Sourcing python-remove-tests-dir-hook Sourcing python-catch-conflicts-hook.sh Sourcing python-remove-bin-bytecode-hook.sh Sourcing pypa-build-hook Using pypaBuildPhase Sourcing python-runtime-deps-check-hook Using pythonRuntimeDepsCheckHook Sourcing pypa-install-hook Using pypaInstallPhase Sourcing python-imports-check-hook.sh Using pythonImportsCheckPhase Sourcing python-metadata-check-hook.sh Using pythonMetadataCheckPhase Sourcing python-namespaces-hook Sourcing python-catch-conflicts-hook.sh Sourcing pytest-check-hook Using pytestCheckPhase Running phase: unpackPhase unpacking source archive /nix/store/8qd97xh7haqn9bsjn93n9pcm4clc036j-source source root is source setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "source/valgrind-python.supp" Running phase: patchPhase Running phase: updateAutotoolsGnuConfigScriptsPhase Running phase: configurePhase no configure script, doing nothing Running phase: buildPhase Executing pypaBuildPhase Creating a wheel... pypa build flags: --no-isolation --outdir dist/ --wheel * Getting build dependencies for wheel... [1/2] Cythonizing primer3/p3helpers.pyx warning: primer3/p3helpers.pyx:34:28: 'COMP_BASE_LUT' redeclared warning: primer3/p3helpers.pyx:35:27: 'SANITIZE_LUT' redeclared warning: primer3/p3helpers.pyx:36:29: 'ACGT_UPPER_LUT' redeclared warning: primer3/p3helpers.pyx:37:36: 'IS_UPPERCASE_ACGT_LUT' redeclared [2/2] Cythonizing primer3/thermoanalysis.pyx warning: primer3/thermoanalysis.pyx:1406:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running egg_info creating primer3_py.egg-info writing primer3_py.egg-info/PKG-INFO writing dependency_links to primer3_py.egg-info/dependency_links.txt writing requirements to primer3_py.egg-info/requires.txt writing top-level names to primer3_py.egg-info/top_level.txt writing manifest file 'primer3_py.egg-info/SOURCES.txt' dependency /build/source/primer3/src/libprimer3/libprimer3.h won't be automatically included in the manifest: the path must be relative dependency /build/source/primer3/src/libprimer3/masker.h won't be automatically included in the manifest: the path must be relative dependency /build/source/primer3/src/libprimer3/oligotm.h won't be automatically included in the manifest: the path must be relative dependency /build/source/primer3/src/libprimer3/p3_seq_lib.h won't be automatically included in the manifest: the path must be relative dependency /build/source/primer3/src/libprimer3/read_boulder.h won't be automatically included in the manifest: the path must be relative dependency /build/source/primer3/src/libprimer3/thal.h won't be automatically included in the manifest: the path must be relative reading manifest file 'primer3_py.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.rst' under directory 'docs' 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 '*.pyd' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '*.dylib' found anywhere in distribution warning: no previously-included files matching '*.dll' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution warning: no previously-included files matching '*.egg-info' found anywhere in distribution warning: no previously-included files matching '.DS_Store' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution no previously-included directories found matching 'primer3/thermoanalysis.c' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'primer3_py.egg-info/SOURCES.txt' * Building wheel... [1/2] Cythonizing primer3/p3helpers.pyx warning: primer3/p3helpers.pyx:34:28: 'COMP_BASE_LUT' redeclared warning: primer3/p3helpers.pyx:35:27: 'SANITIZE_LUT' redeclared warning: primer3/p3helpers.pyx:36:29: 'ACGT_UPPER_LUT' redeclared warning: primer3/p3helpers.pyx:37:36: 'IS_UPPERCASE_ACGT_LUT' redeclared [2/2] Cythonizing primer3/thermoanalysis.pyx warning: primer3/thermoanalysis.pyx:1406:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+) 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-314/primer3 copying primer3/__init__.py -> build/lib.linux-x86_64-cpython-314/primer3 copying primer3/argdefaults.py -> build/lib.linux-x86_64-cpython-314/primer3 copying primer3/bindings.py -> build/lib.linux-x86_64-cpython-314/primer3 running egg_info writing primer3_py.egg-info/PKG-INFO writing dependency_links to primer3_py.egg-info/dependency_links.txt writing requirements to primer3_py.egg-info/requires.txt writing top-level names to primer3_py.egg-info/top_level.txt dependency /build/source/primer3/src/libprimer3/libprimer3.h won't be automatically included in the manifest: the path must be relative dependency /build/source/primer3/src/libprimer3/masker.h won't be automatically included in the manifest: the path must be relative dependency /build/source/primer3/src/libprimer3/oligotm.h won't be automatically included in the manifest: the path must be relative dependency /build/source/primer3/src/libprimer3/p3_seq_lib.h won't be automatically included in the manifest: the path must be relative dependency /build/source/primer3/src/libprimer3/read_boulder.h won't be automatically included in the manifest: the path must be relative dependency /build/source/primer3/src/libprimer3/thal.h won't be automatically included in the manifest: the path must be relative reading manifest file 'primer3_py.