D: [iurt_root_command] chroot
Building target platforms: x86_64
Building for target x86_64
Installing /home/pterjan/rpmbuild/SRPMS/python-biopython-1.84-2.mga10.src.rpm
Executing(%mkbuilddir): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.sbY4MY
Executing(%prep): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.ikvnT3
+ umask 022
+ cd /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ '[' 1 -eq 1 ']'
+ '[' 1 -eq 1 ']'
+ '[' 1 -eq 1 ']'
+ cd /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ rm -rf biopython-1.84
+ /usr/lib/rpm/rpmuncompress -x /home/pterjan/rpmbuild/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 /home/pterjan/rpmbuild/SOURCES/biopython-1.84-linking.patch
+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f
+ /usr/lib/rpm/rpmuncompress /home/pterjan/rpmbuild/SOURCES/python-biopython-1.84-replace_deprecated_function.patch
+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f
+ find Scripts -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec sed -i 's/\r//' '{}' ';'
+ find Bio -type f -exec chmod -x '{}' ';'
+ find Bio -type f -name '*.py' -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' '{}' ';'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%generate_buildrequires): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.L65mmf
+ umask 022
+ cd /home/pterjan/rpmbuild/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'
+ for f in pyproject.toml setup.py setup.cfg
+ '[' -f pyproject.toml ']'
+ for f in pyproject.toml setup.py setup.cfg
+ '[' -f setup.py ']'
+ sed -i -E -e '/^requires/s/(['\''"]\s*flit_core\s*>=\s*[0-9]+(\.[0-9]+)+)\s*,\s*<\s*[0-9]+(\.[0-9]+)*(\s*['\''"])/\1\4/' setup.py
+ sed -i -E -e '/python_requires/s/(['\''"]?\s*\S*\s*>=\s*[0-9]+(\.[0-9]+)*)\s*(,\s*(<|!=)\s*[0-9]+(\.[0-9]+)*(\.\*)*)+(\s*['\''"]?)/\1\7/' setup.py
+ sed -i -E -e 's/(['\''"]?\s*\S*\s*>=\s*[0-9]+(\.[0-9a-z]+)*)\s*,\s*(<|!=|<=)\s*[0-9]+(\.[0-9a-z]+)*(-?dev[0-9]*)?(\.\*)*(\s*['\''"]?)/\1\7/g' setup.py
+ sed -i -E -e 's/(['\''"]\w+\s*)!=(\s*([0-9])+(\.[0-9]+)*\s*['\''"])/\1>\2/g' setup.py
+ sed -i -E -e 's/(['\''"]\s*>=\s*[0-9]+(\.[0-9]+)*)\s*,\s*(<|!=)\s*[0-9]+(\.[0-9]+)*(\s*['\''"])/\1\5/g' setup.py
+ sed -i -E -e 's/(['\''"]?\s*\S*\s*>=\s*[0-9]+(\.[0-9]+)*)\s*(,\s*(<|!=)\s*[0-9]+(\.[0-9]+)*(\.\*)*)+(\s*['\''"]?)/\1\7/g' setup.py
+ sed -i -E -e 's/(['\''"]\s*)\^(\s*[0-9]+(\.[0-9]+)*\s*['\''"])/\1>=\2/g' setup.py
+ sed -i -e 's/~=/>=/g' setup.py
+ sed -i -E -e 's/(['\''"]\s*\S*\s*)==(\s*[0-9]+(\.[0-9]+)*)\.\*(\s*['\''"])/\1>=\2\4/g' setup.py
+ sed -i -E -e 's/(['\''"]?\w*\s*>=\s*[0-9]+(\.[0-9]+)*)\s*,\s*(<|!=)[0-9]+(\.[0-9]+)*\s*(['\''"]?)/\1\5/g' setup.py
+ for f in pyproject.toml setup.py setup.cfg
+ '[' -f setup.cfg ']'
+ sed -i -E -e '/^requires/s/(['\''"]\s*flit_core\s*>=\s*[0-9]+(\.[0-9]+)+)\s*,\s*<\s*[0-9]+(\.[0-9]+)*(\s*['\''"])/\1\4/' setup.cfg
+ sed -i -E -e '/python_requires/s/(['\''"]?\s*\S*\s*>=\s*[0-9]+(\.[0-9]+)*)\s*(,\s*(<|!=)\s*[0-9]+(\.[0-9]+)*(\.\*)*)+(\s*['\''"]?)/\1\7/' setup.cfg
+ sed -i -E -e 's/(['\''"]?\s*\S*\s*>=\s*[0-9]+(\.[0-9a-z]+)*)\s*,\s*(<|!=|<=)\s*[0-9]+(\.[0-9a-z]+)*(-?dev[0-9]*)?(\.\*)*(\s*['\''"]?)/\1\7/g' setup.cfg
+ sed -i -E -e 's/(['\''"]\w+\s*)!=(\s*([0-9])+(\.[0-9]+)*\s*['\''"])/\1>\2/g' setup.cfg
+ sed -i -E -e 's/(['\''"]\s*>=\s*[0-9]+(\.[0-9]+)*)\s*,\s*(<|!=)\s*[0-9]+(\.[0-9]+)*(\s*['\''"])/\1\5/g' setup.cfg
+ sed -i -E -e 's/(['\''"]?\s*\S*\s*>=\s*[0-9]+(\.[0-9]+)*)\s*(,\s*(<|!=)\s*[0-9]+(\.[0-9]+)*(\.\*)*)+(\s*['\''"]?)/\1\7/g' setup.cfg
+ sed -i -E -e 's/(['\''"]\s*)\^(\s*[0-9]+(\.[0-9]+)*\s*['\''"])/\1>=\2/g' setup.cfg
+ sed -i -e 's/~=/>=/g' setup.cfg
+ sed -i -E -e 's/(['\''"]\s*\S*\s*)==(\s*[0-9]+(\.[0-9]+)*)\.\*(\s*['\''"])/\1>=\2\4/g' setup.cfg
+ sed -i -E -e 's/(['\''"]?\w*\s*>=\s*[0-9]+(\.[0-9]+)*)\s*,\s*(<|!=)[0-9]+(\.[0-9]+)*\s*(['\''"]?)/\1\5/g' setup.cfg
+ rm -rfv '*.dist-info/'
+ '[' -f /usr/bin/python3 ']'
+ mkdir -p /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir
+ echo -n
+ CFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full'
+ CXXFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full'
+ FFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full '
+ FCFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full '
+ VALAFLAGS=-g
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none --cap-lints=warn'
+ LDFLAGS='-Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ CXX=g++
+ TMPDIR=/home/pterjan/rpmbuild/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 /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir --output /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/python-biopython-1.84-2.mga10.x86_64-pyproject-buildrequires -x tests
Handling setuptools >= 40.8 from default build backend
Requirement satisfied: setuptools >= 40.8
   (installed: setuptools 78.1.0)
/usr/lib/python3.13/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!

        ********************************************************************************
        Please consider removing the following classifiers in favor of a SPDX license expression:

        License :: Freely Distributable

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  self._finalize_license_expression()
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 '/home/pterjan/rpmbuild/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 2.1.3)
+ cat /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/python-biopython-1.84-2.mga10.x86_64-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/licenses/LICENSE.rst'
removed 'biopython-1.84.dist-info/licenses/LICENSE'
removed directory 'biopython-1.84.dist-info/licenses'
removed directory 'biopython-1.84.dist-info/'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.hmicU1
+ umask 022
+ cd /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ CFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full '
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ 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
+ '[' 1 -eq 1 ']'
+ '[' 1 -eq 1 ']'
+ mkdir -p /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir
+ CFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full'
+ CXXFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full'
+ FFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full '
+ FCFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full '
+ VALAFLAGS=-g
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none --cap-lints=warn'
+ LDFLAGS='-Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ CXX=g++
+ TMPDIR=/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir
+ /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_wheel.py /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir
Processing /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84
  Preparing metadata (pyproject.toml): started
  Running command Preparing metadata (pyproject.toml)
  /usr/lib/python3.13/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
  !!

          ********************************************************************************
          Please consider removing the following classifiers in favor of a SPDX license expression:

          License :: Freely Distributable

          See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
          ********************************************************************************

  !!
    self._finalize_license_expression()
  running dist_info
  creating /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-_7iywwzx/biopython.egg-info
  writing /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-_7iywwzx/biopython.egg-info/PKG-INFO
  writing dependency_links to /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-_7iywwzx/biopython.egg-info/dependency_links.txt
  writing requirements to /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-_7iywwzx/biopython.egg-info/requires.txt
  writing top-level names to /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-_7iywwzx/biopython.egg-info/top_level.txt
  writing manifest file '/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-_7iywwzx/biopython.egg-info/SOURCES.txt'
  reading manifest file '/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-_7iywwzx/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 '/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-_7iywwzx/biopython.egg-info/SOURCES.txt'
  creating '/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-_7iywwzx/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)
  /usr/lib/python3.13/site-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
  !!

