prosite.py -> build/bdist.linux-aarch64/wheel/./Bio/ExPASy copying build/lib.linux-aarch64-cpython-313/Bio/ExPASy/ScanProsite.py -> build/bdist.linux-aarch64/wheel/./Bio/ExPASy copying build/lib.linux-aarch64-cpython-313/Bio/ExPASy/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/ExPASy copying build/lib.linux-aarch64-cpython-313/Bio/ExPASy/cellosaurus.py -> build/bdist.linux-aarch64/wheel/./Bio/ExPASy creating build/bdist.linux-aarch64/wheel/Bio/GenBank copying build/lib.linux-aarch64-cpython-313/Bio/GenBank/Record.py -> build/bdist.linux-aarch64/wheel/./Bio/GenBank copying build/lib.linux-aarch64-cpython-313/Bio/GenBank/Scanner.py -> build/bdist.linux-aarch64/wheel/./Bio/GenBank copying build/lib.linux-aarch64-cpython-313/Bio/GenBank/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/GenBank copying build/lib.linux-aarch64-cpython-313/Bio/GenBank/utils.py -> build/bdist.linux-aarch64/wheel/./Bio/GenBank creating build/bdist.linux-aarch64/wheel/Bio/Geo copying build/lib.linux-aarch64-cpython-313/Bio/Geo/Record.py -> build/bdist.linux-aarch64/wheel/./Bio/Geo copying build/lib.linux-aarch64-cpython-313/Bio/Geo/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Geo creating build/bdist.linux-aarch64/wheel/Bio/Graphics copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/BasicChromosome.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/ColorSpiral.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/Comparative.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/DisplayRepresentation.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/Distribution.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/KGML_vis.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics creating build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_Colors.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_Diagram.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_Feature.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_Graph.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/_Track.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-aarch64-cpython-313/Bio/Graphics/GenomeDiagram/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Graphics/GenomeDiagram creating build/bdist.linux-aarch64/wheel/Bio/HMM copying build/lib.linux-aarch64-cpython-313/Bio/HMM/DynamicProgramming.py -> build/bdist.linux-aarch64/wheel/./Bio/HMM copying build/lib.linux-aarch64-cpython-313/Bio/HMM/MarkovModel.py -> build/bdist.linux-aarch64/wheel/./Bio/HMM copying build/lib.linux-aarch64-cpython-313/Bio/HMM/Trainer.py -> build/bdist.linux-aarch64/wheel/./Bio/HMM copying build/lib.linux-aarch64-cpython-313/Bio/HMM/Utilities.py -> build/bdist.linux-aarch64/wheel/./Bio/HMM copying build/lib.linux-aarch64-cpython-313/Bio/HMM/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/HMM creating build/bdist.linux-aarch64/wheel/Bio/KEGG copying build/lib.linux-aarch64-cpython-313/Bio/KEGG/REST.py -> build/bdist.linux-aarch64/wheel/./Bio/KEGG copying build/lib.linux-aarch64-cpython-313/Bio/KEGG/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/KEGG creating build/bdist.linux-aarch64/wheel/Bio/KEGG/Compound copying build/lib.linux-aarch64-cpython-313/Bio/KEGG/Compound/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/KEGG/Compound creating build/bdist.linux-aarch64/wheel/Bio/KEGG/Enzyme copying build/lib.linux-aarch64-cpython-313/Bio/KEGG/Enzyme/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/KEGG/Enzyme creating build/bdist.linux-aarch64/wheel/Bio/KEGG/Gene copying build/lib.linux-aarch64-cpython-313/Bio/KEGG/Gene/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/KEGG/Gene creating build/bdist.linux-aarch64/wheel/Bio/KEGG/Map copying build/lib.linux-aarch64-cpython-313/Bio/KEGG/Map/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/KEGG/Map creating build/bdist.linux-aarch64/wheel/Bio/KEGG/KGML copying build/lib.linux-aarch64-cpython-313/Bio/KEGG/KGML/KGML_parser.py -> build/bdist.linux-aarch64/wheel/./Bio/KEGG/KGML copying build/lib.linux-aarch64-cpython-313/Bio/KEGG/KGML/KGML_pathway.py -> build/bdist.linux-aarch64/wheel/./Bio/KEGG/KGML copying build/lib.linux-aarch64-cpython-313/Bio/KEGG/KGML/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/KEGG/KGML creating build/bdist.linux-aarch64/wheel/Bio/PDB creating build/bdist.linux-aarch64/wheel/Bio/PDB/mmtf copying build/lib.linux-aarch64-cpython-313/Bio/PDB/mmtf/DefaultParser.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB/mmtf copying build/lib.linux-aarch64-cpython-313/Bio/PDB/mmtf/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB/mmtf copying build/lib.linux-aarch64-cpython-313/Bio/PDB/mmtf/mmtfio.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB/mmtf copying build/lib.linux-aarch64-cpython-313/Bio/PDB/AbstractPropertyMap.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/Atom.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/Chain.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/DSSP.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/Dice.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/Entity.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/FragmentMapper.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/HSExposure.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/MMCIF2Dict.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/MMCIFParser.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/Model.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/NACCESS.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/NeighborSearch.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/PDBExceptions.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/PDBIO.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/PDBList.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/PDBMLParser.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/PDBParser.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/PICIO.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/PSEA.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/Polypeptide.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/Residue.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/ResidueDepth.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/SASA.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/SCADIO.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/Selection.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/Structure.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/StructureAlignment.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/StructureBuilder.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/Superimposer.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/alphafold_db.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/binary_cif.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/cealign.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/ic_data.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/ic_rebuild.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/internal_coords.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/mmcifio.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/parse_pdb_header.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/qcprot.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/vectors.py -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/bcifhelpermodule.c -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/ccealignmodule.c -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/kdtrees.c -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/ccealign.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/kdtrees.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio/PDB copying build/lib.linux-aarch64-cpython-313/Bio/PDB/_bcif_helper.