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.rst' under directory 'docs' 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 '*.pyd' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '*.dylib' found anywhere in distribution warning: no previously-included files matching '*.dll' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution warning: no previously-included files matching '*.egg-info' found anywhere in distribution warning: no previously-included files matching '.DS_Store' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution no previously-included directories found matching 'primer3/thermoanalysis.c' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'primer3_py.egg-info/SOURCES.txt' /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'primer3.src.libprimer3' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'primer3.src.libprimer3' 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 'primer3.src.libprimer3' 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 'primer3.src.libprimer3' to be distributed and are already explicitly excluding 'primer3.src.libprimer3' 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) /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'primer3.src.libprimer3.klib' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'primer3.src.libprimer3.klib' 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 'primer3.src.libprimer3.klib' 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 'primer3.src.libprimer3.klib' to be distributed and are already explicitly excluding 'primer3.src.libprimer3.klib' 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) /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'primer3.src.libprimer3.klib.test' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'primer3.src.libprimer3.klib.test' 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 'primer3.src.libprimer3.klib.test' 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 'primer3.src.libprimer3.klib.test' to be distributed and are already explicitly excluding 'primer3.src.libprimer3.klib.test' 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) /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'primer3.src.libprimer3.primer3_config' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'primer3.src.libprimer3.primer3_config' 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 'primer3.src.libprimer3.primer3_config' 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 'primer3.src.libprimer3.primer3_config' to be distributed and are already explicitly excluding 'primer3.src.libprimer3.primer3_config' 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) /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/command/build_py.py:215: _Warning: Package 'primer3.src.libprimer3.primer3_config.interpretations' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'primer3.src.libprimer3.primer3_config.interpretations' 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 'primer3.src.libprimer3.primer3_config.interpretations' 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 'primer3.src.libprimer3.primer3_config.interpretations' to be distributed and are already explicitly excluding 'primer3.src.libprimer3.primer3_config.interpretations' 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 primer3/p3helpers.c -> build/lib.linux-x86_64-cpython-314/primer3 copying primer3/p3helpers.h -> build/lib.linux-x86_64-cpython-314/primer3 copying primer3/p3helpers.pxd -> build/lib.linux-x86_64-cpython-314/primer3 copying primer3/p3helpers.pyx -> build/lib.linux-x86_64-cpython-314/primer3 copying primer3/thermoanalysis.c -> build/lib.linux-x86_64-cpython-314/primer3 copying primer3/thermoanalysis.pxd -> build/lib.linux-x86_64-cpython-314/primer3 copying primer3/thermoanalysis.pxi -> build/lib.linux-x86_64-cpython-314/primer3 copying primer3/thermoanalysis.pyx -> build/lib.linux-x86_64-cpython-314/primer3 creating build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/ABOUT.txt -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/LICENSE.txt -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/Makefile -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/amplicontm.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/amplicontm.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/amplicontm_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/dpal.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/dpal.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/format_output.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/format_output.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/gpl-2.0.txt -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/humrep_and_simple.txt -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/libprimer3.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/libprimer3.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/libprimer3flex.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/libprimer3flex.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/long_seq_tm_test_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/masker.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/masker.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/masker_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/ntdpal_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/oligotm.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/oligotm.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/oligotm_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/p3_seq_lib.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/p3_seq_lib.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/primer3_boulder_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/print_boulder.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/print_boulder.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/read_boulder.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/read_boulder.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/release_notes.txt -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/thal.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/thal.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/thal_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/thal_parameters.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/thal_parameters.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/thalflex.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/thalflex.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 copying primer3/src/libprimer3/thalflexsignatures.