python3.14-primer3-py-2.3.1
checks.x86_64-linux.pkgs-primer3-py
· build #73
· raw
1Sourcing python-remove-tests-dir-hook2Sourcing python-catch-conflicts-hook.sh3Sourcing python-remove-bin-bytecode-hook.sh4Sourcing pypa-build-hook5Using pypaBuildPhase6Sourcing python-runtime-deps-check-hook7Using pythonRuntimeDepsCheckHook8Sourcing pypa-install-hook9Using pypaInstallPhase10Sourcing python-imports-check-hook.sh11Using pythonImportsCheckPhase12Sourcing python-metadata-check-hook.sh13Using pythonMetadataCheckPhase14Sourcing python-namespaces-hook15Sourcing python-catch-conflicts-hook.sh16Sourcing pytest-check-hook17Using pytestCheckPhase
unpackPhase
18unpacking source archive /nix/store/8qd97xh7haqn9bsjn93n9pcm4clc036j-source19source root is source20setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "source/valgrind-python.supp"configurePhase
21no configure script, doing nothingbuildPhase
22Executing pypaBuildPhase23Creating a wheel...24pypa build flags: --no-isolation --outdir dist/ --wheel25* Getting build dependencies for wheel...26[1/2] Cythonizing primer3/p3helpers.pyx27warning: primer3/p3helpers.pyx:34:28: 'COMP_BASE_LUT' redeclared 28warning: primer3/p3helpers.pyx:35:27: 'SANITIZE_LUT' redeclared 29warning: primer3/p3helpers.pyx:36:29: 'ACGT_UPPER_LUT' redeclared 30warning: primer3/p3helpers.pyx:37:36: 'IS_UPPERCASE_ACGT_LUT' redeclared 31[2/2] Cythonizing primer3/thermoanalysis.pyx32warning: 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/431033/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-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 deprecated34!!3536 ********************************************************************************37 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).3839 By 2027-Feb-18, you need to update your project and remove deprecated calls40 or your builds will no longer be supported.4142 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.43 ********************************************************************************4445!!46 corresp(dist, value, root_dir)47/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.48!!4950 ********************************************************************************51 Please consider removing the following classifiers in favor of a SPDX license expression:5253 License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)5455 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.56 ********************************************************************************5758!!59 dist._finalize_license_expression()60/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.61!!6263 ********************************************************************************64 Please consider removing the following classifiers in favor of a SPDX license expression:6566 License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)6768 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.69 ********************************************************************************7071!!72 self._finalize_license_expression()73running egg_info74creating primer3_py.egg-info75writing primer3_py.egg-info/PKG-INFO76writing dependency_links to primer3_py.egg-info/dependency_links.txt77writing requirements to primer3_py.egg-info/requires.txt78writing top-level names to primer3_py.egg-info/top_level.txt79writing manifest file 'primer3_py.egg-info/SOURCES.txt'80dependency /build/source/primer3/src/libprimer3/libprimer3.h won't be automatically included in the manifest: the path must be relative81dependency /build/source/primer3/src/libprimer3/masker.h won't be automatically included in the manifest: the path must be relative82dependency /build/source/primer3/src/libprimer3/oligotm.h won't be automatically included in the manifest: the path must be relative83dependency /build/source/primer3/src/libprimer3/p3_seq_lib.h won't be automatically included in the manifest: the path must be relative84dependency /build/source/primer3/src/libprimer3/read_boulder.h won't be automatically included in the manifest: the path must be relative85dependency /build/source/primer3/src/libprimer3/thal.h won't be automatically included in the manifest: the path must be relative86reading manifest file 'primer3_py.egg-info/SOURCES.txt'87reading manifest template 'MANIFEST.in'88warning: no files found matching '*.rst' under directory 'docs'89warning: no previously-included files matching '*.pyc' found anywhere in distribution90warning: no previously-included files matching '*.pyo' found anywhere in distribution91warning: no previously-included files matching '*.pyd' found anywhere in distribution92warning: no previously-included files matching '*.so' found anywhere in distribution93warning: no previously-included files matching '*.dylib' found anywhere in distribution94warning: no previously-included files matching '*.dll' found anywhere in distribution95warning: no previously-included files matching '__pycache__' found anywhere in distribution96warning: no previously-included files matching '*.egg-info' found anywhere in distribution97warning: no previously-included files matching '.DS_Store' found anywhere in distribution98warning: no previously-included files matching '.*.swp' found anywhere in distribution99no previously-included directories found matching 'primer3/thermoanalysis.c'100adding license file 'LICENSE'101adding license file 'AUTHORS'102writing manifest file 'primer3_py.egg-info/SOURCES.txt'103* Building wheel...104[1/2] Cythonizing primer3/p3helpers.pyx105warning: primer3/p3helpers.pyx:34:28: 'COMP_BASE_LUT' redeclared 106warning: primer3/p3helpers.pyx:35:27: 'SANITIZE_LUT' redeclared 107warning: primer3/p3helpers.pyx:36:29: 'ACGT_UPPER_LUT' redeclared 108warning: primer3/p3helpers.pyx:37:36: 'IS_UPPERCASE_ACGT_LUT' redeclared 109[2/2] Cythonizing primer3/thermoanalysis.pyx110warning: 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/4310111/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-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 deprecated112!!113114 ********************************************************************************115 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).116117 By 2027-Feb-18, you need to update your project and remove deprecated calls118 or your builds will no longer be supported.119120 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.121 ********************************************************************************122123!!124 corresp(dist, value, root_dir)125/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.126!!127128 ********************************************************************************129 Please consider removing the following classifiers in favor of a SPDX license expression:130131 License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)132133 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.134 ********************************************************************************135136!!137 dist._finalize_license_expression()138/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.139!!140141 ********************************************************************************142 Please consider removing the following classifiers in favor of a SPDX license expression:143144 License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)145146 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.147 ********************************************************************************148149!!150 self._finalize_license_expression()151running bdist_wheel152running build153running build_py154creating build/lib.linux-x86_64-cpython-314/primer3155copying primer3/__init__.py -> build/lib.linux-x86_64-cpython-314/primer3156copying primer3/argdefaults.py -> build/lib.linux-x86_64-cpython-314/primer3157copying primer3/bindings.py -> build/lib.linux-x86_64-cpython-314/primer3158running egg_info159writing primer3_py.egg-info/PKG-INFO160writing dependency_links to primer3_py.egg-info/dependency_links.txt161writing requirements to primer3_py.egg-info/requires.txt162writing top-level names to primer3_py.egg-info/top_level.txt163dependency /build/source/primer3/src/libprimer3/libprimer3.h won't be automatically included in the manifest: the path must be relative164dependency /build/source/primer3/src/libprimer3/masker.h won't be automatically included in the manifest: the path must be relative165dependency /build/source/primer3/src/libprimer3/oligotm.h won't be automatically included in the manifest: the path must be relative166dependency /build/source/primer3/src/libprimer3/p3_seq_lib.h won't be automatically included in the manifest: the path must be relative167dependency /build/source/primer3/src/libprimer3/read_boulder.h won't be automatically included in the manifest: the path must be relative168dependency /build/source/primer3/src/libprimer3/thal.h won't be automatically included in the manifest: the path must be relative169reading manifest file 'primer3_py.egg-info/SOURCES.txt'170reading manifest template 'MANIFEST.in'171warning: no files found matching '*.rst' under directory 'docs'172warning: no previously-included files matching '*.pyc' found anywhere in distribution173warning: no previously-included files matching '*.pyo' found anywhere in distribution174warning: no previously-included files matching '*.pyd' found anywhere in distribution175warning: no previously-included files matching '*.so' found anywhere in distribution176warning: no previously-included files matching '*.dylib' found anywhere in distribution177warning: no previously-included files matching '*.dll' found anywhere in distribution178warning: no previously-included files matching '__pycache__' found anywhere in distribution179warning: no previously-included files matching '*.egg-info' found anywhere in distribution180warning: no previously-included files matching '.DS_Store' found anywhere in distribution181warning: no previously-included files matching '.*.swp' found anywhere in distribution182no previously-included directories found matching 'primer3/thermoanalysis.c'183adding license file 'LICENSE'184adding license file 'AUTHORS'185writing manifest file 'primer3_py.egg-info/SOURCES.txt'186/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-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.187!!188189 ********************************************************************************190 ############################191 # Package would be ignored #192 ############################193 Python recognizes 'primer3.src.libprimer3' as an importable package[^1],194 but it is absent from setuptools' `packages` configuration.195196 This leads to an ambiguous overall configuration. If you want to distribute this197 package, please make sure that 'primer3.src.libprimer3' is explicitly added198 to the `packages` configuration field.199200 Alternatively, you can also rely on setuptools' discovery methods201 (for example by using `find_namespace_packages(...)`/`find_namespace:`202 instead of `find_packages(...)`/`find:`).203204 You can read more about "package discovery" on setuptools documentation page:205206 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html207208 If you don't want 'primer3.src.libprimer3' to be distributed and are209 already explicitly excluding 'primer3.src.libprimer3' via210 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,211 you can try to use `exclude_package_data`, or `include-package-data=False` in212 combination with a more fine grained `package-data` configuration.213214 You can read more about "package data files" on setuptools documentation page:215216 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html217218219 [^1]: For Python, any directory (with suitable naming) can be imported,220 even if it does not contain any `.py` files.221 On the other hand, currently there is no concept of package data222 directory, all directories are treated like packages.223 ********************************************************************************224225!!226 check.warn(importable)227/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-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.228!!229230 ********************************************************************************231 ############################232 # Package would be ignored #233 ############################234 Python recognizes 'primer3.src.libprimer3.klib' as an importable package[^1],235 but it is absent from setuptools' `packages` configuration.236237 This leads to an ambiguous overall configuration. If you want to distribute this238 package, please make sure that 'primer3.src.libprimer3.klib' is explicitly added239 to the `packages` configuration field.240241 Alternatively, you can also rely on setuptools' discovery methods242 (for example by using `find_namespace_packages(...)`/`find_namespace:`243 instead of `find_packages(...)`/`find:`).244245 You can read more about "package discovery" on setuptools documentation page:246247 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html248249 If you don't want 'primer3.src.libprimer3.klib' to be distributed and are250 already explicitly excluding 'primer3.src.libprimer3.klib' via251 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,252 you can try to use `exclude_package_data`, or `include-package-data=False` in253 combination with a more fine grained `package-data` configuration.254255 You can read more about "package data files" on setuptools documentation page:256257 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html258259260 [^1]: For Python, any directory (with suitable naming) can be imported,261 even if it does not contain any `.py` files.262 On the other hand, currently there is no concept of package data263 directory, all directories are treated like packages.264 ********************************************************************************265266!!267 check.warn(importable)268/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-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.269!!270271 ********************************************************************************272 ############################273 # Package would be ignored #274 ############################275 Python recognizes 'primer3.src.libprimer3.klib.test' as an importable package[^1],276 but it is absent from setuptools' `packages` configuration.277278 This leads to an ambiguous overall configuration. If you want to distribute this279 package, please make sure that 'primer3.src.libprimer3.klib.test' is explicitly added280 to the `packages` configuration field.281282 Alternatively, you can also rely on setuptools' discovery methods283 (for example by using `find_namespace_packages(...)