          ********************************************************************************
          Please consider removing the following classifiers in favor of a SPDX license expression:

          License :: Freely Distributable

          See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
          ********************************************************************************

  !!
    self._finalize_license_expression()
  running bdist_wheel
  running build
  running build_py
  creating build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/File.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/MaxEntropy.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/NaiveBayes.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/SeqFeature.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/_utils.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/kNN.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/SeqRecord.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/pairwise2.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/MarkovModel.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/LogisticRegression.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/Seq.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/bgzf.py -> build/lib.linux-x86_64-cpython-313/Bio
  creating build/lib.linux-x86_64-cpython-313/Bio/Affy
  copying Bio/Affy/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Affy
  copying Bio/Affy/CelFile.py -> build/lib.linux-x86_64-cpython-313/Bio/Affy
  creating build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/nexus.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/phylip.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/chain.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/bed.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/a2m.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/tabular.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/mauve.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/interfaces.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/clustal.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/maf.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/AlignInfo.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/sam.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/hhr.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/exonerate.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/fasta.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/bigmaf.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/stockholm.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/emboss.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/bigpsl.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/psl.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/analysis.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/bigbed.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/msf.py -> build/lib.linux-x86_64-cpython-313/Bio/Align
  creating build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  copying Bio/Align/Applications/_Prank.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  copying Bio/Align/Applications/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications
  creating build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices
  copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices
  creating build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/FastaIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/MafIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/Interfaces.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/MsfIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/MauveIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  copying Bio/AlignIO/NexusIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO
  creating build/lib.linux-x86_64-cpython-313/Bio/Alphabet
  copying Bio/Alphabet/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Alphabet
  creating build/lib.linux-x86_64-cpython-313/Bio/Application
  copying Bio/Application/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Application
  creating build/lib.linux-x86_64-cpython-313/Bio/Blast
  copying Bio/Blast/_parser.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast
  copying Bio/Blast/NCBIXML.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast
  copying Bio/Blast/NCBIWWW.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast
  copying Bio/Blast/Applications.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast
  copying Bio/Blast/_writers.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast
  copying Bio/Blast/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast
  creating build/lib.linux-x86_64-cpython-313/Bio/CAPS
  copying Bio/CAPS/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/CAPS
  creating build/lib.linux-x86_64-cpython-313/Bio/Cluster
  copying Bio/Cluster/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Cluster
  creating build/lib.linux-x86_64-cpython-313/Bio/codonalign
  copying Bio/codonalign/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/codonalign
  copying Bio/codonalign/codonseq.py -> build/lib.linux-x86_64-cpython-313/Bio/codonalign
  copying Bio/codonalign/codonalignment.py -> build/lib.linux-x86_64-cpython-313/Bio/codonalign
  creating build/lib.linux-x86_64-cpython-313/Bio/Compass
  copying Bio/Compass/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Compass
  creating build/lib.linux-x86_64-cpython-313/Bio/Data
  copying Bio/Data/CodonTable.py -> build/lib.linux-x86_64-cpython-313/Bio/Data
  copying Bio/Data/IUPACData.py -> build/lib.linux-x86_64-cpython-313/Bio/Data
  copying Bio/Data/PDBData.py -> build/lib.linux-x86_64-cpython-313/Bio/Data
  copying Bio/Data/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Data
  creating build/lib.linux-x86_64-cpython-313/Bio/Emboss
  copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-x86_64-cpython-313/Bio/Emboss
  copying Bio/Emboss/Applications.py -> build/lib.linux-x86_64-cpython-313/Bio/Emboss
  copying Bio/Emboss/Primer3.py -> build/lib.linux-x86_64-cpython-313/Bio/Emboss
  copying Bio/Emboss/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Emboss
  creating build/lib.linux-x86_64-cpython-313/Bio/Entrez
  copying Bio/Entrez/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Entrez
  copying Bio/Entrez/Parser.py -> build/lib.linux-x86_64-cpython-313/Bio/Entrez
  creating build/lib.linux-x86_64-cpython-313/Bio/ExPASy
  copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy
  copying Bio/ExPASy/Enzyme.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy
  copying Bio/ExPASy/Prodoc.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy
  copying Bio/ExPASy/Prosite.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy
  copying Bio/ExPASy/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy
  copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy
  creating build/lib.linux-x86_64-cpython-313/Bio/GenBank
  copying Bio/GenBank/Record.py -> build/lib.linux-x86_64-cpython-313/Bio/GenBank
  copying Bio/GenBank/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/GenBank
  copying Bio/GenBank/Scanner.py -> build/lib.linux-x86_64-cpython-313/Bio/GenBank
  copying Bio/GenBank/utils.py -> build/lib.linux-x86_64-cpython-313/Bio/GenBank
  creating build/lib.linux-x86_64-cpython-313/Bio/Geo
  copying Bio/Geo/Record.py -> build/lib.linux-x86_64-cpython-313/Bio/Geo
  copying Bio/Geo/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Geo
  creating build/lib.linux-x86_64-cpython-313/Bio/Graphics
  copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics
  copying Bio/Graphics/KGML_vis.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics
  copying Bio/Graphics/Distribution.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics
  copying Bio/Graphics/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics
  copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics
  copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics
  copying Bio/Graphics/Comparative.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics
  creating build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram
  creating build/lib.linux-x86_64-cpython-313/Bio/HMM
  copying Bio/HMM/Trainer.py -> build/lib.linux-x86_64-cpython-313/Bio/HMM
  copying Bio/HMM/MarkovModel.py -> build/lib.linux-x86_64-cpython-313/Bio/HMM
  copying Bio/HMM/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/HMM
  copying Bio/HMM/Utilities.py -> build/lib.linux-x86_64-cpython-313/Bio/HMM
  copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-x86_64-cpython-313/Bio/HMM
  creating build/lib.linux-x86_64-cpython-313/Bio/KEGG
  copying Bio/KEGG/REST.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG
  copying Bio/KEGG/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG
  creating build/lib.linux-x86_64-cpython-313/Bio/KEGG/Compound
  copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/Compound
  creating build/lib.linux-x86_64-cpython-313/Bio/KEGG/Enzyme
  copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/Enzyme
  creating build/lib.linux-x86_64-cpython-313/Bio/KEGG/Gene
  copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/Gene
  creating build/lib.linux-x86_64-cpython-313/Bio/KEGG/Map
  copying Bio/KEGG/Map/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/Map
  creating build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf
  copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf
  copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf
  copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf
  creating build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML
  copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML
  copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML
  copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML
  creating build/lib.linux-x86_64-cpython-313/Bio/Medline
  copying Bio/Medline/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Medline
  creating build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/thresholds.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/transfac.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/matrix.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/mast.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/pfm.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/xms.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/alignace.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/meme.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/clusterbuster.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/motifs/minimal.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  creating build/lib.linux-x86_64-cpython-313/Bio/motifs/applications
  copying Bio/motifs/applications/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs/applications
  copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs/applications
  creating build/lib.linux-x86_64-cpython-313/Bio/motifs/jaspar
  copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs/jaspar
  copying Bio/motifs/jaspar/db.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs/jaspar
  creating build/lib.linux-x86_64-cpython-313/Bio/Nexus
  copying Bio/Nexus/StandardData.py -> build/lib.linux-x86_64-cpython-313/Bio/Nexus
  copying Bio/Nexus/Trees.py -> build/lib.linux-x86_64-cpython-313/Bio/Nexus
  copying Bio/Nexus/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Nexus
  copying Bio/Nexus/Nodes.py -> build/lib.linux-x86_64-cpython-313/Bio/Nexus
  copying Bio/Nexus/Nexus.py -> build/lib.linux-x86_64-cpython-313/Bio/Nexus
  creating build/lib.linux-x86_64-cpython-313/Bio/NMR
  copying Bio/NMR/xpktools.py -> build/lib.linux-x86_64-cpython-313/Bio/NMR
  copying Bio/NMR/NOEtools.py -> build/lib.linux-x86_64-cpython-313/Bio/NMR
  copying Bio/NMR/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/NMR
  creating build/lib.linux-x86_64-cpython-313/Bio/Pathway
  copying Bio/Pathway/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Pathway
  creating build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep
  copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep
  copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep
  copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep
  copying Bio/PDB/StructureBuilder.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/Chain.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/SASA.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/binary_cif.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/alphafold_db.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/PDBIO.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/NeighborSearch.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/HSExposure.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/Polypeptide.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/PDBMLParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/PDBExceptions.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/ResidueDepth.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/PSEA.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/Dice.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/DSSP.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/mmcifio.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/PICIO.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/NACCESS.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/MMCIFParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/PDBList.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/ic_data.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/vectors.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/StructureAlignment.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/Structure.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/internal_coords.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/Superimposer.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/qcprot.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/PDBParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/cealign.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/Selection.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/ic_rebuild.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/Residue.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/Atom.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/SCADIO.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/Model.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/Entity.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/FragmentMapper.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  creating build/lib.linux-x86_64-cpython-313/Bio/phenotype
  copying Bio/phenotype/phen_micro.py -> build/lib.linux-x86_64-cpython-313/Bio/phenotype
  copying Bio/phenotype/pm_fitting.py -> build/lib.linux-x86_64-cpython-313/Bio/phenotype
  copying Bio/phenotype/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/phenotype
  creating build/lib.linux-x86_64-cpython-313/Bio/PopGen
  copying Bio/PopGen/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen
  creating build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop
  copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop
  copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop
  copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop
  copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop
  copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop
  creating build/lib.linux-x86_64-cpython-313/Bio/Restriction
  copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-x86_64-cpython-313/Bio/Restriction
  copying Bio/Restriction/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Restriction
  copying Bio/Restriction/PrintFormat.py -> build/lib.linux-x86_64-cpython-313/Bio/Restriction
  copying Bio/Restriction/Restriction.py -> build/lib.linux-x86_64-cpython-313/Bio/Restriction
  creating build/lib.linux-x86_64-cpython-313/Bio/SCOP
  copying Bio/SCOP/Raf.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP
  copying Bio/SCOP/Cla.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP
  copying Bio/SCOP/Dom.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP
  copying Bio/SCOP/Des.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP
  copying Bio/SCOP/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP
  copying Bio/SCOP/Residues.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP
  copying Bio/SCOP/Hie.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP
  creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO
  copying Bio/SearchIO/_index.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO
  copying Bio/SearchIO/FastaIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO
  copying Bio/SearchIO/_utils.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO
  copying Bio/SearchIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO
  copying Bio/SearchIO/BlatIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO
  creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model
  copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model
  copying Bio/SearchIO/_model/hit.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model
  copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model
  copying Bio/SearchIO/_model/query.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model
  copying Bio/SearchIO/_model/_base.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model
  creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO
  copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO
  copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO
  copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO
  creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HHsuiteIO
  copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HHsuiteIO
  copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HHsuiteIO
  creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO
  creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO
  copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO
  copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO
  copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO
  copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO
  copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO
  creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/InterproscanIO
  copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/InterproscanIO
  copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/InterproscanIO
  creating build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/_index.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/AceIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/GfaIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/FastaIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/TabIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/PdbIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/PhdIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/IgIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/PirIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/NibIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/Interfaces.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/SwissIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/AbiIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/QualityIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/GckIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying Bio/SeqIO/SffIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  creating build/lib.linux-x86_64-cpython-313/Bio/SeqUtils
  copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils
  copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils
  copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils
  copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils
  copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils
  copying Bio/SeqUtils/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils
  copying Bio/SeqUtils/lcc.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils
  creating build/lib.linux-x86_64-cpython-313/Bio/Sequencing
  copying Bio/Sequencing/Ace.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing
  copying Bio/Sequencing/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing
  copying Bio/Sequencing/Phd.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing
  creating build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications
  copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications
  copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications
  copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications
  copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications
  creating build/lib.linux-x86_64-cpython-313/Bio/SVDSuperimposer
  copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SVDSuperimposer
  creating build/lib.linux-x86_64-cpython-313/Bio/SwissProt
  copying Bio/SwissProt/KeyWList.py -> build/lib.linux-x86_64-cpython-313/Bio/SwissProt
  copying Bio/SwissProt/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SwissProt
  creating build/lib.linux-x86_64-cpython-313/Bio/TogoWS
  copying Bio/TogoWS/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/TogoWS
  creating build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/NeXML.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/CDAOIO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/_utils.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/_io.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/CDAO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/PhyloXML.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/Consensus.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/Newick.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/BaseTree.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/NexusIO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  copying Bio/Phylo/NewickIO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo
  creating build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications
  copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications
  copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications
  copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications
  copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications
  creating build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML
  creating build/lib.linux-x86_64-cpython-313/Bio/UniGene
  copying Bio/UniGene/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/UniGene
  creating build/lib.linux-x86_64-cpython-313/Bio/UniProt
  copying Bio/UniProt/GOA.py -> build/lib.linux-x86_64-cpython-313/Bio/UniProt
  copying Bio/UniProt/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/UniProt
  creating build/lib.linux-x86_64-cpython-313/BioSQL
  copying BioSQL/BioSeq.py -> build/lib.linux-x86_64-cpython-313/BioSQL
  copying BioSQL/BioSeqDatabase.py -> build/lib.linux-x86_64-cpython-313/BioSQL
  copying BioSQL/Loader.py -> build/lib.linux-x86_64-cpython-313/BioSQL
  copying BioSQL/__init__.py -> build/lib.linux-x86_64-cpython-313/BioSQL
  copying BioSQL/DBUtils.py -> build/lib.linux-x86_64-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:212: _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:212: _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:212: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration.
  !!