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3 creating build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib copying primer3/src/libprimer3/klib/README.md -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib copying primer3/src/libprimer3/klib/khash.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib creating build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test copying primer3/src/libprimer3/klib/test/Makefile -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test copying primer3/src/libprimer3/klib/test/khash_keith.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test copying primer3/src/libprimer3/klib/test/khash_keith2.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test copying primer3/src/libprimer3/klib/test/khash_test.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test creating build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/dangle.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/dangle.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/loops.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/loops.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/stack.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/stack.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/stackmm.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/stackmm.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/tetraloop.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/tetraloop.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/triloop.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/triloop.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/tstack.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/tstack2.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/tstack2.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config copying primer3/src/libprimer3/primer3_config/tstack_tm_inf.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config creating build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/dangle_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/dangle_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/loops_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/loops_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/stack_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/stack_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/stackmm_i_mm.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/stackmm_i_mm.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/tetraloop_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/tetraloop_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/triloop_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/triloop_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/tstack2_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/tstack2_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/tstack_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/tstack_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/tstack_tm_inf_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations copying primer3/src/libprimer3/primer3_config/interpretations/tstack_tm_inf_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations running build_ext no windows rm -f *.o primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker *~ libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a libprimer3.so.1.0.0 libdpal.a.so.1.0.0 libthal.a.so.1.0.0 libthalpara.a.so.1.0.0 libamplicontm.so.1.0.0 liboligotm.so.1.2.0 libmasker.a.so.1.0.0 example.for example.rev example.int core ../*~ no windows cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib primer3_boulder_main.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o format_output.o format_output.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o read_boulder.o read_boulder.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o print_boulder.o print_boulder.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -Wno-deprecated -o libprimer3.o libprimer3.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o p3_seq_lib.o p3_seq_lib.c ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: creating libprimer3.a a - libprimer3.o a - p3_seq_lib.o ranlib libprimer3.a cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o dpal_primer.o dpal.c ar rv libdpal.a dpal_primer.o ar: creating libdpal.a a - dpal_primer.o ranlib libdpal.a cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal_primer.o thal.c ar rv libthal.a thal_primer.o ar: creating libthal.a a - thal_primer.o ranlib libthal.a cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal_parameters.o thal_parameters.c ar rv libthalpara.a thal_parameters.o ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -c -o oligotm.o oligotm.c ar rv liboligotm.a oligotm.o ar: creating liboligotm.a a - oligotm.o ranlib liboligotm.a cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -c -o amplicontm.o amplicontm.c ar rv libamplicontm.a amplicontm.o ar: creating libamplicontm.a a - amplicontm.o ranlib libamplicontm.a cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib masker.c ar rv libmasker.a masker.o ar: creating libmasker.a a - masker.o ranlib libmasker.a cc -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -o ntdpal_main.o ntdpal_main.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o dpal.o dpal.c cc -g -o ntdpal ntdpal_main.o dpal.o cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o thal_main.o thal_main.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal.o thal.c cc -g -o ntthal thal_main.o thal.o thal_parameters.o -lm cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o amplicon3_core amplicontm_main.c libamplicontm.a -lm cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o oligotm oligotm_main.c liboligotm.a -lm cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm cc -g -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm building 'primer3.p3helpers' extension creating build/temp.linux-x86_64-cpython-314/primer3 gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3 -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/p3helpers.c -o build/temp.linux-x86_64-cpython-314/primer3/p3helpers.