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio/PDB creating build/bdist.linux-aarch64/wheel/Bio/Medline copying build/lib.linux-aarch64-cpython-313/Bio/Medline/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Medline creating build/bdist.linux-aarch64/wheel/Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/alignace.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/clusterbuster.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/mast.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/matrix.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/meme.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/minimal.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/pfm.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/thresholds.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/transfac.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/xms.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs creating build/bdist.linux-aarch64/wheel/Bio/motifs/applications copying build/lib.linux-aarch64-cpython-313/Bio/motifs/applications/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs/applications copying build/lib.linux-aarch64-cpython-313/Bio/motifs/applications/_xxmotif.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs/applications creating build/bdist.linux-aarch64/wheel/Bio/motifs/jaspar copying build/lib.linux-aarch64-cpython-313/Bio/motifs/jaspar/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs/jaspar copying build/lib.linux-aarch64-cpython-313/Bio/motifs/jaspar/db.py -> build/bdist.linux-aarch64/wheel/./Bio/motifs/jaspar copying build/lib.linux-aarch64-cpython-313/Bio/motifs/_pwm.c -> build/bdist.linux-aarch64/wheel/./Bio/motifs copying build/lib.linux-aarch64-cpython-313/Bio/motifs/_pwm.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio/motifs creating build/bdist.linux-aarch64/wheel/Bio/Nexus copying build/lib.linux-aarch64-cpython-313/Bio/Nexus/Nexus.py -> build/bdist.linux-aarch64/wheel/./Bio/Nexus copying build/lib.linux-aarch64-cpython-313/Bio/Nexus/Nodes.py -> build/bdist.linux-aarch64/wheel/./Bio/Nexus copying build/lib.linux-aarch64-cpython-313/Bio/Nexus/StandardData.py -> build/bdist.linux-aarch64/wheel/./Bio/Nexus copying build/lib.linux-aarch64-cpython-313/Bio/Nexus/Trees.py -> build/bdist.linux-aarch64/wheel/./Bio/Nexus copying build/lib.linux-aarch64-cpython-313/Bio/Nexus/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Nexus copying build/lib.linux-aarch64-cpython-313/Bio/Nexus/cnexus.c -> build/bdist.linux-aarch64/wheel/./Bio/Nexus copying build/lib.linux-aarch64-cpython-313/Bio/Nexus/cnexus.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio/Nexus creating build/bdist.linux-aarch64/wheel/Bio/NMR copying build/lib.linux-aarch64-cpython-313/Bio/NMR/NOEtools.py -> build/bdist.linux-aarch64/wheel/./Bio/NMR copying build/lib.linux-aarch64-cpython-313/Bio/NMR/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/NMR copying build/lib.linux-aarch64-cpython-313/Bio/NMR/xpktools.py -> build/bdist.linux-aarch64/wheel/./Bio/NMR creating build/bdist.linux-aarch64/wheel/Bio/Pathway copying build/lib.linux-aarch64-cpython-313/Bio/Pathway/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Pathway creating build/bdist.linux-aarch64/wheel/Bio/Pathway/Rep copying build/lib.linux-aarch64-cpython-313/Bio/Pathway/Rep/Graph.py -> build/bdist.linux-aarch64/wheel/./Bio/Pathway/Rep copying build/lib.linux-aarch64-cpython-313/Bio/Pathway/Rep/MultiGraph.py -> build/bdist.linux-aarch64/wheel/./Bio/Pathway/Rep copying build/lib.linux-aarch64-cpython-313/Bio/Pathway/Rep/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Pathway/Rep creating build/bdist.linux-aarch64/wheel/Bio/phenotype copying build/lib.linux-aarch64-cpython-313/Bio/phenotype/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/phenotype copying build/lib.linux-aarch64-cpython-313/Bio/phenotype/phen_micro.py -> build/bdist.linux-aarch64/wheel/./Bio/phenotype copying build/lib.linux-aarch64-cpython-313/Bio/phenotype/pm_fitting.py -> build/bdist.linux-aarch64/wheel/./Bio/phenotype creating build/bdist.linux-aarch64/wheel/Bio/PopGen copying build/lib.linux-aarch64-cpython-313/Bio/PopGen/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/PopGen creating build/bdist.linux-aarch64/wheel/Bio/PopGen/GenePop copying build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop/Controller.py -> build/bdist.linux-aarch64/wheel/./Bio/PopGen/GenePop copying build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop/EasyController.py -> build/bdist.linux-aarch64/wheel/./Bio/PopGen/GenePop copying build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop/FileParser.py -> build/bdist.linux-aarch64/wheel/./Bio/PopGen/GenePop copying build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop/LargeFileParser.py -> build/bdist.linux-aarch64/wheel/./Bio/PopGen/GenePop copying build/lib.linux-aarch64-cpython-313/Bio/PopGen/GenePop/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/PopGen/GenePop creating build/bdist.linux-aarch64/wheel/Bio/Restriction copying build/lib.linux-aarch64-cpython-313/Bio/Restriction/PrintFormat.py -> build/bdist.linux-aarch64/wheel/./Bio/Restriction copying build/lib.linux-aarch64-cpython-313/Bio/Restriction/Restriction.py -> build/bdist.linux-aarch64/wheel/./Bio/Restriction copying build/lib.linux-aarch64-cpython-313/Bio/Restriction/Restriction_Dictionary.py -> build/bdist.linux-aarch64/wheel/./Bio/Restriction copying build/lib.linux-aarch64-cpython-313/Bio/Restriction/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Restriction creating build/bdist.linux-aarch64/wheel/Bio/SCOP copying build/lib.linux-aarch64-cpython-313/Bio/SCOP/Cla.py -> build/bdist.linux-aarch64/wheel/./Bio/SCOP copying build/lib.linux-aarch64-cpython-313/Bio/SCOP/Des.py -> build/bdist.linux-aarch64/wheel/./Bio/SCOP copying build/lib.linux-aarch64-cpython-313/Bio/SCOP/Dom.py -> build/bdist.linux-aarch64/wheel/./Bio/SCOP copying build/lib.linux-aarch64-cpython-313/Bio/SCOP/Hie.py -> build/bdist.linux-aarch64/wheel/./Bio/SCOP copying build/lib.linux-aarch64-cpython-313/Bio/SCOP/Raf.py -> build/bdist.linux-aarch64/wheel/./Bio/SCOP copying build/lib.linux-aarch64-cpython-313/Bio/SCOP/Residues.py -> build/bdist.linux-aarch64/wheel/./Bio/SCOP copying build/lib.linux-aarch64-cpython-313/Bio/SCOP/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SCOP creating build/bdist.linux-aarch64/wheel/Bio/SearchIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/BlatIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/FastaIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_index.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_utils.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO creating build/bdist.linux-aarch64/wheel/Bio/SearchIO/_model copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/_model copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model/_base.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/_model copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model/hit.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/_model copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model/hsp.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/_model copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/_model/query.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/_model creating build/bdist.linux-aarch64/wheel/Bio/SearchIO/BlastIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/BlastIO/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/BlastIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/BlastIO/blast_tab.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/BlastIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/BlastIO/blast_xml.