          ********************************************************************************
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'Bio.Entrez.XSDs' as an importable package[^1],
          but it is absent from setuptools' `packages` configuration.

          This leads to an ambiguous overall configuration. If you want to distribute this
          package, please make sure that 'Bio.Entrez.XSDs' is explicitly added
          to the `packages` configuration field.

          Alternatively, you can also rely on setuptools' discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).

          You can read more about "package discovery" on setuptools documentation page:

          - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

          If you don't want 'Bio.Entrez.XSDs' to be distributed and are
          already explicitly excluding 'Bio.Entrez.XSDs' via
          `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
          you can try to use `exclude_package_data`, or `include-package-data=False` in
          combination with a more fine grained `package-data` configuration.

          You can read more about "package data files" on setuptools documentation page:

          - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


          [^1]: For Python, any directory (with suitable naming) can be imported,
                even if it does not contain any `.py` files.
                On the other hand, currently there is no concept of package data
                directory, all directories are treated like packages.
          ********************************************************************************

  !!
    check.warn(importable)
  copying Bio/cpairwise2module.c -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/py.typed -> build/lib.linux-x86_64-cpython-313/Bio
  copying Bio/Align/_aligncore.c -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/_codonaligner.c -> build/lib.linux-x86_64-cpython-313/Bio/Align
  copying Bio/Align/_pairwisealigner.c -> build/lib.linux-x86_64-cpython-313/Bio/Align
  creating build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data
  copying Bio/Cluster/cluster.c -> build/lib.linux-x86_64-cpython-313/Bio/Cluster
  copying Bio/Cluster/cluster.h -> build/lib.linux-x86_64-cpython-313/Bio/Cluster
  copying Bio/Cluster/clustermodule.c -> build/lib.linux-x86_64-cpython-313/Bio/Cluster
  creating build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/elink.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/epost.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/esummary_clinvar.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/esummary_gene.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs
  creating build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs
  copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs
  copying Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs
  copying Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs
  copying Bio/motifs/_pwm.c -> build/lib.linux-x86_64-cpython-313/Bio/motifs
  copying Bio/Nexus/cnexus.c -> build/lib.linux-x86_64-cpython-313/Bio/Nexus
  copying Bio/PDB/bcifhelpermodule.c -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/ccealignmodule.c -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/PDB/kdtrees.c -> build/lib.linux-x86_64-cpython-313/Bio/PDB
  copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO
  copying BioSQL/py.typed -> build/lib.linux-x86_64-cpython-313/BioSQL
  running build_ext
  building 'Bio.Align._codonaligner' extension
  creating build/temp.linux-x86_64-cpython-313/Bio/Align
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/Align/_codonaligner.c -o build/temp.linux-x86_64-cpython-313/Bio/Align/_codonaligner.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/Align/_codonaligner.o -L/usr/lib64 -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/Align/_codonaligner.cpython-313-x86_64-linux-gnu.so
  building 'Bio.Align._pairwisealigner' extension
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/Align/_pairwisealigner.c -o build/temp.linux-x86_64-cpython-313/Bio/Align/_pairwisealigner.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/Align/_pairwisealigner.o -L/usr/lib64 -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/Align/_pairwisealigner.cpython-313-x86_64-linux-gnu.so
  building 'Bio.Align._aligncore' extension
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/Align/_aligncore.c -o build/temp.linux-x86_64-cpython-313/Bio/Align/_aligncore.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/Align/_aligncore.o -L/usr/lib64 -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/Align/_aligncore.cpython-313-x86_64-linux-gnu.so
  building 'Bio.cpairwise2' extension
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/cpairwise2module.c -o build/temp.linux-x86_64-cpython-313/Bio/cpairwise2module.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/cpairwise2module.o -L/usr/lib64 -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/cpairwise2.cpython-313-x86_64-linux-gnu.so
  building 'Bio.Nexus.cnexus' extension
  creating build/temp.linux-x86_64-cpython-313/Bio/Nexus
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/Nexus/cnexus.c -o build/temp.linux-x86_64-cpython-313/Bio/Nexus/cnexus.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/Nexus/cnexus.o -L/usr/lib64 -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/Nexus/cnexus.cpython-313-x86_64-linux-gnu.so
  building 'Bio.motifs._pwm' extension
  creating build/temp.linux-x86_64-cpython-313/Bio/motifs
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/motifs/_pwm.c -o build/temp.linux-x86_64-cpython-313/Bio/motifs/_pwm.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/motifs/_pwm.o -L/usr/lib64 -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/motifs/_pwm.cpython-313-x86_64-linux-gnu.so
  building 'Bio.Cluster._cluster' extension
  creating build/temp.linux-x86_64-cpython-313/Bio/Cluster
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/Cluster/cluster.c -o build/temp.linux-x86_64-cpython-313/Bio/Cluster/cluster.o
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/Cluster/clustermodule.c -o build/temp.linux-x86_64-cpython-313/Bio/Cluster/clustermodule.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/Cluster/cluster.o build/temp.linux-x86_64-cpython-313/Bio/Cluster/clustermodule.o -L/usr/lib64 -lm -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/Cluster/_cluster.cpython-313-x86_64-linux-gnu.so
  building 'Bio.PDB.ccealign' extension
  creating build/temp.linux-x86_64-cpython-313/Bio/PDB
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-x86_64-cpython-313/Bio/PDB/ccealignmodule.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/PDB/ccealignmodule.o -L/usr/lib64 -lm -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/PDB/ccealign.cpython-313-x86_64-linux-gnu.so
  building 'Bio.PDB.kdtrees' extension
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/PDB/kdtrees.c -o build/temp.linux-x86_64-cpython-313/Bio/PDB/kdtrees.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/PDB/kdtrees.o -L/usr/lib64 -lm -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/PDB/kdtrees.cpython-313-x86_64-linux-gnu.so
  building 'Bio.PDB._bcif_helper' extension
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/PDB/bcifhelpermodule.c -o build/temp.linux-x86_64-cpython-313/Bio/PDB/bcifhelpermodule.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/PDB/bcifhelpermodule.o -L/usr/lib64 -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/PDB/_bcif_helper.cpython-313-x86_64-linux-gnu.so
  building 'Bio.SeqIO._twoBitIO' extension
  creating build/temp.linux-x86_64-cpython-313/Bio/SeqIO
  gcc -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full -fPIC -I/usr/include/python3.13 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-x86_64-cpython-313/Bio/SeqIO/_twoBitIO.o
  gcc -shared -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full build/temp.linux-x86_64-cpython-313/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -lpython3.13 -o build/lib.linux-x86_64-cpython-313/Bio/SeqIO/_twoBitIO.cpython-313-x86_64-linux-gnu.so
  installing to build/bdist.linux-x86_64/wheel
  running install
  running install_lib
  creating build/bdist.linux-x86_64/wheel
  creating build/bdist.linux-x86_64/wheel/BioSQL
  copying build/lib.linux-x86_64-cpython-313/BioSQL/BioSeq.py -> build/bdist.linux-x86_64/wheel/./BioSQL
  copying build/lib.linux-x86_64-cpython-313/BioSQL/BioSeqDatabase.py -> build/bdist.linux-x86_64/wheel/./BioSQL
  copying build/lib.linux-x86_64-cpython-313/BioSQL/Loader.py -> build/bdist.linux-x86_64/wheel/./BioSQL
  copying build/lib.linux-x86_64-cpython-313/BioSQL/__init__.py -> build/bdist.linux-x86_64/wheel/./BioSQL
  copying build/lib.linux-x86_64-cpython-313/BioSQL/DBUtils.py -> build/bdist.linux-x86_64/wheel/./BioSQL
  copying build/lib.linux-x86_64-cpython-313/BioSQL/py.typed -> build/bdist.linux-x86_64/wheel/./BioSQL
  creating build/bdist.linux-x86_64/wheel/Bio
  copying build/lib.linux-x86_64-cpython-313/Bio/File.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/UniProt
  copying build/lib.linux-x86_64-cpython-313/Bio/UniProt/GOA.py -> build/bdist.linux-x86_64/wheel/./Bio/UniProt
  copying build/lib.linux-x86_64-cpython-313/Bio/UniProt/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/UniProt
  creating build/bdist.linux-x86_64/wheel/Bio/HMM
  copying build/lib.linux-x86_64-cpython-313/Bio/HMM/Trainer.py -> build/bdist.linux-x86_64/wheel/./Bio/HMM
  copying build/lib.linux-x86_64-cpython-313/Bio/HMM/MarkovModel.py -> build/bdist.linux-x86_64/wheel/./Bio/HMM
  copying build/lib.linux-x86_64-cpython-313/Bio/HMM/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/HMM
  copying build/lib.linux-x86_64-cpython-313/Bio/HMM/Utilities.py -> build/bdist.linux-x86_64/wheel/./Bio/HMM
  copying build/lib.linux-x86_64-cpython-313/Bio/HMM/DynamicProgramming.py -> build/bdist.linux-x86_64/wheel/./Bio/HMM
  creating build/bdist.linux-x86_64/wheel/Bio/SeqUtils
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/IsoelectricPoint.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/CheckSum.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/ProtParamData.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/MeltingTemp.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/ProtParam.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/lcc.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils
  copying build/lib.linux-x86_64-cpython-313/Bio/cpairwise2.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/codonalign
  copying build/lib.linux-x86_64-cpython-313/Bio/codonalign/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/codonalign
  copying build/lib.linux-x86_64-cpython-313/Bio/codonalign/codonseq.py -> build/bdist.linux-x86_64/wheel/./Bio/codonalign
  copying build/lib.linux-x86_64-cpython-313/Bio/codonalign/codonalignment.py -> build/bdist.linux-x86_64/wheel/./Bio/codonalign