`/`find_namespace:`284 instead of `find_packages(...)`/`find:`).285286 You can read more about "package discovery" on setuptools documentation page:287288 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html289290 If you don't want 'primer3.src.libprimer3.klib.test' to be distributed and are291 already explicitly excluding 'primer3.src.libprimer3.klib.test' via292 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,293 you can try to use `exclude_package_data`, or `include-package-data=False` in294 combination with a more fine grained `package-data` configuration.295296 You can read more about "package data files" on setuptools documentation page:297298 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html299300301 [^1]: For Python, any directory (with suitable naming) can be imported,302 even if it does not contain any `.py` files.303 On the other hand, currently there is no concept of package data304 directory, all directories are treated like packages.305 ********************************************************************************306307!!308 check.warn(importable)309/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-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.310!!311312 ********************************************************************************313 ############################314 # Package would be ignored #315 ############################316 Python recognizes 'primer3.src.libprimer3.primer3_config' as an importable package[^1],317 but it is absent from setuptools' `packages` configuration.318319 This leads to an ambiguous overall configuration. If you want to distribute this320 package, please make sure that 'primer3.src.libprimer3.primer3_config' is explicitly added321 to the `packages` configuration field.322323 Alternatively, you can also rely on setuptools' discovery methods324 (for example by using `find_namespace_packages(...)`/`find_namespace:`325 instead of `find_packages(...)`/`find:`).326327 You can read more about "package discovery" on setuptools documentation page:328329 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html330331 If you don't want 'primer3.src.libprimer3.primer3_config' to be distributed and are332 already explicitly excluding 'primer3.src.libprimer3.primer3_config' via333 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,334 you can try to use `exclude_package_data`, or `include-package-data=False` in335 combination with a more fine grained `package-data` configuration.336337 You can read more about "package data files" on setuptools documentation page:338339 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html340341342 [^1]: For Python, any directory (with suitable naming) can be imported,343 even if it does not contain any `.py` files.344 On the other hand, currently there is no concept of package data345 directory, all directories are treated like packages.346 ********************************************************************************347348!!349 check.warn(importable)350/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-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.351!!352353 ********************************************************************************354 ############################355 # Package would be ignored #356 ############################357 Python recognizes 'primer3.src.libprimer3.primer3_config.interpretations' as an importable package[^1],358 but it is absent from setuptools' `packages` configuration.359360 This leads to an ambiguous overall configuration. If you want to distribute this361 package, please make sure that 'primer3.src.libprimer3.primer3_config.interpretations' is explicitly added362 to the `packages` configuration field.363364 Alternatively, you can also rely on setuptools' discovery methods365 (for example by using `find_namespace_packages(...)`/`find_namespace:`366 instead of `find_packages(...)`/`find:`).367368 You can read more about "package discovery" on setuptools documentation page:369370 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html371372 If you don't want 'primer3.src.libprimer3.primer3_config.interpretations' to be distributed and are373 already explicitly excluding 'primer3.src.libprimer3.primer3_config.interpretations' via374 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,375 you can try to use `exclude_package_data`, or `include-package-data=False` in376 combination with a more fine grained `package-data` configuration.377378 You can read more about "package data files" on setuptools documentation page:379380 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html381382383 [^1]: For Python, any directory (with suitable naming) can be imported,384 even if it does not contain any `.py` files.385 On the other hand, currently there is no concept of package data386 directory, all directories are treated like packages.387 ********************************************************************************388389!!390 check.warn(importable)391copying primer3/p3helpers.c -> build/lib.linux-x86_64-cpython-314/primer3392copying primer3/p3helpers.h -> build/lib.linux-x86_64-cpython-314/primer3393copying primer3/p3helpers.pxd -> build/lib.linux-x86_64-cpython-314/primer3394copying primer3/p3helpers.pyx -> build/lib.linux-x86_64-cpython-314/primer3395copying primer3/thermoanalysis.c -> build/lib.linux-x86_64-cpython-314/primer3396copying primer3/thermoanalysis.pxd -> build/lib.linux-x86_64-cpython-314/primer3397copying primer3/thermoanalysis.pxi -> build/lib.linux-x86_64-cpython-314/primer3398copying primer3/thermoanalysis.pyx -> build/lib.linux-x86_64-cpython-314/primer3399creating build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3400copying primer3/src/libprimer3/ABOUT.txt -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3401copying primer3/src/libprimer3/LICENSE.txt -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3402copying primer3/src/libprimer3/Makefile -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3403copying primer3/src/libprimer3/amplicontm.