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/BlastIO creating build/bdist.linux-aarch64/wheel/Bio/SearchIO/HHsuiteIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HHsuiteIO/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/HHsuiteIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/HHsuiteIO creating build/bdist.linux-aarch64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO/_base.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/HmmerIO creating build/bdist.linux-aarch64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO/_base.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/ExonerateIO creating build/bdist.linux-aarch64/wheel/Bio/SearchIO/InterproscanIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/InterproscanIO/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/InterproscanIO copying build/lib.linux-aarch64-cpython-313/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/bdist.linux-aarch64/wheel/./Bio/SearchIO/InterproscanIO creating build/bdist.linux-aarch64/wheel/Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/AbiIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/AceIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/FastaIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/GckIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/GfaIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/IgIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/InsdcIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/Interfaces.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/NibIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/PdbIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/PhdIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/PirIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/QualityIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/SeqXmlIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/SffIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/SnapGeneIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/SwissIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/TabIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/TwoBitIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/UniprotIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/XdnaIO.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/_index.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/_twoBitIO.c -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO copying build/lib.linux-aarch64-cpython-313/Bio/SeqIO/_twoBitIO.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio/SeqIO creating build/bdist.linux-aarch64/wheel/Bio/SeqUtils copying build/lib.linux-aarch64-cpython-313/Bio/SeqUtils/CheckSum.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqUtils copying build/lib.linux-aarch64-cpython-313/Bio/SeqUtils/IsoelectricPoint.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqUtils copying build/lib.linux-aarch64-cpython-313/Bio/SeqUtils/MeltingTemp.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqUtils copying build/lib.linux-aarch64-cpython-313/Bio/SeqUtils/ProtParam.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqUtils copying build/lib.linux-aarch64-cpython-313/Bio/SeqUtils/ProtParamData.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqUtils copying build/lib.linux-aarch64-cpython-313/Bio/SeqUtils/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqUtils copying build/lib.linux-aarch64-cpython-313/Bio/SeqUtils/lcc.py -> build/bdist.linux-aarch64/wheel/./Bio/SeqUtils creating build/bdist.linux-aarch64/wheel/Bio/Sequencing copying build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Ace.py -> build/bdist.linux-aarch64/wheel/./Bio/Sequencing copying build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Phd.py -> build/bdist.linux-aarch64/wheel/./Bio/Sequencing copying build/lib.linux-aarch64-cpython-313/Bio/Sequencing/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Sequencing creating build/bdist.linux-aarch64/wheel/Bio/Sequencing/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Applications/_Novoalign.py -> build/bdist.linux-aarch64/wheel/./Bio/Sequencing/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Applications/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Sequencing/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Applications/_bwa.py -> build/bdist.linux-aarch64/wheel/./Bio/Sequencing/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Sequencing/Applications/_samtools.py -> build/bdist.linux-aarch64/wheel/./Bio/Sequencing/Applications creating build/bdist.linux-aarch64/wheel/Bio/SVDSuperimposer copying build/lib.linux-aarch64-cpython-313/Bio/SVDSuperimposer/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SVDSuperimposer creating build/bdist.linux-aarch64/wheel/Bio/SwissProt copying build/lib.linux-aarch64-cpython-313/Bio/SwissProt/KeyWList.py -> build/bdist.linux-aarch64/wheel/./Bio/SwissProt copying build/lib.linux-aarch64-cpython-313/Bio/SwissProt/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/SwissProt creating build/bdist.linux-aarch64/wheel/Bio/TogoWS copying build/lib.linux-aarch64-cpython-313/Bio/TogoWS/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/TogoWS creating build/bdist.linux-aarch64/wheel/Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/BaseTree.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/CDAO.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/CDAOIO.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/Consensus.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/NeXML.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/NeXMLIO.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/Newick.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/NewickIO.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/NexusIO.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PhyloXML.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PhyloXMLIO.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/TreeConstruction.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/_cdao_owl.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/_io.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/_utils.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo creating build/bdist.linux-aarch64/wheel/Bio/Phylo/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/Applications/_Fasttree.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/Applications/_Phyml.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/Applications/_Raxml.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/Applications copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/Applications/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/Applications creating build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/PAML copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML/_paml.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/PAML copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML/_parse_baseml.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/PAML copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML/_parse_codeml.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/PAML copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML/_parse_yn00.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/PAML copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML/baseml.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/PAML copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML/chi2.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/PAML copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML/codeml.