  copying build/lib.linux-x86_64-cpython-313/Bio/MaxEntropy.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/Medline
  copying build/lib.linux-x86_64-cpython-313/Bio/Medline/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Medline
  creating build/bdist.linux-x86_64/wheel/Bio/Restriction
  copying build/lib.linux-x86_64-cpython-313/Bio/Restriction/Restriction_Dictionary.py -> build/bdist.linux-x86_64/wheel/./Bio/Restriction
  copying build/lib.linux-x86_64-cpython-313/Bio/Restriction/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Restriction
  copying build/lib.linux-x86_64-cpython-313/Bio/Restriction/PrintFormat.py -> build/bdist.linux-x86_64/wheel/./Bio/Restriction
  copying build/lib.linux-x86_64-cpython-313/Bio/Restriction/Restriction.py -> build/bdist.linux-x86_64/wheel/./Bio/Restriction
  creating build/bdist.linux-x86_64/wheel/Bio/SVDSuperimposer
  copying build/lib.linux-x86_64-cpython-313/Bio/SVDSuperimposer/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SVDSuperimposer
  creating build/bdist.linux-x86_64/wheel/Bio/Application
  copying build/lib.linux-x86_64-cpython-313/Bio/Application/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Application
  creating build/bdist.linux-x86_64/wheel/Bio/KEGG
  creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Enzyme
  copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/Enzyme/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/Enzyme
  creating build/bdist.linux-x86_64/wheel/Bio/KEGG/KGML
  copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML/KGML_parser.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/KGML
  copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/KGML
  copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML/KGML_pathway.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/KGML
  creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Gene
  copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/Gene/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/Gene
  copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/REST.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG
  creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Map
  copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/Map/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/Map
  copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG
  creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Compound
  copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/Compound/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/Compound
  creating build/bdist.linux-x86_64/wheel/Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/StructureBuilder.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/_bcif_helper.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Chain.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/SASA.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/kdtrees.c -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/binary_cif.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/alphafold_db.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  creating build/bdist.linux-x86_64/wheel/Bio/PDB/mmtf
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf/DefaultParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB/mmtf
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf/mmtfio.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB/mmtf
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB/mmtf
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PDBIO.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/AbstractPropertyMap.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/HSExposure.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Polypeptide.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PDBMLParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PDBExceptions.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/ResidueDepth.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/kdtrees.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PSEA.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Dice.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/MMCIF2Dict.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/DSSP.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/mmcifio.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PICIO.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/NACCESS.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/MMCIFParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PDBList.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/ic_data.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/vectors.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/bcifhelpermodule.c -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/StructureAlignment.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Structure.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/internal_coords.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Superimposer.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/qcprot.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PDBParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/cealign.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Selection.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/ccealign.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/ic_rebuild.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/ccealignmodule.c -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/parse_pdb_header.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Residue.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Atom.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/SCADIO.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Model.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Entity.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  copying build/lib.linux-x86_64-cpython-313/Bio/PDB/FragmentMapper.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB
  creating build/bdist.linux-x86_64/wheel/Bio/Entrez
  creating build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isodia.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/elink_020122.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_all.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/ePost_020511.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
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  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/journalmeta.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs
  creating build/bdist.linux-x86_64/wheel/Bio/Entrez/XSDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs/IPGReportSet.xsd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/XSDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/XSDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/XSDs
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Entrez
  copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/Parser.py -> build/bdist.linux-x86_64/wheel/./Bio/Entrez
  creating build/bdist.linux-x86_64/wheel/Bio/Cluster
  copying build/lib.linux-x86_64-cpython-313/Bio/Cluster/clustermodule.c -> build/bdist.linux-x86_64/wheel/./Bio/Cluster
  copying build/lib.linux-x86_64-cpython-313/Bio/Cluster/cluster.c -> build/bdist.linux-x86_64/wheel/./Bio/Cluster
  copying build/lib.linux-x86_64-cpython-313/Bio/Cluster/_cluster.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/Cluster
  copying build/lib.linux-x86_64-cpython-313/Bio/Cluster/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Cluster
  copying build/lib.linux-x86_64-cpython-313/Bio/Cluster/cluster.h -> build/bdist.linux-x86_64/wheel/./Bio/Cluster
  creating build/bdist.linux-x86_64/wheel/Bio/Affy
  copying build/lib.linux-x86_64-cpython-313/Bio/Affy/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Affy
  copying build/lib.linux-x86_64-cpython-313/Bio/Affy/CelFile.py -> build/bdist.linux-x86_64/wheel/./Bio/Affy
  creating build/bdist.linux-x86_64/wheel/Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/MafIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/Interfaces.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/EmbossIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/StockholmIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/PhylipIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/MsfIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/MauveIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/ClustalIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/NexusIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO
  copying build/lib.linux-x86_64-cpython-313/Bio/NaiveBayes.py -> build/bdist.linux-x86_64/wheel/./Bio
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqFeature.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/SearchIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_index.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO
  creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/HHsuiteIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HHsuiteIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HHsuiteIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HHsuiteIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO
  creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/InterproscanIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/InterproscanIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/InterproscanIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/InterproscanIO
  creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/BlastIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO/blast_tab.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/BlastIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO/blast_xml.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/BlastIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/BlastIO
  creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model/hsp.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/_model
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model/hit.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/_model
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/_model
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model/query.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/_model
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model/_base.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/_model
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_utils.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO
  creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/ExonerateIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/ExonerateIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/ExonerateIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/ExonerateIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO/_base.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/ExonerateIO
  creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/_base.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlatIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO