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3404copying primer3/src/libprimer3/amplicontm.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3405copying primer3/src/libprimer3/amplicontm_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3406copying primer3/src/libprimer3/dpal.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3407copying primer3/src/libprimer3/dpal.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3408copying primer3/src/libprimer3/format_output.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3409copying primer3/src/libprimer3/format_output.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3410copying primer3/src/libprimer3/gpl-2.0.txt -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3411copying primer3/src/libprimer3/humrep_and_simple.txt -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3412copying primer3/src/libprimer3/libprimer3.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3413copying primer3/src/libprimer3/libprimer3.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3414copying primer3/src/libprimer3/libprimer3flex.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3415copying primer3/src/libprimer3/libprimer3flex.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3416copying primer3/src/libprimer3/long_seq_tm_test_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3417copying primer3/src/libprimer3/masker.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3418copying primer3/src/libprimer3/masker.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3419copying primer3/src/libprimer3/masker_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3420copying primer3/src/libprimer3/ntdpal_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3421copying primer3/src/libprimer3/oligotm.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3422copying primer3/src/libprimer3/oligotm.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3423copying primer3/src/libprimer3/oligotm_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3424copying primer3/src/libprimer3/p3_seq_lib.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3425copying primer3/src/libprimer3/p3_seq_lib.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3426copying primer3/src/libprimer3/primer3_boulder_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3427copying primer3/src/libprimer3/print_boulder.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3428copying primer3/src/libprimer3/print_boulder.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3429copying primer3/src/libprimer3/read_boulder.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3430copying primer3/src/libprimer3/read_boulder.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3431copying primer3/src/libprimer3/release_notes.txt -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3432copying primer3/src/libprimer3/thal.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3433copying primer3/src/libprimer3/thal.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3434copying primer3/src/libprimer3/thal_main.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3435copying primer3/src/libprimer3/thal_parameters.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3436copying primer3/src/libprimer3/thal_parameters.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3437copying primer3/src/libprimer3/thalflex.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3438copying primer3/src/libprimer3/thalflex.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3439copying primer3/src/libprimer3/thalflexsignatures.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3440creating build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib441copying primer3/src/libprimer3/klib/README.md -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib442copying primer3/src/libprimer3/klib/khash.h -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib443creating build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test444copying primer3/src/libprimer3/klib/test/Makefile -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test445copying primer3/src/libprimer3/klib/test/khash_keith.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test446copying primer3/src/libprimer3/klib/test/khash_keith2.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test447copying primer3/src/libprimer3/klib/test/khash_test.c -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test448creating build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config449copying primer3/src/libprimer3/primer3_config/dangle.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config450copying primer3/src/libprimer3/primer3_config/dangle.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config451copying primer3/src/libprimer3/primer3_config/loops.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config452copying primer3/src/libprimer3/primer3_config/loops.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config453copying primer3/src/libprimer3/primer3_config/stack.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config454copying primer3/src/libprimer3/primer3_config/stack.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config455copying primer3/src/libprimer3/primer3_config/stackmm.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config456copying primer3/src/libprimer3/primer3_config/stackmm.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config457copying primer3/src/libprimer3/primer3_config/tetraloop.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config458copying primer3/src/libprimer3/primer3_config/tetraloop.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config459copying primer3/src/libprimer3/primer3_config/triloop.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config460copying primer3/src/libprimer3/primer3_config/triloop.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config461copying primer3/src/libprimer3/primer3_config/tstack.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config462copying primer3/src/libprimer3/primer3_config/tstack2.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config463copying primer3/src/libprimer3/primer3_config/tstack2.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config464copying primer3/src/libprimer3/primer3_config/tstack_tm_inf.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config465creating build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations466copying primer3/src/libprimer3/primer3_config/interpretations/dangle_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations467copying primer3/src/libprimer3/primer3_config/interpretations/dangle_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations468copying primer3/src/libprimer3/primer3_config/interpretations/loops_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations469copying primer3/src/libprimer3/primer3_config/interpretations/loops_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations470copying primer3/src/libprimer3/primer3_config/interpretations/stack_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations471copying primer3/src/libprimer3/primer3_config/interpretations/stack_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations472copying primer3/src/libprimer3/primer3_config/interpretations/stackmm_i_mm.