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/PAML copying build/lib.linux-aarch64-cpython-313/Bio/Phylo/PAML/yn00.py -> build/bdist.linux-aarch64/wheel/./Bio/Phylo/PAML creating build/bdist.linux-aarch64/wheel/Bio/UniGene copying build/lib.linux-aarch64-cpython-313/Bio/UniGene/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/UniGene creating build/bdist.linux-aarch64/wheel/Bio/UniProt copying build/lib.linux-aarch64-cpython-313/Bio/UniProt/GOA.py -> build/bdist.linux-aarch64/wheel/./Bio/UniProt copying build/lib.linux-aarch64-cpython-313/Bio/UniProt/__init__.py -> build/bdist.linux-aarch64/wheel/./Bio/UniProt copying build/lib.linux-aarch64-cpython-313/Bio/cpairwise2module.c -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/py.typed -> build/bdist.linux-aarch64/wheel/./Bio copying build/lib.linux-aarch64-cpython-313/Bio/cpairwise2.cpython-313-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/./Bio creating build/bdist.linux-aarch64/wheel/BioSQL copying build/lib.linux-aarch64-cpython-313/BioSQL/BioSeq.py -> build/bdist.linux-aarch64/wheel/./BioSQL copying build/lib.linux-aarch64-cpython-313/BioSQL/BioSeqDatabase.py -> build/bdist.linux-aarch64/wheel/./BioSQL copying build/lib.linux-aarch64-cpython-313/BioSQL/DBUtils.py -> build/bdist.linux-aarch64/wheel/./BioSQL copying build/lib.linux-aarch64-cpython-313/BioSQL/Loader.py -> build/bdist.linux-aarch64/wheel/./BioSQL copying build/lib.linux-aarch64-cpython-313/BioSQL/__init__.py -> build/bdist.linux-aarch64/wheel/./BioSQL copying build/lib.linux-aarch64-cpython-313/BioSQL/py.typed -> build/bdist.linux-aarch64/wheel/./BioSQL running install_egg_info Copying biopython.egg-info to build/bdist.linux-aarch64/wheel/./biopython-1.84-py3.13.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/biopython-1.84.dist-info/WHEEL creating '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-wheel-ynd1w7if/.tmp-isa6t683/biopython-1.84-cp313-cp313-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it adding 'Bio/File.py' adding 'Bio/LogisticRegression.py' adding 'Bio/MarkovModel.py' adding 'Bio/MaxEntropy.py' adding 'Bio/NaiveBayes.py' adding 'Bio/Seq.py' adding 'Bio/SeqFeature.py' adding 'Bio/SeqRecord.py' adding 'Bio/__init__.py' adding 'Bio/_utils.py' adding 'Bio/bgzf.py' adding 'Bio/cpairwise2.cpython-313-aarch64-linux-gnu.so' adding 'Bio/cpairwise2module.c' adding 'Bio/kNN.py' adding 'Bio/pairwise2.py' adding 'Bio/py.typed' adding 'Bio/Affy/CelFile.py' adding 'Bio/Affy/__init__.py' adding 'Bio/Align/AlignInfo.py' adding 'Bio/Align/__init__.py' adding 'Bio/Align/_aligncore.c' adding 'Bio/Align/_aligncore.cpython-313-aarch64-linux-gnu.so' adding 'Bio/Align/_codonaligner.c' adding 'Bio/Align/_codonaligner.cpython-313-aarch64-linux-gnu.so' adding 'Bio/Align/_pairwisealigner.c' adding 'Bio/Align/_pairwisealigner.cpython-313-aarch64-linux-gnu.so' adding 'Bio/Align/a2m.py' adding 'Bio/Align/analysis.py' adding 'Bio/Align/bed.py' adding 'Bio/Align/bigbed.py' adding 'Bio/Align/bigmaf.py' adding 'Bio/Align/bigpsl.py' adding 'Bio/Align/chain.py' adding 'Bio/Align/clustal.py' adding 'Bio/Align/emboss.py' adding 'Bio/Align/exonerate.py' adding 'Bio/Align/fasta.py' adding 'Bio/Align/hhr.py' adding 'Bio/Align/interfaces.py' adding 'Bio/Align/maf.py' adding 'Bio/Align/mauve.py' adding 'Bio/Align/msf.py' adding 'Bio/Align/nexus.py' adding 'Bio/Align/phylip.py' adding 'Bio/Align/psl.py' adding 'Bio/Align/sam.py' adding 'Bio/Align/stockholm.py' adding 'Bio/Align/tabular.py' adding 'Bio/Align/Applications/_ClustalOmega.py' adding 'Bio/Align/Applications/_Clustalw.py' adding 'Bio/Align/Applications/_Dialign.py' adding 'Bio/Align/Applications/_MSAProbs.py' adding 'Bio/Align/Applications/_Mafft.py' adding 'Bio/Align/Applications/_Muscle.py' adding 'Bio/Align/Applications/_Prank.py' adding 'Bio/Align/Applications/_Probcons.py' adding 'Bio/Align/Applications/_TCoffee.py' adding 'Bio/Align/Applications/__init__.py' adding 'Bio/Align/substitution_matrices/__init__.py' adding 'Bio/Align/substitution_matrices/data/BENNER22' adding 'Bio/Align/substitution_matrices/data/BENNER6' adding 'Bio/Align/substitution_matrices/data/BENNER74' adding 'Bio/Align/substitution_matrices/data/BLASTN' adding 'Bio/Align/substitution_matrices/data/BLASTP' adding 'Bio/Align/substitution_matrices/data/BLOSUM45' adding 'Bio/Align/substitution_matrices/data/BLOSUM50' adding 'Bio/Align/substitution_matrices/data/BLOSUM62' adding 'Bio/Align/substitution_matrices/data/BLOSUM80' adding 'Bio/Align/substitution_matrices/data/BLOSUM90' adding 'Bio/Align/substitution_matrices/data/DAYHOFF' adding 'Bio/Align/substitution_matrices/data/FENG' adding 'Bio/Align/substitution_matrices/data/GENETIC' adding 'Bio/Align/substitution_matrices/data/GONNET1992' adding 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'Bio/PDB/__init__.py' adding 'Bio/PDB/_bcif_helper.cpython-313-aarch64-linux-gnu.so' adding 'Bio/PDB/alphafold_db.py' adding 'Bio/PDB/bcifhelpermodule.c' adding 'Bio/PDB/binary_cif.py' adding 'Bio/PDB/ccealign.cpython-313-aarch64-linux-gnu.so' adding 'Bio/PDB/ccealignmodule.c' adding 'Bio/PDB/cealign.py' adding 'Bio/PDB/ic_data.py' adding 'Bio/PDB/ic_rebuild.py' adding 'Bio/PDB/internal_coords.py' adding 'Bio/PDB/kdtrees.c' adding 'Bio/PDB/kdtrees.cpython-313-aarch64-linux-gnu.so' adding 'Bio/PDB/mmcifio.py' adding 'Bio/PDB/parse_pdb_header.py' adding 'Bio/PDB/qcprot.py' adding 'Bio/PDB/vectors.py' adding 'Bio/PDB/mmtf/DefaultParser.py' adding 'Bio/PDB/mmtf/__init__.py' adding 'Bio/PDB/mmtf/mmtfio.py' adding 'Bio/Pathway/__init__.py' adding 'Bio/Pathway/Rep/Graph.py' adding 'Bio/Pathway/Rep/MultiGraph.py' adding 'Bio/Pathway/Rep/__init__.py' adding 'Bio/Phylo/BaseTree.py' adding 'Bio/Phylo/CDAO.py' adding 'Bio/Phylo/CDAOIO.py' adding 'Bio/Phylo/Consensus.py' adding 'Bio/Phylo/NeXML.py' adding 'Bio/Phylo/NeXMLIO.py' adding 'Bio/Phylo/Newick.py' adding 'Bio/Phylo/NewickIO.py' adding 'Bio/Phylo/NexusIO.py' adding 'Bio/Phylo/PhyloXML.py' adding 'Bio/Phylo/PhyloXMLIO.py' adding 'Bio/Phylo/TreeConstruction.py' adding 'Bio/Phylo/__init__.py' adding 'Bio/Phylo/_cdao_owl.py' adding 'Bio/Phylo/_io.py' adding 'Bio/Phylo/_utils.py' adding 'Bio/Phylo/Applications/_Fasttree.py' adding 'Bio/Phylo/Applications/_Phyml.py' adding 'Bio/Phylo/Applications/_Raxml.py' adding 'Bio/Phylo/Applications/__init__.py' adding 'Bio/Phylo/PAML/__init__.py' adding 'Bio/Phylo/PAML/_paml.py' adding 'Bio/Phylo/PAML/_parse_baseml.py' adding 'Bio/Phylo/PAML/_parse_codeml.py' adding 'Bio/Phylo/PAML/_parse_yn00.py' adding 'Bio/Phylo/PAML/baseml.py' adding 'Bio/Phylo/PAML/chi2.py' adding 'Bio/Phylo/PAML/codeml.py' adding 'Bio/Phylo/PAML/yn00.py' adding 'Bio/PopGen/__init__.py' adding 'Bio/PopGen/GenePop/Controller.py' adding 'Bio/PopGen/GenePop/EasyController.py' adding 'Bio/PopGen/GenePop/FileParser.py' adding 'Bio/PopGen/GenePop/LargeFileParser.py' adding 'Bio/PopGen/GenePop/__init__.py' adding 'Bio/Restriction/PrintFormat.py' adding 'Bio/Restriction/Restriction.py' adding 'Bio/Restriction/Restriction_Dictionary.py' adding 'Bio/Restriction/__init__.py' adding 'Bio/SCOP/Cla.py' adding 'Bio/SCOP/Des.py' adding 'Bio/SCOP/Dom.py' adding 'Bio/SCOP/Hie.py' adding 'Bio/SCOP/Raf.py' adding 'Bio/SCOP/Residues.py' adding 'Bio/SCOP/__init__.py' adding 'Bio/SVDSuperimposer/__init__.py' adding 'Bio/SearchIO/BlatIO.py' adding 'Bio/SearchIO/FastaIO.py' adding 'Bio/SearchIO/__init__.py' adding 'Bio/SearchIO/_index.py' adding 'Bio/SearchIO/_utils.py' adding 'Bio/SearchIO/BlastIO/__init__.py' adding 'Bio/SearchIO/BlastIO/blast_tab.py' adding 'Bio/SearchIO/BlastIO/blast_xml.py' adding 'Bio/SearchIO/ExonerateIO/__init__.py' adding 'Bio/SearchIO/ExonerateIO/_base.py' adding 'Bio/SearchIO/ExonerateIO/exonerate_cigar.py' adding 'Bio/SearchIO/ExonerateIO/exonerate_text.py' adding 'Bio/SearchIO/ExonerateIO/exonerate_vulgar.py' adding 'Bio/SearchIO/HHsuiteIO/__init__.py' adding 'Bio/SearchIO/HHsuiteIO/hhsuite2_text.py' adding 'Bio/SearchIO/HmmerIO/__init__.py' adding 'Bio/SearchIO/HmmerIO/_base.py' adding 'Bio/SearchIO/HmmerIO/hmmer2_text.py' adding 'Bio/SearchIO/HmmerIO/hmmer3_domtab.py' adding 