  creating build/bdist.linux-x86_64/wheel/Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/thresholds.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  creating build/bdist.linux-x86_64/wheel/Bio/motifs/jaspar
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/jaspar/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs/jaspar
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/jaspar/db.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs/jaspar
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/transfac.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/matrix.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/mast.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/pfm.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/_pwm.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/xms.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/alignace.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/meme.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  creating build/bdist.linux-x86_64/wheel/Bio/motifs/applications
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/applications/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs/applications
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/applications/_xxmotif.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs/applications
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/_pwm.c -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/clusterbuster.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  copying build/lib.linux-x86_64-cpython-313/Bio/motifs/minimal.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs
  creating build/bdist.linux-x86_64/wheel/Bio/Alphabet
  copying build/lib.linux-x86_64-cpython-313/Bio/Alphabet/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Alphabet
  copying build/lib.linux-x86_64-cpython-313/Bio/_utils.py -> build/bdist.linux-x86_64/wheel/./Bio
  copying build/lib.linux-x86_64-cpython-313/Bio/kNN.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/Emboss
  copying build/lib.linux-x86_64-cpython-313/Bio/Emboss/PrimerSearch.py -> build/bdist.linux-x86_64/wheel/./Bio/Emboss
  copying build/lib.linux-x86_64-cpython-313/Bio/Emboss/Applications.py -> build/bdist.linux-x86_64/wheel/./Bio/Emboss
  copying build/lib.linux-x86_64-cpython-313/Bio/Emboss/Primer3.py -> build/bdist.linux-x86_64/wheel/./Bio/Emboss
  copying build/lib.linux-x86_64-cpython-313/Bio/Emboss/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Emboss
  creating build/bdist.linux-x86_64/wheel/Bio/phenotype
  copying build/lib.linux-x86_64-cpython-313/Bio/phenotype/phen_micro.py -> build/bdist.linux-x86_64/wheel/./Bio/phenotype
  copying build/lib.linux-x86_64-cpython-313/Bio/phenotype/pm_fitting.py -> build/bdist.linux-x86_64/wheel/./Bio/phenotype
  copying build/lib.linux-x86_64-cpython-313/Bio/phenotype/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/phenotype
  creating build/bdist.linux-x86_64/wheel/Bio/Data
  copying build/lib.linux-x86_64-cpython-313/Bio/Data/CodonTable.py -> build/bdist.linux-x86_64/wheel/./Bio/Data
  copying build/lib.linux-x86_64-cpython-313/Bio/Data/IUPACData.py -> build/bdist.linux-x86_64/wheel/./Bio/Data
  copying build/lib.linux-x86_64-cpython-313/Bio/Data/PDBData.py -> build/bdist.linux-x86_64/wheel/./Bio/Data
  copying build/lib.linux-x86_64-cpython-313/Bio/Data/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Data
  creating build/bdist.linux-x86_64/wheel/Bio/Pathway
  creating build/bdist.linux-x86_64/wheel/Bio/Pathway/Rep
  copying build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep/MultiGraph.py -> build/bdist.linux-x86_64/wheel/./Bio/Pathway/Rep
  copying build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Pathway/Rep
  copying build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep/Graph.py -> build/bdist.linux-x86_64/wheel/./Bio/Pathway/Rep
  copying build/lib.linux-x86_64-cpython-313/Bio/Pathway/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Pathway
  creating build/bdist.linux-x86_64/wheel/Bio/TogoWS
  copying build/lib.linux-x86_64-cpython-313/Bio/TogoWS/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/TogoWS
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqRecord.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/nexus.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/phylip.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/chain.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/bed.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/a2m.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/tabular.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/_codonaligner.c -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/mauve.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/interfaces.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/clustal.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/maf.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/_pairwisealigner.c -> build/bdist.linux-x86_64/wheel/./Bio/Align
  creating build/bdist.linux-x86_64/wheel/Bio/Align/Applications
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  copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_MSAProbs.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Dialign.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Probcons.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Muscle.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_ClustalOmega.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Mafft.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_TCoffee.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Clustalw.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/AlignInfo.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/sam.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/hhr.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/exonerate.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/fasta.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/bigmaf.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/stockholm.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/_pairwisealigner.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/_aligncore.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/emboss.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  creating build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices
  creating build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/JOHNSON -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM62 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/FENG -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BENNER22 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLASTP -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/PAM70 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/DAYHOFF -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/JONES -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLASTN -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/LEVIN -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/NUC.4.4 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM50 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/RAO -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM45 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/HOXD70 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/MEGABLAST -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/STR -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM80 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/MDM78 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/RISLER -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/PAM30 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM90 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/TRANS -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/GONNET1992 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/SCHNEIDER -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BENNER6 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/PAM250 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BENNER74 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/MCLACHLAN -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/GENETIC -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/bigpsl.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/psl.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/_codonaligner.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/analysis.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/bigbed.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/_aligncore.c -> build/bdist.linux-x86_64/wheel/./Bio/Align
  copying build/lib.linux-x86_64-cpython-313/Bio/Align/msf.py -> build/bdist.linux-x86_64/wheel/./Bio/Align
  creating build/bdist.linux-x86_64/wheel/Bio/Compass
  copying build/lib.linux-x86_64-cpython-313/Bio/Compass/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Compass
  copying build/lib.linux-x86_64-cpython-313/Bio/pairwise2.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/NMR
  copying build/lib.linux-x86_64-cpython-313/Bio/NMR/xpktools.py -> build/bdist.linux-x86_64/wheel/./Bio/NMR
  copying build/lib.linux-x86_64-cpython-313/Bio/NMR/NOEtools.py -> build/bdist.linux-x86_64/wheel/./Bio/NMR
  copying build/lib.linux-x86_64-cpython-313/Bio/NMR/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/NMR
  copying build/lib.linux-x86_64-cpython-313/Bio/MarkovModel.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/Blast
  copying build/lib.linux-x86_64-cpython-313/Bio/Blast/_parser.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast
  copying build/lib.linux-x86_64-cpython-313/Bio/Blast/NCBIXML.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast
  copying build/lib.linux-x86_64-cpython-313/Bio/Blast/NCBIWWW.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast
  copying build/lib.linux-x86_64-cpython-313/Bio/Blast/Applications.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast
  copying build/lib.linux-x86_64-cpython-313/Bio/Blast/_writers.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast
  copying build/lib.linux-x86_64-cpython-313/Bio/Blast/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast
  creating build/bdist.linux-x86_64/wheel/Bio/SwissProt
  copying build/lib.linux-x86_64-cpython-313/Bio/SwissProt/KeyWList.py -> build/bdist.linux-x86_64/wheel/./Bio/SwissProt
  copying build/lib.linux-x86_64-cpython-313/Bio/SwissProt/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SwissProt
  copying build/lib.linux-x86_64-cpython-313/Bio/LogisticRegression.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/UniGene
  copying build/lib.linux-x86_64-cpython-313/Bio/UniGene/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/UniGene
  copying build/lib.linux-x86_64-cpython-313/Bio/Seq.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/Nexus
  copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/StandardData.py -> build/bdist.linux-x86_64/wheel/./Bio/Nexus
  copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/cnexus.c -> build/bdist.linux-x86_64/wheel/./Bio/Nexus
  copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/Trees.py -> build/bdist.linux-x86_64/wheel/./Bio/Nexus
  copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/cnexus.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/Nexus
  copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Nexus
  copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/Nodes.py -> build/bdist.linux-x86_64/wheel/./Bio/Nexus
  copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/Nexus.py -> build/bdist.linux-x86_64/wheel/./Bio/Nexus
  creating build/bdist.linux-x86_64/wheel/Bio/SCOP
  copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Raf.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP
  copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Cla.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP
  copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Dom.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP
  copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Des.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP
  copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP
  copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Residues.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP
  copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Hie.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP
  creating build/bdist.linux-x86_64/wheel/Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/NeXML.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  creating build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/_parse_codeml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/_parse_yn00.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/baseml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/codeml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/yn00.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/_paml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/chi2.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/_parse_baseml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PhyloXMLIO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/CDAOIO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/TreeConstruction.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  creating build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications/_Fasttree.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications/_Raxml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications/_Phyml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/_utils.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/_io.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/CDAO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PhyloXML.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Consensus.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/NeXMLIO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/_cdao_owl.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Newick.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/BaseTree.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/NexusIO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/NewickIO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo
  copying build/lib.linux-x86_64-cpython-313/Bio/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/Geo
  copying build/lib.linux-x86_64-cpython-313/Bio/Geo/Record.py -> build/bdist.linux-x86_64/wheel/./Bio/Geo
  copying build/lib.linux-x86_64-cpython-313/Bio/Geo/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Geo
  creating build/bdist.linux-x86_64/wheel/Bio/GenBank
  copying build/lib.linux-x86_64-cpython-313/Bio/GenBank/Record.py -> build/bdist.linux-x86_64/wheel/./Bio/GenBank
  copying build/lib.linux-x86_64-cpython-313/Bio/GenBank/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/GenBank
  copying build/lib.linux-x86_64-cpython-313/Bio/GenBank/Scanner.py -> build/bdist.linux-x86_64/wheel/./Bio/GenBank
  copying build/lib.linux-x86_64-cpython-313/Bio/GenBank/utils.py -> build/bdist.linux-x86_64/wheel/./Bio/GenBank
  creating build/bdist.linux-x86_64/wheel/Bio/PopGen
  copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen
  creating build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop
  copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop/Controller.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen/GenePop
  copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop/EasyController.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen/GenePop
  copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop/FileParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen/GenePop
  copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen/GenePop
  copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop/LargeFileParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen/GenePop
  creating build/bdist.linux-x86_64/wheel/Bio/Sequencing
  creating build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications/_samtools.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications/_Novoalign.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications/_bwa.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing/Applications
  copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Ace.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing
  copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing
  copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Phd.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing
  creating build/bdist.linux-x86_64/wheel/Bio/Graphics
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/BasicChromosome.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/KGML_vis.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/Distribution.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/DisplayRepresentation.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/ColorSpiral.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/Comparative.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics
  creating build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_Feature.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_Graph.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_Diagram.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_Colors.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_Track.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram
  copying build/lib.linux-x86_64-cpython-313/Bio/cpairwise2module.c -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/_index.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/AceIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/GfaIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/TabIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/PdbIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/PhdIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/IgIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/InsdcIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/UniprotIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/PirIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/SeqXmlIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/NibIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/Interfaces.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/XdnaIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/SwissIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/AbiIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/QualityIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/_twoBitIO.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/SnapGeneIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/TwoBitIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/GckIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/_twoBitIO.c -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/SffIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO
  creating build/bdist.linux-x86_64/wheel/Bio/CAPS
  copying build/lib.linux-x86_64-cpython-313/Bio/CAPS/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/CAPS
  copying build/lib.linux-x86_64-cpython-313/Bio/py.typed -> build/bdist.linux-x86_64/wheel/./Bio
  copying build/lib.linux-x86_64-cpython-313/Bio/bgzf.py -> build/bdist.linux-x86_64/wheel/./Bio
  creating build/bdist.linux-x86_64/wheel/Bio/ExPASy
  copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/cellosaurus.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy
  copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/Enzyme.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy
  copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/Prodoc.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy
  copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/Prosite.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy
  copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy
  copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/ScanProsite.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy
  running install_egg_info
  Copying biopython.egg-info to build/bdist.linux-x86_64/wheel/./biopython-1.84-py3.13.egg-info
  running install_scripts
  creating build/bdist.linux-x86_64/wheel/biopython-1.84.dist-info/WHEEL
  creating '/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-wheel-o8g5i53c/.tmp-0u2e4pmg/biopython-1.84-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/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-x86_64-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-x86_64-linux-gnu.so'
  adding 'Bio/Align/_codonaligner.c'
  adding 'Bio/Align/_codonaligner.cpython-313-x86_64-linux-gnu.so'
  adding 'Bio/Align/_pairwisealigner.c'
  adding 'Bio/Align/_pairwisealigner.cpython-313-x86_64-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 'Bio/Align/substitution_matrices/data/HOXD70'
  adding 'Bio/Align/substitution_matrices/data/JOHNSON'
  adding 'Bio/Align/substitution_matrices/data/JONES'
  adding 'Bio/Align/substitution_matrices/data/LEVIN'
  adding 'Bio/Align/substitution_matrices/data/MCLACHLAN'
  adding 'Bio/Align/substitution_matrices/data/MDM78'
  adding 'Bio/Align/substitution_matrices/data/MEGABLAST'
  adding 'Bio/Align/substitution_matrices/data/NUC.4.4'
  adding 'Bio/Align/substitution_matrices/data/PAM250'
  adding 'Bio/Align/substitution_matrices/data/PAM30'
  adding 'Bio/Align/substitution_matrices/data/PAM70'
  adding 'Bio/Align/substitution_matrices/data/RAO'
  adding 'Bio/Align/substitution_matrices/data/RISLER'
  adding 'Bio/Align/substitution_matrices/data/SCHNEIDER'
  adding 'Bio/Align/substitution_matrices/data/STR'
  adding 'Bio/Align/substitution_matrices/data/TRANS'
  adding 'Bio/AlignIO/ClustalIO.py'
  adding 'Bio/AlignIO/EmbossIO.py'
  adding 'Bio/AlignIO/FastaIO.py'
  adding 'Bio/AlignIO/Interfaces.py'
  adding 'Bio/AlignIO/MafIO.py'
  adding 'Bio/AlignIO/MauveIO.py'
  adding 'Bio/AlignIO/MsfIO.py'