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations473copying primer3/src/libprimer3/primer3_config/interpretations/stackmm_i_mm.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations474copying primer3/src/libprimer3/primer3_config/interpretations/tetraloop_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations475copying primer3/src/libprimer3/primer3_config/interpretations/tetraloop_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations476copying primer3/src/libprimer3/primer3_config/interpretations/triloop_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations477copying primer3/src/libprimer3/primer3_config/interpretations/triloop_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations478copying primer3/src/libprimer3/primer3_config/interpretations/tstack2_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations479copying primer3/src/libprimer3/primer3_config/interpretations/tstack2_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations480copying primer3/src/libprimer3/primer3_config/interpretations/tstack_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations481copying primer3/src/libprimer3/primer3_config/interpretations/tstack_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations482copying primer3/src/libprimer3/primer3_config/interpretations/tstack_tm_inf_i.dh -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations483copying primer3/src/libprimer3/primer3_config/interpretations/tstack_tm_inf_i.ds -> build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/interpretations484running build_ext485no windows486rm -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 ../*~487no windows488cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib primer3_boulder_main.c489cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o format_output.o format_output.c490cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o read_boulder.o read_boulder.c491cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o print_boulder.o print_boulder.c492cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -Wno-deprecated -o libprimer3.o libprimer3.c493cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o p3_seq_lib.o p3_seq_lib.c494ar rv libprimer3.a libprimer3.o p3_seq_lib.o495ar: creating libprimer3.a496a - libprimer3.o497a - p3_seq_lib.o498ranlib libprimer3.a499cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o dpal_primer.o dpal.c500ar rv libdpal.a dpal_primer.o501ar: creating libdpal.a502a - dpal_primer.o503ranlib libdpal.a504cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal_primer.o thal.c505ar rv libthal.a thal_primer.o506ar: creating libthal.a507a - thal_primer.o508ranlib libthal.a509cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal_parameters.o thal_parameters.c510ar rv libthalpara.a thal_parameters.o511ar: creating libthalpara.a512a - thal_parameters.o513ranlib libthalpara.a514cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -c -o oligotm.o oligotm.c515ar rv liboligotm.a oligotm.o516ar: creating liboligotm.a517a - oligotm.o518ranlib liboligotm.a519cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -c -o amplicontm.o amplicontm.c520ar rv libamplicontm.a amplicontm.o521ar: creating libamplicontm.a522a - amplicontm.o523ranlib libamplicontm.a524cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib masker.c525ar rv libmasker.a masker.o526ar: creating libmasker.a527a - masker.o528ranlib libmasker.a529cc -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 -lm530cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -o ntdpal_main.o ntdpal_main.c531cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o dpal.o dpal.c532cc -g -o ntdpal ntdpal_main.o dpal.o533cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o thal_main.o thal_main.c534cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal.o thal.c535cc -g -o ntthal thal_main.o thal.o thal_parameters.o -lm536cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o amplicon3_core amplicontm_main.c libamplicontm.a -lm537cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o oligotm oligotm_main.c liboligotm.a -lm538cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm539cc -g -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm540building 'primer3.p3helpers' extension541creating build/temp.linux-x86_64-cpython-314/primer3542gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3 -I/nix/store/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function543gcc -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-2.42.2-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-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/p0ff33dca0fbkskqwrl3spvxcn5974h0-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-2.42.2-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-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/p0ff33dca0fbkskqwrl3spvxcn5974h0-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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/primer3/p3helpers.cpython-314-x86_64-linux-gnu.so544building 'primer3.thermoanalysis' extension545creating build/temp.linux-x86_64-cpython-314/primer3/src/libprimer3546gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function547gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function548gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function549gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function550gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function551gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function552gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function553gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function554In file included from /nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/string.h:548,555 from primer3/src/libprimer3/thalflex.c:66:556In function ‘strcpy’,557 inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5,558 inlined from ‘calc_hairpin’ at primer3/src/libprimer3/thalflex.c:1842:18:559/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-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]560 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));561 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~562/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’563In function ‘strcpy’,564 inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5,565 inlined from ‘calc_bulge_internal.constprop’ at