'Bio/SearchIO/HmmerIO/hmmer3_tab.py' adding 'Bio/SearchIO/HmmerIO/hmmer3_text.py' adding 'Bio/SearchIO/InterproscanIO/__init__.py' adding 'Bio/SearchIO/InterproscanIO/interproscan_xml.py' adding 'Bio/SearchIO/_model/__init__.py' adding 'Bio/SearchIO/_model/_base.py' adding 'Bio/SearchIO/_model/hit.py' adding 'Bio/SearchIO/_model/hsp.py' adding 'Bio/SearchIO/_model/query.py' adding 'Bio/SeqIO/AbiIO.py' adding 'Bio/SeqIO/AceIO.py' adding 'Bio/SeqIO/FastaIO.py' adding 'Bio/SeqIO/GckIO.py' adding 'Bio/SeqIO/GfaIO.py' adding 'Bio/SeqIO/IgIO.py' adding 'Bio/SeqIO/InsdcIO.py' adding 'Bio/SeqIO/Interfaces.py' adding 'Bio/SeqIO/NibIO.py' adding 'Bio/SeqIO/PdbIO.py' adding 'Bio/SeqIO/PhdIO.py' adding 'Bio/SeqIO/PirIO.py' adding 'Bio/SeqIO/QualityIO.py' adding 'Bio/SeqIO/SeqXmlIO.py' adding 'Bio/SeqIO/SffIO.py' adding 'Bio/SeqIO/SnapGeneIO.py' adding 'Bio/SeqIO/SwissIO.py' adding 'Bio/SeqIO/TabIO.py' adding 'Bio/SeqIO/TwoBitIO.py' adding 'Bio/SeqIO/UniprotIO.py' adding 'Bio/SeqIO/XdnaIO.py' adding 'Bio/SeqIO/__init__.py' adding 'Bio/SeqIO/_index.py' adding 'Bio/SeqIO/_twoBitIO.c' adding 'Bio/SeqIO/_twoBitIO.cpython-313-aarch64-linux-gnu.so' adding 'Bio/SeqUtils/CheckSum.py' adding 'Bio/SeqUtils/IsoelectricPoint.py' adding 'Bio/SeqUtils/MeltingTemp.py' adding 'Bio/SeqUtils/ProtParam.py' adding 'Bio/SeqUtils/ProtParamData.py' adding 'Bio/SeqUtils/__init__.py' adding 'Bio/SeqUtils/lcc.py' adding 'Bio/Sequencing/Ace.py' adding 'Bio/Sequencing/Phd.py' adding 'Bio/Sequencing/__init__.py' adding 'Bio/Sequencing/Applications/_Novoalign.py' adding 'Bio/Sequencing/Applications/__init__.py' adding 'Bio/Sequencing/Applications/_bwa.py' adding 'Bio/Sequencing/Applications/_samtools.py' adding 'Bio/SwissProt/KeyWList.py' adding 'Bio/SwissProt/__init__.py' adding 'Bio/TogoWS/__init__.py' adding 'Bio/UniGene/__init__.py' adding 'Bio/UniProt/GOA.py' adding 'Bio/UniProt/__init__.py' adding 'Bio/codonalign/__init__.py' adding 'Bio/codonalign/codonalignment.py' adding 'Bio/codonalign/codonseq.py' adding 'Bio/motifs/__init__.py' adding 'Bio/motifs/_pwm.c' adding 'Bio/motifs/_pwm.cpython-313-aarch64-linux-gnu.so' adding 'Bio/motifs/alignace.py' adding 'Bio/motifs/clusterbuster.py' adding 'Bio/motifs/mast.py' adding 'Bio/motifs/matrix.py' adding 'Bio/motifs/meme.py' adding 'Bio/motifs/minimal.py' adding 'Bio/motifs/pfm.py' adding 'Bio/motifs/thresholds.py' adding 'Bio/motifs/transfac.py' adding 'Bio/motifs/xms.py' adding 'Bio/motifs/applications/__init__.py' adding 'Bio/motifs/applications/_xxmotif.py' adding 'Bio/motifs/jaspar/__init__.py' adding 'Bio/motifs/jaspar/db.py' adding 'Bio/phenotype/__init__.py' adding 'Bio/phenotype/phen_micro.py' adding 'Bio/phenotype/pm_fitting.py' adding 'BioSQL/BioSeq.py' adding 'BioSQL/BioSeqDatabase.py' adding 'BioSQL/DBUtils.py' adding 'BioSQL/Loader.py' adding 'BioSQL/__init__.py' adding 'BioSQL/py.typed' adding 'biopython-1.84.dist-info/LICENSE' adding 'biopython-1.84.dist-info/LICENSE.rst' adding 'biopython-1.84.dist-info/METADATA' adding 'biopython-1.84.dist-info/WHEEL' adding 'biopython-1.84.dist-info/top_level.txt' adding 'biopython-1.84.dist-info/RECORD' removing build/bdist.linux-aarch64/wheel Building wheel for biopython (pyproject.toml): finished with status 'done' Created wheel for biopython: filename=biopython-1.84-cp313-cp313-linux_aarch64.whl size=3151294 sha256=8a795c17190bbde5f50edb1453b7c02c972b1a119ebbfd67d14209fbe029231c Stored in directory: /builddir/.cache/pip/wheels/fa/1c/1f/5139d73471cb8006e195b0c98d34603006f6d66d4eae28da02 Successfully built biopython + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.EWJS9J + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + '[' /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT ++ dirname /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build + mkdir /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 biopython-1.84 ++ ls /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir/biopython-1.84-cp313-cp313-linux_aarch64.whl ++ xargs basename --multiple ++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/' + specifier=biopython==1.84 + '[' -z biopython==1.84 ']' + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + /usr/bin/python3 -m pip install --root /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT --prefix /usr --no-deps --disable-pip-version-check --progress-bar off --verbose --ignore-installed --no-warn-script-location --no-index --no-cache-dir --find-links /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir biopython==1.84 Using pip 24.3.1 from /usr/lib/python3.13/site-packages/pip (python 3.13) Looking in links: /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir Processing ./pyproject-wheeldir/biopython-1.84-cp313-cp313-linux_aarch64.whl Installing collected packages: biopython Successfully installed biopython-1.84 + '[' -d /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin ']' + rm -f /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages ']' + '[' /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages '!=' /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages ']' + '[' -d /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages ']' + site_dirs+=("/usr/lib64/python3.13/site-packages") + for site_dir in ${site_dirs[@]} + for distinfo in /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT$site_dir/*.dist-info + echo '%ghost /usr/lib64/python3.13/site-packages/biopython-1.84.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/INSTALLER + PYTHONPATH=/usr/lib/rpm/redhat + /usr/bin/python3 -B /usr/lib/rpm/redhat/pyproject_preprocess_record.py --buildroot /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT --record /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/RECORD --output /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-record + rm -fv /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/RECORD removed '/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/RECORD' + rm -fv /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/REQUESTED removed '/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/REQUESTED' ++ wc -l /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-ghost-distinfo ++ cut -f1 '-d ' + lines=1 + '[' 1 -ne 1 ']' + RPM_FILES_ESCAPE=4.19 + /usr/bin/python3 /usr/lib/rpm/redhat/pyproject_save_files.py --output-files /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-files --output-modules /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-modules --buildroot /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT --sitelib /usr/lib/python3.13/site-packages --sitearch /usr/lib64/python3.13/site-packages --python-version 3.13 --pyproject-record /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.aarch64-pyproject-record --prefix /usr Bio BioSQL + /usr/bin/find-debuginfo -j12 --strict-build-id -m -i --build-id-seed 1.84-3.fc42 --unique-debug-suffix -1.84-3.fc42.aarch64 --unique-debug-src-base python-biopython-1.84-3.fc42.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84 find-debuginfo: starting Extracting debug info from 11 files DWARF-compressing 11 files sepdebugcrcfix: Updated 11 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-1.84-3.fc42.aarch64 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 -j12 Bytecompiling .py files below /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13 using python3.13 Bytecompiling .py files below /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.13 using python3.13 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j12 /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Affy/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/Applications/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/Applications/__pycache__/_TCoffee.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/Applications/__pycache__/_Probcons.