  adding 'Bio/AlignIO/NexusIO.py'
  adding 'Bio/AlignIO/PhylipIO.py'
  adding 'Bio/AlignIO/StockholmIO.py'
  adding 'Bio/AlignIO/__init__.py'
  adding 'Bio/Alphabet/__init__.py'
  adding 'Bio/Application/__init__.py'
  adding 'Bio/Blast/Applications.py'
  adding 'Bio/Blast/NCBIWWW.py'
  adding 'Bio/Blast/NCBIXML.py'
  adding 'Bio/Blast/__init__.py'
  adding 'Bio/Blast/_parser.py'
  adding 'Bio/Blast/_writers.py'
  adding 'Bio/CAPS/__init__.py'
  adding 'Bio/Cluster/__init__.py'
  adding 'Bio/Cluster/_cluster.cpython-313-x86_64-linux-gnu.so'
  adding 'Bio/Cluster/cluster.c'
  adding 'Bio/Cluster/cluster.h'
  adding 'Bio/Cluster/clustermodule.c'
  adding 'Bio/Compass/__init__.py'
  adding 'Bio/Data/CodonTable.py'
  adding 'Bio/Data/IUPACData.py'
  adding 'Bio/Data/PDBData.py'
  adding 'Bio/Data/__init__.py'
  adding 'Bio/Emboss/Applications.py'
  adding 'Bio/Emboss/Primer3.py'
  adding 'Bio/Emboss/PrimerSearch.py'
  adding 'Bio/Emboss/__init__.py'
  adding 'Bio/Entrez/Parser.py'
  adding 'Bio/Entrez/__init__.py'
  adding 'Bio/Entrez/DTDs/BITS-embedded-index2.ent'
  adding 'Bio/Entrez/DTDs/BITS-question-answer2.ent'
  adding 'Bio/Entrez/DTDs/Docsum_3_0.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_0.mod.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_1.dtd'
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  adding 'Bio/Entrez/DTDs/Docsum_3_2.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_2.mod.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_3.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_3.mod.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_4.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_4.mod.dtd'
  adding 'Bio/Entrez/DTDs/EMBL_General.dtd'
  adding 'Bio/Entrez/DTDs/EMBL_General.mod.dtd'
  adding 'Bio/Entrez/DTDs/GenBank_General.dtd'
  adding 'Bio/Entrez/DTDs/GenBank_General.mod.dtd'
  adding 'Bio/Entrez/DTDs/HomoloGene.dtd'
  adding 'Bio/Entrez/DTDs/HomoloGene.mod.dtd'
  adding 'Bio/Entrez/DTDs/INSD_INSDSeq.dtd'
  adding 'Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd'
  adding 'Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd'
  adding 'Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-articlemeta1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-backmatter1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-chars1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-common-atts1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-common1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-default-classes1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-default-mixes1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-display1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-format1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-funding1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-journalmeta1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-link1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-list1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-math1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-modules1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-notat1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-para1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-phrase1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-references1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-related-object1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-section1-3.ent'
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  adding 'Bio/Entrez/DTDs/MMDB.dtd'
  adding 'Bio/Entrez/DTDs/MMDB.mod.dtd'
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  adding 'Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd'
  adding 'Bio/Entrez/DTDs/MMDB_Features.dtd'
  adding 'Bio/Entrez/DTDs/MMDB_Features.mod.dtd'
  adding 'Bio/Entrez/DTDs/MMDB_Structural_model.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_Access.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Biblio.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_BioSource.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_BioTree.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Blast4.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BlastOutput.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Cdd.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_Gene.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_General.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_ID1Access.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_ID2Access.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_MedArchive.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Medlars.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Medline.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_Mim.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_Pub.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Pub.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_PubMed.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_RNA.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_SeqTable.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Seqalign.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_Seqres.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Sequence.dtd'
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  adding 'Bio/Entrez/DTDs/NCBI_TxInit.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Variation.dtd'
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  adding 'Bio/Entrez/DTDs/NSE.dtd'
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  adding 'Bio/Entrez/DTDs/PIR_General.mod.dtd'
  adding 'Bio/Entrez/DTDs/PRF_General.dtd'
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  adding 'Bio/Entrez/DTDs/SP_General.dtd'
  adding 'Bio/Entrez/DTDs/SP_General.mod.dtd'
  adding 'Bio/Entrez/DTDs/XHTMLtablesetup.ent'
  adding 'Bio/Entrez/DTDs/archivearticle.dtd'
  adding 'Bio/Entrez/DTDs/archivecustom-classes.ent'
  adding 'Bio/Entrez/DTDs/archivecustom-mixes.ent'
  adding 'Bio/Entrez/DTDs/archivecustom-models.ent'
  adding 'Bio/Entrez/DTDs/archivecustom-modules.ent'
  adding 'Bio/Entrez/DTDs/articlemeta.ent'
  adding 'Bio/Entrez/DTDs/backmatter.ent'
  adding 'Bio/Entrez/DTDs/bookdoc_100301.dtd'
  adding 'Bio/Entrez/DTDs/bookdoc_110101.dtd'
  adding 'Bio/Entrez/DTDs/bookdoc_120101.dtd'
  adding 'Bio/Entrez/DTDs/bookdoc_130101.dtd'
  adding 'Bio/Entrez/DTDs/bookdoc_140101.dtd'
  adding 'Bio/Entrez/DTDs/bookdoc_150101.dtd'
  adding 'Bio/Entrez/DTDs/chars.ent'
  adding 'Bio/Entrez/DTDs/common.ent'
  adding 'Bio/Entrez/DTDs/default-classes.ent'
  adding 'Bio/Entrez/DTDs/default-mixes.ent'
  adding 'Bio/Entrez/DTDs/display.ent'
  adding 'Bio/Entrez/DTDs/eInfo_020511.dtd'
  adding 'Bio/Entrez/DTDs/eLink_090910.dtd'
  adding 'Bio/Entrez/DTDs/eLink_101123.dtd'
  adding 'Bio/Entrez/DTDs/ePost_020511.dtd'
  adding 'Bio/Entrez/DTDs/eSearch_020511.dtd'
  adding 'Bio/Entrez/DTDs/eSpell.dtd'
  adding 'Bio/Entrez/DTDs/eSummary_041029.dtd'
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  adding 'Bio/Entrez/DTDs/math.ent'
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  adding 'Bio/Entrez/DTDs/taxon.dtd'
  adding 'Bio/Entrez/DTDs/xhtml-inlstyle-1.mod'
  adding 'Bio/Entrez/DTDs/xhtml-table-1.mod'
  adding 'Bio/Entrez/DTDs/xmlspecchars.ent'
  adding 'Bio/Entrez/XSDs/IPGReportSet.xsd'
  adding 'Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd'
  adding 'Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd'
  adding 'Bio/ExPASy/Enzyme.py'
  adding 'Bio/ExPASy/Prodoc.py'
  adding 'Bio/ExPASy/Prosite.py'
  adding 'Bio/ExPASy/ScanProsite.py'
  adding 'Bio/ExPASy/__init__.py'
  adding 'Bio/ExPASy/cellosaurus.py'
  adding 'Bio/GenBank/Record.py'
  adding 'Bio/GenBank/Scanner.py'
  adding 'Bio/GenBank/__init__.py'
  adding 'Bio/GenBank/utils.py'
  adding 'Bio/Geo/Record.py'
  adding 'Bio/Geo/__init__.py'
  adding 'Bio/Graphics/BasicChromosome.py'
  adding 'Bio/Graphics/ColorSpiral.py'
  adding 'Bio/Graphics/Comparative.py'
  adding 'Bio/Graphics/DisplayRepresentation.py'
  adding 'Bio/Graphics/Distribution.py'
  adding 'Bio/Graphics/KGML_vis.py'
  adding 'Bio/Graphics/__init__.py'
  adding 'Bio/Graphics/GenomeDiagram/_AbstractDrawer.py'
  adding 'Bio/Graphics/GenomeDiagram/_CircularDrawer.py'
  adding 'Bio/Graphics/GenomeDiagram/_Colors.py'
  adding 'Bio/Graphics/GenomeDiagram/_CrossLink.py'
  adding 'Bio/Graphics/GenomeDiagram/_Diagram.py'
  adding 'Bio/Graphics/GenomeDiagram/_Feature.py'
  adding 'Bio/Graphics/GenomeDiagram/_FeatureSet.py'
  adding 'Bio/Graphics/GenomeDiagram/_Graph.py'
  adding 'Bio/Graphics/GenomeDiagram/_GraphSet.py'
  adding 'Bio/Graphics/GenomeDiagram/_LinearDrawer.py'
  adding 'Bio/Graphics/GenomeDiagram/_Track.py'
  adding 'Bio/Graphics/GenomeDiagram/__init__.py'
  adding 'Bio/HMM/DynamicProgramming.py'
  adding 'Bio/HMM/MarkovModel.py'
  adding 'Bio/HMM/Trainer.py'
  adding 'Bio/HMM/Utilities.py'
  adding 'Bio/HMM/__init__.py'
  adding 'Bio/KEGG/REST.py'
  adding 'Bio/KEGG/__init__.py'
  adding 'Bio/KEGG/Compound/__init__.py'
  adding 'Bio/KEGG/Enzyme/__init__.py'
  adding 'Bio/KEGG/Gene/__init__.py'
  adding 'Bio/KEGG/KGML/KGML_parser.py'
  adding 'Bio/KEGG/KGML/KGML_pathway.py'
  adding 'Bio/KEGG/KGML/__init__.py'
  adding 'Bio/KEGG/Map/__init__.py'
  adding 'Bio/Medline/__init__.py'
  adding 'Bio/NMR/NOEtools.py'
  adding 'Bio/NMR/__init__.py'
  adding 'Bio/NMR/xpktools.py'
  adding 'Bio/Nexus/Nexus.py'
  adding 'Bio/Nexus/Nodes.py'
  adding 'Bio/Nexus/StandardData.py'
  adding 'Bio/Nexus/Trees.py'
  adding 'Bio/Nexus/__init__.py'
  adding 'Bio/Nexus/cnexus.c'
  adding 'Bio/Nexus/cnexus.cpython-313-x86_64-linux-gnu.so'
  adding 'Bio/PDB/AbstractPropertyMap.py'
  adding 'Bio/PDB/Atom.py'
  adding 'Bio/PDB/Chain.py'
  adding 'Bio/PDB/DSSP.py'
  adding 'Bio/PDB/Dice.py'
  adding 'Bio/PDB/Entity.py'
  adding 'Bio/PDB/FragmentMapper.py'
  adding 'Bio/PDB/HSExposure.py'
  adding 'Bio/PDB/MMCIF2Dict.py'
  adding 'Bio/PDB/MMCIFParser.py'
  adding 'Bio/PDB/Model.py'
  adding 'Bio/PDB/NACCESS.py'
  adding 'Bio/PDB/NeighborSearch.py'
  adding 'Bio/PDB/PDBExceptions.py'
  adding 'Bio/PDB/PDBIO.py'
  adding 'Bio/PDB/PDBList.py'
  adding 'Bio/PDB/PDBMLParser.py'
  adding 'Bio/PDB/PDBParser.py'
  adding 'Bio/PDB/PICIO.py'
  adding 'Bio/PDB/PSEA.py'
  adding 'Bio/PDB/Polypeptide.py'
  adding 'Bio/PDB/Residue.py'
  adding 'Bio/PDB/ResidueDepth.py'
  adding 'Bio/PDB/SASA.py'
  adding 'Bio/PDB/SCADIO.py'
  adding 'Bio/PDB/Selection.py'
  adding 'Bio/PDB/Structure.py'
  adding 'Bio/PDB/StructureAlignment.py'
  adding 'Bio/PDB/StructureBuilder.py'
  adding 'Bio/PDB/Superimposer.py'
  adding 'Bio/PDB/__init__.py'
  adding 'Bio/PDB/_bcif_helper.cpython-313-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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/licenses/LICENSE'
  adding 'biopython-1.84.dist-info/licenses/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-x86_64/wheel
  Building wheel for biopython (pyproject.toml): finished with status 'done'