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/fh8svr4ds87z84iarfnxrlfpjlbmc816-tzdata-2026c/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/fh8svr4ds87z84iarfnxrlfpjlbmc816-tzdata-2026c/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib build/temp.linux-x86_64-cpython-314/primer3/p3helpers.o -L/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/primer3/p3helpers.cpython-314-x86_64-linux-gnu.so building 'primer3.thermoanalysis' extension creating build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3 gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/dpal.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/dpal.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/libprimer3flex.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3flex.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/masker.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/masker.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/oligotm.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/oligotm.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/p3_seq_lib.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/p3_seq_lib.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/read_boulder.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/read_boulder.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/thal_parameters.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/thal_parameters.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/thalflex.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/thalflex.o -Wno-error=declaration-after-statement -Wno-unused-function In file included from /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/string.h:548, from primer3/src/libprimer3/thalflex.c:66: In function ‘strcpy’, inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5, inlined from ‘calc_hairpin’ at primer3/src/libprimer3/thalflex.c:1842:18: /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’ In function ‘strcpy’, inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5, inlined from ‘calc_bulge_internal.constprop’ at primer3/src/libprimer3/thalflex.c:1946:18: /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’ In function ‘strcpy’, inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5, inlined from ‘maxTM’ at primer3/src/libprimer3/thalflex.h:752:18, inlined from ‘fillMatrix.constprop’ at primer3/src/libprimer3/thalflex.c:1701:11: /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’ In function ‘strcpy’, inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5, inlined from ‘calc_bulge_internal’ at primer3/src/libprimer3/thalflex.c:1946:18, inlined from ‘fillMatrix.constprop’ at primer3/src/libprimer3/thalflex.c:1721:17: /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’ gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/thermoanalysis.c -o build/temp.linux-x86_64-cpython-314/primer3/thermoanalysis.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/fh8svr4ds87z84iarfnxrlfpjlbmc816-tzdata-2026c/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/fh8svr4ds87z84iarfnxrlfpjlbmc816-tzdata-2026c/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/dpal.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3flex.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/masker.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/oligotm.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/p3_seq_lib.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/read_boulder.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/thal_parameters.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/thalflex.o build/temp.linux-x86_64-cpython-314/primer3/thermoanalysis.o -L/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.cpython-314-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/primer3 copying build/lib.linux-x86_64-cpython-314/primer3/__init__.py -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/argdefaults.py -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/bindings.py -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.c -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.h -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.pxd -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.pyx -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.c -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.pxd -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.pxi -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.pyx -> build/bdist.linux-x86_64/wheel/./primer3 creating build/bdist.linux-x86_64/wheel/primer3/src creating build/bdist.linux-x86_64/wheel/primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/ABOUT.txt -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/LICENSE.txt -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/Makefile -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/amplicontm.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/amplicontm.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/amplicontm_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/dpal.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/dpal.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/format_output.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/format_output.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/gpl-2.0.txt -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/humrep_and_simple.txt -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3flex.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3flex.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/long_seq_tm_test_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/masker.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/masker.