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/Applications/__pycache__/_MSAProbs.cpython-313.pyc: rewriting with normalized contents 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/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/__pycache__/Seq.cpython-313.pyc: replacing with normalized version /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/__pycache__/SeqFeature.cpython-313.opt-1.pyc: replacing with normalized version Scanned 159 directories and 1362 files, processed 438 inodes, 438 modified (220 replaced + 218 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/python-biopython-1.84-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.6ISWKp + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-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 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS ~/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests ~/build/BUILD/python-biopython-1.84-build/biopython-1.84 + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 biopython-1.84 + pushd Tests ++ grep -v test_Align_bigbed.py ++ grep -v test_Tutorial.py ++ 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_chain.py test_Align_clustal.py test_Align_codonalign.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_Blast_parser.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_NCBIXML.py test_NCBI_BLAST_tools.py test_NCBI_qblast.py test_NMR.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDB_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_PDBList.py test_PDB_PDBMLParser.py test_PDB_PDBParser.py test_PDB_PSEA.py test_PDB_Polypeptide.py test_PDB_QCPSuperimposer.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_alphafold_db.py test_PDB_binary_cif.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_igraph.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_SVDSuperimposer.py test_SearchIO_blast_tab.py test_SearchIO_blast_tab_index.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_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_Gfa.py test_SeqIO_Insdc.py test_SeqIO_NibIO.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_SnapGene.py test_SeqIO_TwoBitIO.py test_SeqIO_Xdna.py test_SeqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_UniProt.py test_UniProt_GOA.py test_UniProt_Parser.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 + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.063 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.034 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 2.427 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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_empty (test_AlignIO_ClustalIO.TestClustalIO.test_empty) 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 0.064 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.063 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.074 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.097 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.063 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.175 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.108 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_Alignment.py test_Align_Alignment ... ok test_mapall (test_Align_Alignment.TestAlign_mapall.test_mapall) ... ok test_nucleotide_nucleotide_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_nucleotide_nucleotide_str) ... ok test_protein_nucleotide_many_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_protein_nucleotide_many_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_add (test_Align_Alignment.TestMultipleAlignment.test_add) ... 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_add (test_Align_Alignment.TestPairwiseAlignment.test_add) ... ok test_aligned_indices (test_Align_Alignment.TestPairwiseAlignment.test_aligned_indices) ... ok test_indexing_slicing (test_Align_Alignment.TestPairwiseAlignment.test_indexing_slicing) ... ok test_reverse_complement (test_Align_Alignment.TestPairwiseAlignment.test_reverse_complement) ... 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 0.357 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.090 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 test_reading (test_Align_bed.TestAlign_searching.test_reading) Test reading bigbedtest.bed. ... ok test_writing (test_Align_bed.TestAlign_searching.test_writing) Test writing bigbedtest.bed. ... ok test_format (test_Align_bed.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.187 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bigmaf.py test_Align_bigmaf ... ok test_reading (test_Align_bigmaf.TestAlign_bundle_without_target.test_reading) Test parsing bundle_without_target.bb. ... ok test_writing (test_Align_bigmaf.TestAlign_bundle_without_target.test_writing) Test writing bundle_without_target.bb. ... ok test_declaration (test_Align_bigmaf.TestAlign_declaration.test_declaration) ... 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 test_reading (test_Align_bigmaf.TestAlign_ucsc_mm9_chr10.test_reading) Test parsing file ucsc_mm9_chr10.bb. ... ok test_writing (test_Align_bigmaf.TestAlign_ucsc_mm9_chr10.test_writing) Test writing file ucsc_mm9_chr10.bb. ... ok test_reading (test_Align_bigmaf.TestAlign_ucsc_test.test_reading) Test reading ucsc_test.bb. ... ok test_writing (test_Align_bigmaf.TestAlign_ucsc_test.test_writing) Test writing ucsc_test.bb. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.529 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bigpsl.py test_Align_bigpsl ... ok test_reading (test_Align_bigpsl.TestAlign_bigpsl.test_reading) Test parsing bigPsl.bb. ... ok test_writing (test_Align_bigpsl.TestAlign_bigpsl.test_writing) Test writing bigPsl.bb. ... ok test_declaration (test_Align_bigpsl.TestAlign_declaration.test_declaration) ... 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_writing_psl_34_001 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_001) Test writing psl_34_001.psl.bb. ... ok test_writing_psl_34_003 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_003) Test writing psl_34_003.psl.bb. ... ok test_writing_psl_34_004 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_004) Test writing psl_34_004.psl.bb. ... ok test_writing_psl_34_005 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_005) Test writing psl_34_005.psl.bb. ... ok test_reading (test_Align_bigpsl.TestAlign_dna_rna.test_reading) Test parsing dna_rna.psl.bb. ... ok test_writing (test_Align_bigpsl.TestAlign_dna_rna.test_writing) Test writing 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_writing_psl_35_001 (test_Align_bigpsl.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing psl_35_001.psl.bb. ... ok test_writing_psl_35_002 (test_Align_bigpsl.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing 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 0.452 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_chain.py test_Align_chain ... ok test_reading_chain_34_002 (test_Align_chain.TestAlign_dna.test_reading_chain_34_002) Test parsing psl_34_002.chain. ... ok test_reading_psl_34_001 (test_Align_chain.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.chain. ... ok test_reading_psl_34_003 (test_Align_chain.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.chain. ... ok test_reading_psl_34_004 (test_Align_chain.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.chain. ... ok test_reading_psl_34_005 (test_Align_chain.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.chain. ... ok test_writing_chain_34_001 (test_Align_chain.TestAlign_dna.test_writing_chain_34_001) Test writing the alignments in psl_34_001.chain. ... ok test_writing_psl_34_002 (test_Align_chain.TestAlign_dna.test_writing_psl_34_002) Test writing the alignments in psl_34_002.chain. ... ok test_writing_psl_34_003 (test_Align_chain.