primer3/src/libprimer3/thalflex.c:1946:18:566/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-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]567 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));568 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~569/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’570In function ‘strcpy’,571 inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5,572 inlined from ‘maxTM’ at primer3/src/libprimer3/thalflex.h:752:18,573 inlined from ‘fillMatrix.constprop’ at primer3/src/libprimer3/thalflex.c:1701:11:574/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-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]575 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));576 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~577/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’578In function ‘strcpy’,579 inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5,580 inlined from ‘calc_bulge_internal’ at primer3/src/libprimer3/thalflex.c:1946:18,581 inlined from ‘fillMatrix.constprop’ at primer3/src/libprimer3/thalflex.c:1721:17:582/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-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]583 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));584 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~585/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’586gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function587gcc -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-2.42.2-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-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/p0ff33dca0fbkskqwrl3spvxcn5974h0-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-2.42.2-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-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/p0ff33dca0fbkskqwrl3spvxcn5974h0-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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so588installing to build/bdist.linux-x86_64/wheel589running install590running install_lib591creating build/bdist.linux-x86_64/wheel592creating build/bdist.linux-x86_64/wheel/primer3593copying build/lib.linux-x86_64-cpython-314/primer3/__init__.py -> build/bdist.linux-x86_64/wheel/./primer3594copying build/lib.linux-x86_64-cpython-314/primer3/argdefaults.py -> build/bdist.linux-x86_64/wheel/./primer3595copying build/lib.linux-x86_64-cpython-314/primer3/bindings.py -> build/bdist.linux-x86_64/wheel/./primer3596copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.c -> build/bdist.linux-x86_64/wheel/./primer3597copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.h -> build/bdist.linux-x86_64/wheel/./primer3598copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.pxd -> build/bdist.linux-x86_64/wheel/./primer3599copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.pyx -> build/bdist.linux-x86_64/wheel/./primer3600copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.c -> build/bdist.linux-x86_64/wheel/./primer3601copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.pxd -> build/bdist.linux-x86_64/wheel/./primer3602copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.pxi -> build/bdist.linux-x86_64/wheel/./primer3603copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.pyx -> build/bdist.linux-x86_64/wheel/./primer3604creating build/bdist.linux-x86_64/wheel/primer3/src605creating build/bdist.linux-x86_64/wheel/primer3/src/libprimer3606copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/ABOUT.txt -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3607copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/LICENSE.txt -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3608copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/Makefile -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3609copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/amplicontm.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3610copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/amplicontm.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3611copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/amplicontm_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3612copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/dpal.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3613copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/dpal.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3614copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/format_output.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3615copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/format_output.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3616copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/gpl-2.0.txt -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3617copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/humrep_and_simple.txt -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3618copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3619copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3620copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3flex.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3621copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/libprimer3flex.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3622copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/long_seq_tm_test_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3623copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/masker.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3624copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/masker.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3625copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/masker_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3626copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/ntdpal_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3627copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/oligotm.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3628copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/oligotm.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3629copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/oligotm_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3630copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/p3_seq_lib.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3631copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/p3_seq_lib.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3632copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_boulder_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3633copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/print_boulder.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3634copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/print_boulder.