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/masker_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/ntdpal_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/oligotm.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/oligotm.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/oligotm_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/p3_seq_lib.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/p3_seq_lib.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_boulder_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/print_boulder.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/print_boulder.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/read_boulder.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/read_boulder.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/release_notes.txt -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thal.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thal.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thal_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thal_parameters.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thal_parameters.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thalflex.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thalflex.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thalflexsignatures.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3 creating build/bdist.linux-x86_64/wheel/primer3/src/libprimer3/klib copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/README.md -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/klib copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/khash.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/klib creating build/bdist.linux-x86_64/wheel/primer3/src/libprimer3/klib/test copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test/Makefile -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/klib/test copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test/khash_keith.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/klib/test copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test/khash_keith2.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/klib/test copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test/khash_test.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/klib/test creating build/bdist.linux-x86_64/wheel/primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/dangle.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/dangle.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/loops.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/loops.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/stack.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/stack.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/stackmm.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/stackmm.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tetraloop.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tetraloop.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/triloop.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/triloop.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tstack.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tstack2.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tstack2.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tstack_tm_inf.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config creating build/bdist.linux-x86_64/wheel/primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/dangle_i.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/dangle_i.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/loops_i.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/loops_i.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/stack_i.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/stack_i.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/stackmm_i_mm.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/stackmm_i_mm.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/tetraloop_i.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/tetraloop_i.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/triloop_i.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/triloop_i.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/tstack2_i.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/tstack2_i.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/tstack_i.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/tstack_i.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/tstack_tm_inf_i.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations/tstack_tm_inf_i.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config/interpretations copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./primer3 copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./primer3 Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/amplicon3_core (mode is now 755) Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/oligotm (mode is now 755) Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/ntdpal (mode is now 755) Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/ntthal (mode is now 755) Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_core (mode is now 755) Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_masker (mode is now 755) running install_egg_info Copying primer3_py.egg-info to build/bdist.linux-x86_64/wheel/./primer3_py-2.3.1-py3.14.