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.chain. ... ok test_writing_psl_34_004 (test_Align_chain.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.chain. ... ok test_writing_psl_34_005 (test_Align_chain.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.chain. ... ok test_reading (test_Align_chain.TestAlign_dna_rna.test_reading) Test parsing dna_rna.chain. ... ok test_writing (test_Align_chain.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.chain. ... ok test_format (test_Align_chain.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.193 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.093 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_codonalign.py test_Align_codonalign ... ok test_aligner (test_Align_codonalign.TestBasic.test_aligner) ... ok test_alignments (test_Align_codonalign.TestBasic.test_alignments) ... ok test1 (test_Align_codonalign.TestBuildAndIO.test1) ... ok test2 (test_Align_codonalign.TestBuildAndIO.test2) ... ok test3 (test_Align_codonalign.TestBuildAndIO.test3) ... ok test4 (test_Align_codonalign.TestBuildAndIO.test4) ... ok test5 (test_Align_codonalign.TestBuildAndIO.test5) ... ok test_mk (test_Align_codonalign.Test_MK.test_mk) ... ok test_build1 (test_Align_codonalign.Test_build.test_build1) ... ok test_build2 (test_Align_codonalign.Test_build.test_build2) ... ok test_build3 (test_Align_codonalign.Test_build.test_build3) ... ok test_dn_ds (test_Align_codonalign.Test_dn_ds.test_dn_ds) ... ok ---------------------------------------------------------------------- Ran 1 test in 3.084 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.103 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.155 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.091 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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_reading (test_Align_hhr.Align_hhr_7rbx_A_hhsearch_trunc.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 0.344 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.827 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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_empty (test_Align_mauve.TestMauveBasic.test_empty) ... ok test_parse (test_Align_mauve.TestSeparateFiles.test_parse) ... ok test_write_read (test_Align_mauve.TestSeparateFiles.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.119 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_msf.py test_Align_msf ... ok test_empty (test_Align_msf.TestMSF.test_empty) Checking empty file. ... ok test_protein1 (test_Align_msf.TestMSF.test_protein1) ... ok test_protein2 (test_Align_msf.TestMSF.test_protein2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.069 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 0.108 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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_interlaced (test_Align_phylip.TestPhylipReading.test_interlaced) ... ok test_interlaced2 (test_Align_phylip.TestPhylipReading.test_interlaced2) ... ok test_one (test_Align_phylip.TestPhylipReading.test_one) ... ok test_sequential (test_Align_phylip.TestPhylipReading.test_sequential) ... ok test_sequential2 (test_Align_phylip.TestPhylipReading.test_sequential2) ... ok test_two_and_three (test_Align_phylip.TestPhylipReading.test_two_and_three) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.121 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -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 test_format (test_Align_psl.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.408 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_sam.py test_Align_sam ... ok test_4D8I6M (test_Align_sam.TestAlign_clipping.test_4D8I6M) Test alignment starting with deletion followed by insertion. ... ok test_4I8D6M (test_Align_sam.TestAlign_clipping.test_4I8D6M) Test alignment starting with insertion followed by deletion. ... ok test_4S6M (test_Align_sam.TestAlign_clipping.test_4S6M) Test alignment starting with soft clip at non-zero position. ... ok test_4S8D6M (test_Align_sam.TestAlign_clipping.test_4S8D6M) Test alignment starting with soft clip followed by deletion. ... ok test_4S8I6M (test_Align_sam.TestAlign_clipping.test_4S8I6M) Test alignment starting with soft clip followed by insertion. ... ok test_6M (test_Align_sam.TestAlign_clipping.test_6M) Test alignment starting at non-zero position. ... ok test_8D6M_ex1 (test_Align_sam.TestAlign_clipping.test_8D6M_ex1) Test alignment starting with deletion. ... ok test_8D6M_ex2 (test_Align_sam.TestAlign_clipping.test_8D6M_ex2) Test alignment starting with deletion at non-zero position. ... ok test_8I6M_ex1 (test_Align_sam.TestAlign_clipping.test_8I6M_ex1) Test alignment starting with insertion. ... ok test_8I6M_ex2 (test_Align_sam.TestAlign_clipping.test_8I6M_ex2) Test alignment starting with insertion at non-zero position. ... ok test_8S6M (test_Align_sam.TestAlign_clipping.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 test_format (test_Align_sam.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.367 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=12 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_stockholm.py test_Align_stockholm ... FAIL test_io_nonstandard_annotations (test_Align_stockholm.TestStockholm_reading.test_io_nonstandard_annotations) Test input and output of nonstandard GC, GS and GR annotation lines. ... ERROR test_reading_alignments_cath1 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath1) Test parsing CATH record 3.30.160.60/FF/004774. ... ERROR test_reading_alignments_cath2 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath2) Test parsing CATH record 2.105.10.10/FF/000002. ... ERROR test_reading_alignments_cath3 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath3) Test parsing CATH record 1.10.275.10/FF/000026. ... ERROR test_reading_example (test_Align_stockholm.TestStockholm_reading.test_reading_example) Test parsing Pfam record HAT as the docstring example. ... ERROR test_reading_writing_alignments_globins45 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_globins45) Test parsing hmmalign output. ... ERROR test_reading_writing_alignments_pfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam1) Test parsing Pfam record 120_Rick_ant. ... ERROR test_reading_writing_alignments_pfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam2) Test parsing Pfam record 7kD_DNA_binding. ... ERROR test_reading_writing_alignments_pfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam3) Test parsing Pfam record 12TM_1. ... ERROR test_reading_writing_alignments_pfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam4) Test parsing Pfam record 3Beta_HSD. ... ERROR test_reading_writing_alignments_pfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam5) Test parsing Pfam record ArsP_1. ... ERROR test_reading_writing_alignments_pfam6 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam6) Test parsing Pfam record COX2_TM. ... ERROR test_reading_writing_alignments_pfam7 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam7) Test parsing Pfam record Alpha_E1_glycop. ... ERROR test_reading_writing_alignments_pfam8 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam8) Test parsing Pfam record Cyclin_N. ... ERROR test_reading_writing_alignments_pfam9 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam9) Test parsing Pfam record SH3_11. ... ERROR test_reading_writing_alignments_rfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam1) Test parsing Rfam record BTnc005. ... ERROR test_reading_writing_alignments_rfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam2) Test parsing Rfam record SraC_RyeA. ... ERROR test_reading_writing_alignments_rfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam3) Test parsing Rfam record McaS. ... ERROR test_reading_writing_alignments_rfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam4) Test parsing Rfam record IRES_KSHV. ... ERROR test_reading_writing_alignments_rfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam5) Test parsing Rfam record BMV3_UPD-PK3. ... ERROR ====================================================================== ERROR: test_io_nonstandard_annotations (test_Align_stockholm.TestStockholm_reading.test_io_nonstandard_annotations) Test input and output of nonstandard GC, GS and GR annotation lines. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6696, in test_io_nonstandard_annotations alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_alignments_cath1 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath1) Test parsing CATH record 3.30.160.60/FF/004774. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6556, in test_reading_alignments_cath1 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_alignments_cath2 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath2) Test parsing CATH record 2.105.10.10/FF/000002. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6564, in test_reading_alignments_cath2 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_alignments_cath3 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath3) Test parsing CATH record 1.10.275.10/FF/000026. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6606, in test_reading_alignments_cath3 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_example (test_Align_stockholm.TestStockholm_reading.test_reading_example) Test parsing Pfam record HAT as the docstring example. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 26, in test_reading_example alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_globins45 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_globins45) Test parsing hmmalign output. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 5902, in test_reading_writing_alignments_globins45 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam1) Test parsing Pfam record 120_Rick_ant. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 5931, in test_reading_writing_alignments_pfam1 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam2) Test parsing Pfam record 7kD_DNA_binding. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6037, in test_reading_writing_alignments_pfam2 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam3) Test parsing Pfam record 12TM_1. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6097, in test_reading_writing_alignments_pfam3 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam4) Test parsing Pfam record 3Beta_HSD. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6115, in test_reading_writing_alignments_pfam4 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam5) Test parsing Pfam record ArsP_1. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6131, in test_reading_writing_alignments_pfam5 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam6 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam6) Test parsing Pfam record COX2_TM. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6147, in test_reading_writing_alignments_pfam6 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam7 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam7) Test parsing Pfam record Alpha_E1_glycop. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6163, in test_reading_writing_alignments_pfam7 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam8 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam8) Test parsing Pfam record Cyclin_N. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6179, in test_reading_writing_alignments_pfam8 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam9 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam9) Test parsing Pfam record SH3_11. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6195, in test_reading_writing_alignments_pfam9 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_rfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam1) Test parsing Rfam record BTnc005. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6238, in test_reading_writing_alignments_rfam1 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_rfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam2) Test parsing Rfam record SraC_RyeA. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6366, in test_reading_writing_alignments_rfam2 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_rfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam3) Test parsing Rfam record McaS. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6382, in test_reading_writing_alignments_rfam3 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_rfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam4) Test parsing Rfam record IRES_KSHV. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6476, in test_reading_writing_alignments_rfam4 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_rfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam5) Test parsing Rfam record BMV3_UPD-PK3. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6492, in test_reading_writing_alignments_rfam5 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ---------------------------------------------------------------------- Ran 1 test in 0.149 seconds FAILED (failures = 1) Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux RPM build errors: error: Bad exit status from /var/tmp/rpm-tmp.6ISWKp (%check) Bad exit status from /var/tmp/rpm-tmp.6ISWKp (%check) Child return code was: 1 EXCEPTION: [Error('Command failed: \n # /usr/bin/systemd-nspawn -q -M 403bd61cef814d95b002ecef9c1c5132 -D /var/lib/mock/f42-build-55747816-6538638/root -a -u mockbuild --capability=cap_ipc_lock --bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf --bind=/dev/btrfs-control --bind=/dev/mapper/control --bind=/dev/fuse --bind=/dev/loop-control --bind=/dev/loop0 --bind=/dev/loop1 --bind=/dev/loop2 --bind=/dev/loop3 --bind=/dev/loop4 --bind=/dev/loop5 --bind=/dev/loop6 --bind=/dev/loop7 --bind=/dev/loop8 --bind=/dev/loop9 --bind=/dev/loop10 --bind=/dev/loop11 --console=pipe --setenv=TERM=vt100 --setenv=SHELL=/bin/bash --setenv=HOME=/builddir --setenv=HOSTNAME=mock --setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin \'--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"\' \'--setenv=PS1= \\s-\\v\\$ \' --setenv=LANG=C.UTF-8 --resolv-conf=off bash --login -c \'/usr/bin/rpmbuild -ba --noprep --noclean --target aarch64 /builddir/build/SPECS/python-biopython.spec\'\n', 1)] Traceback (most recent call last): File "/usr/lib/python3.13/site-packages/mockbuild/trace_decorator.py", line 93, in trace result = func(*args, **kw) File "/usr/lib/python3.13/site-packages/mockbuild/util.py", line 610, in do_with_status raise exception.Error("Command failed: \n # %s\n%s" % (cmd_pretty(command, env), output), child.returncode) mockbuild.exception.Error: Command failed: # /usr/bin/systemd-nspawn -q -M 403bd61cef814d95b002ecef9c1c5132 -D /var/lib/mock/f42-build-55747816-6538638/root -a -u mockbuild --capability=cap_ipc_lock --bind=/tmp/mock-resolv.oxa91rp1:/etc/resolv.conf --bind=/dev/btrfs-control --bind=/dev/mapper/control --bind=/dev/fuse --bind=/dev/loop-control --bind=/dev/loop0 --bind=/dev/loop1 --bind=/dev/loop2 --bind=/dev/loop3 --bind=/dev/loop4 --bind=/dev/loop5 --bind=/dev/loop6 --bind=/dev/loop7 --bind=/dev/loop8 --bind=/dev/loop9 --bind=/dev/loop10 --bind=/dev/loop11 --console=pipe --setenv=TERM=vt100 --setenv=SHELL=/bin/bash --setenv=HOME=/builddir --setenv=HOSTNAME=mock --setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin '--setenv=PROMPT_COMMAND=printf "\033]0;\007"' '--setenv=PS1= \s-\v\$ ' --setenv=LANG=C.UTF-8 --resolv-conf=off bash --login -c '/usr/bin/rpmbuild -ba --noprep --noclean --target aarch64 /builddir/build/SPECS/python-biopython.spec'