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3635copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/read_boulder.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3636copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/read_boulder.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3637copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/release_notes.txt -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3638copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thal.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3639copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thal.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3640copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thal_main.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3641copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thal_parameters.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3642copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thal_parameters.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3643copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thalflex.c -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3644copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thalflex.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3645copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/thalflexsignatures.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3646creating build/bdist.linux-x86_64/wheel/primer3/src/libprimer3/klib647copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/README.md -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/klib648copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/khash.h -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/klib649creating build/bdist.linux-x86_64/wheel/primer3/src/libprimer3/klib/test650copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/klib/test/Makefile -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/klib/test651copying 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/test652copying 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/test653copying 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/test654creating build/bdist.linux-x86_64/wheel/primer3/src/libprimer3/primer3_config655copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/dangle.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config656copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/dangle.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config657copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/loops.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config658copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/loops.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config659copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/stack.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config660copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/stack.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config661copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/stackmm.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config662copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/stackmm.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config663copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tetraloop.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config664copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tetraloop.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config665copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/triloop.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config666copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/triloop.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config667copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tstack.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config668copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tstack2.dh -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config669copying build/lib.linux-x86_64-cpython-314/primer3/src/libprimer3/primer3_config/tstack2.ds -> build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_config670copying 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_config671creating build/bdist.linux-x86_64/wheel/primer3/src/libprimer3/primer3_config/interpretations672copying 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/interpretations673copying 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/interpretations674copying 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/interpretations675copying 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/interpretations676copying 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/interpretations677copying 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/interpretations678copying 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/interpretations679copying 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/interpretations680copying 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/interpretations681copying 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/interpretations682copying 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/interpretations683copying 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/interpretations684copying 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/interpretations685copying 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/interpretations686copying 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/interpretations687copying 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/interpretations688copying 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/interpretations689copying 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/interpretations690copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./primer3691copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./primer3692Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/amplicon3_core (mode is now 755)693Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/oligotm (mode is now 755)694Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/ntdpal (mode is now 755)695Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/ntthal (mode is now 755)696Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_core (mode is now 755)697Adding executable bit to build/bdist.linux-x86_64/wheel/./primer3/src/libprimer3/primer3_masker (mode is now 755)698running install_egg_info699Copying primer3_py.egg-info to build/bdist.linux-x86_64/wheel/./primer3_py-2.3.1-py3.14.egg-info700running install_scripts701creating build/bdist.linux-x86_64/wheel/primer3_py-2.3.1.dist-info/WHEEL702creating '/build/source/dist/.tmp-0bxhwjn4/primer3_py-2.3.1-cp314-cp314-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it703adding 'primer3/__init__.py'704adding 'primer3/argdefaults.py'705adding 