  Created wheel for biopython: filename=biopython-1.84-cp313-cp313-linux_x86_64.whl size=3158351 sha256=8dfa6e2b1bdfd3fa55b77dea0ec872f92e0f20c472a915a1d228d80f42d8c0bd
  Stored in directory: /home/pterjan/.cache/pip/wheels/d4/c8/0c/aa208fec109d47f0d1b5f13df485f9a57a2416c6e834644997
Successfully built biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.z0YHAV
+ umask 022
+ cd /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ '[' 1 -eq 1 ']'
+ '[' /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT '!=' / ']'
+ rm -rf /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT
++ dirname /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT
+ mkdir -p /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ mkdir /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT
+ CFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full '
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wformat -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -m64 -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection=full '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -Wl,-O1 -Wl,--build-id=sha1 -Wl,--enable-new-dtags -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ 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
+ '[' 1 -eq 1 ']'
++ xargs basename --multiple
++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/'
++ ls /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir/biopython-1.84-cp313-cp313-linux_x86_64.whl
+ specifier=biopython==1.84
+ '[' -z biopython==1.84 ']'
+ TMPDIR=/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir
+ /usr/bin/python3 -m pip install --root /home/pterjan/rpmbuild/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 /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir biopython==1.84
Using pip 25.0.1 from /usr/lib/python3.13/site-packages/pip (python 3.13)
Looking in links: /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir
Processing ./pyproject-wheeldir/biopython-1.84-cp313-cp313-linux_x86_64.whl
Installing collected packages: biopython
Successfully installed biopython-1.84
+ '[' -d /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin ']'
+ rm -f /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/python-biopython-1.84-2.mga10.x86_64-pyproject-ghost-distinfo
+ site_dirs=()
+ '[' -d /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages ']'
+ '[' /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages '!=' /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages ']'
+ '[' -d /home/pterjan/rpmbuild/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 ${site_dirs[@]}
+ for distinfo in /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT$site_dir/*.dist-info
+ echo '%ghost /usr/lib64/python3.13/site-packages/biopython-1.84.dist-info'
+ sed -i s/pip/rpm/ /home/pterjan/rpmbuild/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 /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT --record /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/RECORD --output /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/python-biopython-1.84-2.mga10.x86_64-pyproject-record
+ rm -fv /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/RECORD
removed '/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/RECORD'
+ rm -fv /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/REQUESTED
removed '/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/REQUESTED'
++ cut -f1 '-d '
++ wc -l /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/python-biopython-1.84-2.mga10.x86_64-pyproject-ghost-distinfo
+ lines=1
+ '[' 1 -ne 1 ']'
+ /usr/bin/find-debuginfo -j16 --strict-build-id -m -i --build-id-seed 1.84-2.mga10 --unique-debug-suffix -1.84-2.mga10.x86_64 --unique-debug-src-base python-biopython-1.84-2.mga10.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /home/pterjan/rpmbuild/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-1.84-2.mga10.x86_64
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ '[' -n '' ']'
+ /usr/share/spec-helper/clean_files
+ '[' -n '' ']'
+ /usr/share/spec-helper/compress_files .xz
+ '[' -n '' ']'
+ /usr/share/spec-helper/relink_symlinks
+ '[' -n '' ']'
+ /usr/share/spec-helper/clean_perl
+ '[' -n '' ']'
+ /usr/share/spec-helper/lib_symlinks
+ '[' -n '' ']'
+ /usr/share/spec-helper/gprintify
+ '[' -n '' ']'
+ /usr/share/spec-helper/fix_mo
+ '[' -n '' ']'
+ /usr/share/spec-helper/fix_pamd
+ '[' -n '' ']'
+ /usr/share/spec-helper/remove_info_dir
+ '[' -n '' ']'
+ /usr/share/spec-helper/fix_eol
+ '[' -n '' ']'
+ /usr/share/spec-helper/check_desktop_files
+ '[' -n '' ']'
+ /usr/share/spec-helper/check_elf_files
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ env -u SOURCE_DATE_EPOCH /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j16
Bytecompiling .py files below /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13 using python3.13
Not clamping source mtimes, $SOURCE_DATE_EPOCH not set
Bytecompiling .py files below /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.13 using python3.13
Not clamping source mtimes, $SOURCE_DATE_EPOCH not set
+ /usr/lib/rpm/redhat/brp-python-hardlink
Reading /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/SPECPARTS/rpm-debuginfo.specpart
Processing files: python3-biopython-1.84-2.mga10.x86_64
Executing(%doc): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.K4q5x8
+ umask 022
+ cd /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ cd biopython-1.84
+ DOCDIR=/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python3-biopython
+ cp -pr /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/Scripts /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python3-biopython
+ cp -pr /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/CONTRIB.rst /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python3-biopython
+ cp -pr /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/DEPRECATED.rst /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python3-biopython
+ cp -pr /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/NEWS.rst /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python3-biopython
+ cp -pr /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/README.rst /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.NFA3QZ
+ umask 022
+ cd /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ cd biopython-1.84
+ LICENSEDIR=/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/licenses/python3-biopython
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/licenses/python3-biopython
+ cp -pr /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/LICENSE.rst /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/licenses/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython = 1:1.84-2.mga10 python3-biopython = 1:1.84-2.mga10 python3-biopython(x86-64) = 1:1.84-2.mga10 python3.13-biopython = 1:1.84-2.mga10 python3.13dist(biopython) = 1.84 python3dist(biopython) = 1.84
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libpython3.13.so.1.0()(64bit) python(abi) = 3.13 python3.13dist(numpy)
Obsoletes: python-biopython < 1:1.84-2.mga10 wise2 < 2.4.1-11
Recommends: clustalw ncbi-blast
Processing files: python3-biopython-sql-1.84-2.mga10.x86_64
Executing(%license): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.nbdmR4
+ umask 022
+ cd /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ cd biopython-1.84
+ LICENSEDIR=/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/licenses/python3-biopython-sql
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/licenses/python3-biopython-sql
+ cp -pr /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/LICENSE.rst /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/licenses/python3-biopython-sql
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython-sql = 1:1.84-2.mga10 python3-biopython-sql = 1:1.84-2.mga10 python3-biopython-sql(x86-64) = 1:1.84-2.mga10 python3.13-biopython-sql = 1:1.84-2.mga10
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: python(abi) = 3.13
Processing files: python-biopython-doc-1.84-2.mga10.x86_64
Executing(%doc): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.aWbfiu
+ umask 022
+ cd /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ cd biopython-1.84
+ DOCDIR=/home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python-biopython-doc
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python-biopython-doc
+ cp -pr /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/Doc/Biopython_doc.pdf /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python-biopython-doc
+ cp -pr /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/biopython-1.84/Doc/examples /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT/usr/share/doc/python-biopython-doc
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: biopython-doc python-biopython-doc = 1:1.84-2.mga10 python-biopython-doc(x86-64) = 1:1.84-2.mga10
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-biopython-debugsource-1.84-2.mga10.x86_64
Provides: python-biopython-debugsource = 1:1.84-2.mga10 python-biopython-debugsource(x86-64) = 1:1.84-2.mga10
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python3-biopython-debuginfo-1.84-2.mga10.x86_64
Provides: debuginfo(build-id) = 00d8552ff74f6870de67c5eae2353313fecae0ae debuginfo(build-id) = 4bc9c84720dd17b2a16a7574c9bd36bd03d1da99 debuginfo(build-id) = 77fa26cfa5dcc48b8ae9d933b88b3f3f8e210573 debuginfo(build-id) = 96eb95bf535808e8dc399e1251754f5c66f8d2e0 debuginfo(build-id) = 984731bd8a37e711ab233ee0070dae289b4ce8d9 debuginfo(build-id) = b1d305d8658e66473deb40966311fc957fe87edd debuginfo(build-id) = be38fdbedc3b86d65fa1efd7e072843807d9f0a5 debuginfo(build-id) = d36ff1bb502a79c5f965efa9aaa6d7d0b1a998a9 debuginfo(build-id) = d6c3f260eb138467d760a11dc529ce5d7051650d debuginfo(build-id) = e2bcff2c010d17c3d973eaba5949c3324a1a0d5b debuginfo(build-id) = eb829d9ab5e60a2ef9e838d7a6a8c4d1466a9b45 python-biopython-debuginfo = 1:1.84-2.mga10 python3-biopython-debuginfo = 1:1.84-2.mga10 python3-biopython-debuginfo(x86-64) = 1:1.84-2.mga10 python3.13-biopython-debuginfo = 1:1.84-2.mga10
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: python-biopython-debugsource(x86-64) = 1:1.84-2.mga10
Checking for unpackaged file(s): /usr/lib/rpm/check-files /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build/BUILDROOT
Wrote: /home/pterjan/rpmbuild/RPMS/x86_64/python3-biopython-sql-1.84-2.mga10.x86_64.rpm
Wrote: /home/pterjan/rpmbuild/RPMS/x86_64/python-biopython-debugsource-1.84-2.mga10.x86_64.rpm
Wrote: /home/pterjan/rpmbuild/RPMS/x86_64/python3-biopython-debuginfo-1.84-2.mga10.x86_64.rpm
Wrote: /home/pterjan/rpmbuild/RPMS/x86_64/python-biopython-doc-1.84-2.mga10.x86_64.rpm
Wrote: /home/pterjan/rpmbuild/RPMS/x86_64/python3-biopython-1.84-2.mga10.x86_64.rpm
Executing(rmbuild): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.chM5SU
+ umask 022
+ cd /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ test -d /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ rm -rf /home/pterjan/rpmbuild/BUILD/python-biopython-1.84-build
+ RPM_EC=0
++ jobs -p
+ exit 0
D: [iurt_root_command] Success!