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/primer3_py-2.3.1.dist-info/WHEEL creating '/build/source/dist/.tmp-t6w56roe/primer3_py-2.3.1-cp314-cp314-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'primer3/__init__.py' adding 'primer3/argdefaults.py' adding 'primer3/bindings.py' adding 'primer3/p3helpers.c' adding 'primer3/p3helpers.cpython-314-x86_64-linux-gnu.so' adding 'primer3/p3helpers.h' adding 'primer3/p3helpers.pxd' adding 'primer3/p3helpers.pyx' adding 'primer3/thermoanalysis.c' adding 'primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so' adding 'primer3/thermoanalysis.pxd' adding 'primer3/thermoanalysis.pxi' adding 'primer3/thermoanalysis.pyx' adding 'primer3/src/libprimer3/ABOUT.txt' adding 'primer3/src/libprimer3/LICENSE.txt' adding 'primer3/src/libprimer3/Makefile' adding 'primer3/src/libprimer3/amplicon3_core' adding 'primer3/src/libprimer3/amplicontm.c' adding 'primer3/src/libprimer3/amplicontm.h' adding 'primer3/src/libprimer3/amplicontm_main.c' adding 'primer3/src/libprimer3/dpal.c' adding 'primer3/src/libprimer3/dpal.h' adding 'primer3/src/libprimer3/format_output.c' adding 'primer3/src/libprimer3/format_output.h' adding 'primer3/src/libprimer3/gpl-2.0.txt' adding 'primer3/src/libprimer3/humrep_and_simple.txt' adding 'primer3/src/libprimer3/libprimer3.c' adding 'primer3/src/libprimer3/libprimer3.h' adding 'primer3/src/libprimer3/libprimer3flex.c' adding 'primer3/src/libprimer3/libprimer3flex.h' adding 'primer3/src/libprimer3/long_seq_tm_test_main.c' adding 'primer3/src/libprimer3/masker.c' adding 'primer3/src/libprimer3/masker.h' adding 'primer3/src/libprimer3/masker_main.c' adding 'primer3/src/libprimer3/ntdpal' adding 'primer3/src/libprimer3/ntdpal_main.c' adding 'primer3/src/libprimer3/ntthal' adding 'primer3/src/libprimer3/oligotm' adding 'primer3/src/libprimer3/oligotm.c' adding 'primer3/src/libprimer3/oligotm.h' adding 'primer3/src/libprimer3/oligotm_main.c' adding 'primer3/src/libprimer3/p3_seq_lib.c' adding 'primer3/src/libprimer3/p3_seq_lib.h' adding 'primer3/src/libprimer3/primer3_boulder_main.c' adding 'primer3/src/libprimer3/primer3_core' adding 'primer3/src/libprimer3/primer3_masker' adding 'primer3/src/libprimer3/print_boulder.c' adding 'primer3/src/libprimer3/print_boulder.h' adding 'primer3/src/libprimer3/read_boulder.c' adding 'primer3/src/libprimer3/read_boulder.h' adding 'primer3/src/libprimer3/release_notes.txt' adding 'primer3/src/libprimer3/thal.c' adding 'primer3/src/libprimer3/thal.h' adding 'primer3/src/libprimer3/thal_main.c' adding 'primer3/src/libprimer3/thal_parameters.c' adding 'primer3/src/libprimer3/thal_parameters.h' adding 'primer3/src/libprimer3/thalflex.c' adding 'primer3/src/libprimer3/thalflex.h' adding 'primer3/src/libprimer3/thalflexsignatures.h' adding 'primer3/src/libprimer3/klib/README.md' adding 'primer3/src/libprimer3/klib/khash.h' adding 'primer3/src/libprimer3/klib/test/Makefile' adding 'primer3/src/libprimer3/klib/test/khash_keith.c' adding 'primer3/src/libprimer3/klib/test/khash_keith2.c' adding 'primer3/src/libprimer3/klib/test/khash_test.c' adding 'primer3/src/libprimer3/primer3_config/dangle.dh' adding 'primer3/src/libprimer3/primer3_config/dangle.ds' adding 'primer3/src/libprimer3/primer3_config/loops.dh' adding 'primer3/src/libprimer3/primer3_config/loops.ds' adding 'primer3/src/libprimer3/primer3_config/stack.dh' adding 'primer3/src/libprimer3/primer3_config/stack.ds' adding 'primer3/src/libprimer3/primer3_config/stackmm.dh' adding 'primer3/src/libprimer3/primer3_config/stackmm.ds' adding 'primer3/src/libprimer3/primer3_config/tetraloop.dh' adding 'primer3/src/libprimer3/primer3_config/tetraloop.ds' adding 'primer3/src/libprimer3/primer3_config/triloop.dh' adding 'primer3/src/libprimer3/primer3_config/triloop.ds' adding 'primer3/src/libprimer3/primer3_config/tstack.dh' adding 'primer3/src/libprimer3/primer3_config/tstack2.dh' adding 'primer3/src/libprimer3/primer3_config/tstack2.ds' adding 'primer3/src/libprimer3/primer3_config/tstack_tm_inf.ds' adding 'primer3/src/libprimer3/primer3_config/interpretations/dangle_i.dh' adding 'primer3/src/libprimer3/primer3_config/interpretations/dangle_i.ds' adding 'primer3/src/libprimer3/primer3_config/interpretations/loops_i.dh' adding 'primer3/src/libprimer3/primer3_config/interpretations/loops_i.ds' adding 'primer3/src/libprimer3/primer3_config/interpretations/stack_i.dh' adding 'primer3/src/libprimer3/primer3_config/interpretations/stack_i.ds' adding 'primer3/src/libprimer3/primer3_config/interpretations/stackmm_i_mm.dh' adding 'primer3/src/libprimer3/primer3_config/interpretations/stackmm_i_mm.ds' adding 'primer3/src/libprimer3/primer3_config/interpretations/tetraloop_i.dh' adding 'primer3/src/libprimer3/primer3_config/interpretations/tetraloop_i.ds' adding 'primer3/src/libprimer3/primer3_config/interpretations/triloop_i.dh' adding 'primer3/src/libprimer3/primer3_config/interpretations/triloop_i.ds' adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack2_i.dh' adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack2_i.ds' adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack_i.dh' adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack_i.ds' adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack_tm_inf_i.dh' adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack_tm_inf_i.ds' adding 'primer3_py-2.3.1.dist-info/licenses/AUTHORS' adding 'primer3_py-2.3.1.dist-info/licenses/LICENSE' adding 'primer3_py-2.3.1.dist-info/METADATA' adding 'primer3_py-2.3.1.dist-info/WHEEL' adding 'primer3_py-2.3.1.dist-info/top_level.txt' adding 'primer3_py-2.3.1.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built primer3_py-2.3.1-cp314-cp314-linux_x86_64.whl Finished creating a wheel... Finished executing pypaBuildPhase buildPhase completed in 30 seconds Running phase: pythonRuntimeDepsCheckHook Executing pythonRuntimeDepsCheck Checking runtime dependencies for primer3_py-2.3.1-cp314-cp314-linux_x86_64.whl Finished executing pythonRuntimeDepsCheck Running phase: installPhase Executing pypaInstallPhase Successfully installed primer3_py-2.3.1-cp314-cp314-linux_x86_64.whl Finished executing pypaInstallPhase Running phase: pythonOutputDistPhase Executing pythonOutputDistPhase Finished executing pythonOutputDistPhase Running phase: fixupPhase shrinking RPATHs of ELF executables and libraries in /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1 shrinking /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/p3helpers.cpython-314-x86_64-linux-gnu.so shrinking /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so shrinking /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/amplicon3_core shrinking /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/ntdpal shrinking /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/ntthal shrinking /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/oligotm shrinking /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/primer3_core shrinking /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/primer3_masker checking for references to /build/ in /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1... patching script interpreter paths in /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1 stripping (with command strip and flags -S -p) in /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib shrinking RPATHs of ELF executables and libraries in /nix/store/bvkqcvig74mq0a8yib95zgk6p1nmcxpp-python3.14-primer3-py-2.3.1-dist checking for references to /build/ in /nix/store/bvkqcvig74mq0a8yib95zgk6p1nmcxpp-python3.14-primer3-py-2.3.1-dist... patching script interpreter paths in /nix/store/bvkqcvig74mq0a8yib95zgk6p1nmcxpp-python3.14-primer3-py-2.3.1-dist Executing pythonRemoveTestsDir Finished executing pythonRemoveTestsDir Running phase: installCheckPhase no Makefile or custom installCheckPhase, doing nothing Running phase: pythonCatchConflictsPhase Running phase: pythonRemoveBinBytecodePhase Running phase: pythonImportsCheckPhase Executing pythonImportsCheckPhase Check whether the following modules can be imported: primer3 primer3.bindings Running phase: pythonMetadataCheckPhase Executing pythonMetadataCheckPhase Running phase: pytestCheckPhase Executing pytestCheckPhase /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/_distutils_hack/__init__.py:15: UserWarning: Distutils was imported before Setuptools, but importing Setuptools also replaces the `distutils` module in `sys.modules`. This may lead to undesirable behaviors or errors. To avoid these issues, avoid using distutils directly, ensure that setuptools is installed in the traditional way (e.g. not an editable install), and/or make sure that setuptools is always imported before distutils. warnings.warn( /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/_distutils_hack/__init__.py:30: UserWarning: Setuptools is replacing distutils. Support for replacing an already imported distutils is deprecated. In the future, this condition will fail. Register concerns at https://github.com/pypa/setuptools/issues/new?template=distutils-deprecation.yml warnings.warn( no windows rm -f *.o primer3_core ntdpal ntthal amplicon3_core oligotm long_seq_tm_test primer3_masker *~ libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a libprimer3.so.1.0.0 libdpal.a.so.1.0.0 libthal.a.so.1.0.0 libthalpara.a.so.1.0.0 libamplicontm.so.1.0.0 liboligotm.so.1.2.0 libmasker.a.so.1.0.0 example.for example.rev example.int core ../*~ no windows cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib primer3_boulder_main.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o format_output.o format_output.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o read_boulder.o read_boulder.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o print_boulder.o print_boulder.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -Wno-deprecated -o libprimer3.o libprimer3.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o p3_seq_lib.o p3_seq_lib.c ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: creating libprimer3.a a - libprimer3.o a - p3_seq_lib.o ranlib libprimer3.a cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o dpal_primer.o dpal.c ar rv libdpal.a dpal_primer.o ar: creating libdpal.a a - dpal_primer.o ranlib libdpal.a cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal_primer.o thal.c ar rv libthal.a thal_primer.o ar: creating libthal.a a - thal_primer.o ranlib libthal.a cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal_parameters.o thal_parameters.c ar rv libthalpara.a thal_parameters.o ar: creating libthalpara.a a - thal_parameters.o ranlib libthalpara.a cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -c -o oligotm.o oligotm.c ar rv liboligotm.a oligotm.o ar: creating liboligotm.a a - oligotm.o ranlib liboligotm.a cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -c -o amplicontm.o amplicontm.c ar rv libamplicontm.a amplicontm.o ar: creating libamplicontm.a a - amplicontm.o ranlib libamplicontm.a cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib masker.c ar rv libmasker.a masker.o ar: creating libmasker.a a - masker.o ranlib libmasker.a cc -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -o ntdpal_main.o ntdpal_main.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o dpal.o dpal.c cc -g -o ntdpal ntdpal_main.o dpal.o cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o thal_main.o thal_main.c cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal.o thal.c cc -g -o ntthal thal_main.o thal.o thal_parameters.o -lm cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o amplicon3_core amplicontm_main.c libamplicontm.a -lm cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o oligotm oligotm_main.c liboligotm.a -lm cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm cc -g -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm [1/2] Cythonizing primer3/p3helpers.pyx warning: primer3/p3helpers.pyx:34:28: 'COMP_BASE_LUT' redeclared warning: primer3/p3helpers.pyx:35:27: 'SANITIZE_LUT' redeclared warning: primer3/p3helpers.pyx:36:29: 'ACGT_UPPER_LUT' redeclared warning: primer3/p3helpers.pyx:37:36: 'IS_UPPERCASE_ACGT_LUT' redeclared [2/2] Cythonizing primer3/thermoanalysis.pyx warning: primer3/thermoanalysis.pyx:1406:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310 /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2027-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! corresp(dist, value, root_dir) /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! dist._finalize_license_expression() /nix/store/gyficbimx12q5975523ps3kjzz8ys4pq-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build_ext building 'primer3.p3helpers' extension gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3 -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/p3helpers.c -o build/temp.linux-x86_64-cpython-314/primer3/p3helpers.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/fh8svr4ds87z84iarfnxrlfpjlbmc816-tzdata-2026c/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/fh8svr4ds87z84iarfnxrlfpjlbmc816-tzdata-2026c/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib build/temp.linux-x86_64-cpython-314/primer3/p3helpers.o -L/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/primer3/p3helpers.cpython-314-x86_64-linux-gnu.so building 'primer3.thermoanalysis' extension gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/dpal.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/dpal.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/libprimer3flex.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3flex.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/masker.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/masker.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/oligotm.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/oligotm.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/p3_seq_lib.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/p3_seq_lib.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/read_boulder.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/read_boulder.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/thal_parameters.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/thal_parameters.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/src/libprimer3/thalflex.c -o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/thalflex.o -Wno-error=declaration-after-statement -Wno-unused-function In file included from /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/string.h:548, from primer3/src/libprimer3/thalflex.c:66: In function ‘strcpy’, inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5, inlined from ‘calc_hairpin’ at primer3/src/libprimer3/thalflex.c:1842:18: /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’ In function ‘strcpy’, inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5, inlined from ‘calc_bulge_internal.constprop’ at primer3/src/libprimer3/thalflex.c:1946:18: /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’ In function ‘strcpy’, inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5, inlined from ‘maxTM’ at primer3/src/libprimer3/thalflex.h:752:18, inlined from ‘fillMatrix.constprop’ at primer3/src/libprimer3/thalflex.c:1701:11: /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’ In function ‘strcpy’, inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5, inlined from ‘calc_bulge_internal’ at primer3/src/libprimer3/thalflex.c:1946:18, inlined from ‘fillMatrix.constprop’ at primer3/src/libprimer3/thalflex.c:1721:17: /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: warning: argument 1 null where non-null expected because argument 3 is nonzero [-Wnonnull] 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /nix/store/lbjwxax9n0457lgd83rqwpd1l9lgfl7r-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’ gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3/src -I/build/source/primer3/src/libprimer3 -I/build/source/primer3/src/libprimer3/klib -I/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/include/python3.14 -c primer3/thermoanalysis.c -o build/temp.linux-x86_64-cpython-314/primer3/thermoanalysis.o -Wno-error=declaration-after-statement -Wno-unused-function gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/fh8svr4ds87z84iarfnxrlfpjlbmc816-tzdata-2026c/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.8.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-util-linux-minimal-2.42.3-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.6/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.3.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.6.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/fh8svr4ds87z84iarfnxrlfpjlbmc816-tzdata-2026c/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.26-lib/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.3p3/lib build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/dpal.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3flex.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/masker.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/oligotm.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/p3_seq_lib.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/read_boulder.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/thal_parameters.o build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3/thalflex.o build/temp.linux-x86_64-cpython-314/primer3/thermoanalysis.o -L/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.cpython-314-x86_64-linux-gnu.so -> primer3 copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so -> primer3 pytest flags: -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.14.7, pytest-9.1.1, pluggy-1.6.0 rootdir: /build/source configfile: pyproject.toml plugins: typeguard-4.5.2 collected 45 items tests/test_argdefaults.py ... [ 6%] tests/test_ntthal_io.py . [ 8%] tests/test_p3helpers.py ....... [ 24%] tests/test_primerdesign.py ......... [ 44%] tests/test_sequences.py .......... [ 66%] tests/test_str_rep_ifc_compat.py .. [ 71%] tests/test_thermoanalysis.py ........... [ 95%] tests/test_threadsafe.py .. [100%] ============================= 45 passed in 19.02s ============================== Finished executing pytestCheckPhase pytestCheckPhase completed in 47 seconds Running phase: pytestcachePhase Running phase: pytestRemoveBytecodePhase