'primer3/bindings.py'706adding 'primer3/p3helpers.c'707adding 'primer3/p3helpers.cpython-314-x86_64-linux-gnu.so'708adding 'primer3/p3helpers.h'709adding 'primer3/p3helpers.pxd'710adding 'primer3/p3helpers.pyx'711adding 'primer3/thermoanalysis.c'712adding 'primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so'713adding 'primer3/thermoanalysis.pxd'714adding 'primer3/thermoanalysis.pxi'715adding 'primer3/thermoanalysis.pyx'716adding 'primer3/src/libprimer3/ABOUT.txt'717adding 'primer3/src/libprimer3/LICENSE.txt'718adding 'primer3/src/libprimer3/Makefile'719adding 'primer3/src/libprimer3/amplicon3_core'720adding 'primer3/src/libprimer3/amplicontm.c'721adding 'primer3/src/libprimer3/amplicontm.h'722adding 'primer3/src/libprimer3/amplicontm_main.c'723adding 'primer3/src/libprimer3/dpal.c'724adding 'primer3/src/libprimer3/dpal.h'725adding 'primer3/src/libprimer3/format_output.c'726adding 'primer3/src/libprimer3/format_output.h'727adding 'primer3/src/libprimer3/gpl-2.0.txt'728adding 'primer3/src/libprimer3/humrep_and_simple.txt'729adding 'primer3/src/libprimer3/libprimer3.c'730adding 'primer3/src/libprimer3/libprimer3.h'731adding 'primer3/src/libprimer3/libprimer3flex.c'732adding 'primer3/src/libprimer3/libprimer3flex.h'733adding 'primer3/src/libprimer3/long_seq_tm_test_main.c'734adding 'primer3/src/libprimer3/masker.c'735adding 'primer3/src/libprimer3/masker.h'736adding 'primer3/src/libprimer3/masker_main.c'737adding 'primer3/src/libprimer3/ntdpal'738adding 'primer3/src/libprimer3/ntdpal_main.c'739adding 'primer3/src/libprimer3/ntthal'740adding 'primer3/src/libprimer3/oligotm'741adding 'primer3/src/libprimer3/oligotm.c'742adding 'primer3/src/libprimer3/oligotm.h'743adding 'primer3/src/libprimer3/oligotm_main.c'744adding 'primer3/src/libprimer3/p3_seq_lib.c'745adding 'primer3/src/libprimer3/p3_seq_lib.h'746adding 'primer3/src/libprimer3/primer3_boulder_main.c'747adding 'primer3/src/libprimer3/primer3_core'748adding 'primer3/src/libprimer3/primer3_masker'749adding 'primer3/src/libprimer3/print_boulder.c'750adding 'primer3/src/libprimer3/print_boulder.h'751adding 'primer3/src/libprimer3/read_boulder.c'752adding 'primer3/src/libprimer3/read_boulder.h'753adding 'primer3/src/libprimer3/release_notes.txt'754adding 'primer3/src/libprimer3/thal.c'755adding 'primer3/src/libprimer3/thal.h'756adding 'primer3/src/libprimer3/thal_main.c'757adding 'primer3/src/libprimer3/thal_parameters.c'758adding 'primer3/src/libprimer3/thal_parameters.h'759adding 'primer3/src/libprimer3/thalflex.c'760adding 'primer3/src/libprimer3/thalflex.h'761adding 'primer3/src/libprimer3/thalflexsignatures.h'762adding 'primer3/src/libprimer3/klib/README.md'763adding 'primer3/src/libprimer3/klib/khash.h'764adding 'primer3/src/libprimer3/klib/test/Makefile'765adding 'primer3/src/libprimer3/klib/test/khash_keith.c'766adding 'primer3/src/libprimer3/klib/test/khash_keith2.c'767adding 'primer3/src/libprimer3/klib/test/khash_test.c'768adding 'primer3/src/libprimer3/primer3_config/dangle.dh'769adding 'primer3/src/libprimer3/primer3_config/dangle.ds'770adding 'primer3/src/libprimer3/primer3_config/loops.dh'771adding 'primer3/src/libprimer3/primer3_config/loops.ds'772adding 'primer3/src/libprimer3/primer3_config/stack.dh'773adding 'primer3/src/libprimer3/primer3_config/stack.ds'774adding 'primer3/src/libprimer3/primer3_config/stackmm.dh'775adding 'primer3/src/libprimer3/primer3_config/stackmm.ds'776adding 'primer3/src/libprimer3/primer3_config/tetraloop.dh'777adding 'primer3/src/libprimer3/primer3_config/tetraloop.ds'778adding 'primer3/src/libprimer3/primer3_config/triloop.dh'779adding 'primer3/src/libprimer3/primer3_config/triloop.ds'780adding 'primer3/src/libprimer3/primer3_config/tstack.dh'781adding 'primer3/src/libprimer3/primer3_config/tstack2.dh'782adding 'primer3/src/libprimer3/primer3_config/tstack2.ds'783adding 'primer3/src/libprimer3/primer3_config/tstack_tm_inf.ds'784adding 'primer3/src/libprimer3/primer3_config/interpretations/dangle_i.dh'785adding 'primer3/src/libprimer3/primer3_config/interpretations/dangle_i.ds'786adding 'primer3/src/libprimer3/primer3_config/interpretations/loops_i.dh'787adding 'primer3/src/libprimer3/primer3_config/interpretations/loops_i.ds'788adding 'primer3/src/libprimer3/primer3_config/interpretations/stack_i.dh'789adding 'primer3/src/libprimer3/primer3_config/interpretations/stack_i.ds'790adding 'primer3/src/libprimer3/primer3_config/interpretations/stackmm_i_mm.dh'791adding 'primer3/src/libprimer3/primer3_config/interpretations/stackmm_i_mm.ds'792adding 'primer3/src/libprimer3/primer3_config/interpretations/tetraloop_i.dh'793adding 'primer3/src/libprimer3/primer3_config/interpretations/tetraloop_i.ds'794adding 'primer3/src/libprimer3/primer3_config/interpretations/triloop_i.dh'795adding 'primer3/src/libprimer3/primer3_config/interpretations/triloop_i.ds'796adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack2_i.dh'797adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack2_i.ds'798adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack_i.dh'799adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack_i.ds'800adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack_tm_inf_i.dh'801adding 'primer3/src/libprimer3/primer3_config/interpretations/tstack_tm_inf_i.ds'802adding 'primer3_py-2.3.1.dist-info/licenses/AUTHORS'803adding 'primer3_py-2.3.1.dist-info/licenses/LICENSE'804adding 'primer3_py-2.3.1.dist-info/METADATA'805adding 'primer3_py-2.3.1.dist-info/WHEEL'806adding 'primer3_py-2.3.1.dist-info/top_level.txt'807adding 'primer3_py-2.3.1.dist-info/RECORD'808removing build/bdist.linux-x86_64/wheel809Successfully built primer3_py-2.3.1-cp314-cp314-linux_x86_64.whl810Finished creating a wheel...811Finished executing pypaBuildPhase812buildPhase completed in 31 secondspythonRuntimeDepsCheckHook
813Executing pythonRuntimeDepsCheck814Checking runtime dependencies for primer3_py-2.3.1-cp314-cp314-linux_x86_64.whl815Finished executing pythonRuntimeDepsCheckinstallPhase
816Executing pypaInstallPhase817Successfully installed primer3_py-2.3.1-cp314-cp314-linux_x86_64.whl818Finished executing pypaInstallPhasepythonOutputDistPhase
819Executing pythonOutputDistPhase820Finished executing pythonOutputDistPhasefixupPhase
821shrinking RPATHs of ELF executables and libraries in /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1822shrinking /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/p3helpers.cpython-314-x86_64-linux-gnu.so823shrinking /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so824shrinking /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/amplicon3_core825shrinking /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/ntdpal826shrinking /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/ntthal827shrinking /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/oligotm828shrinking /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/primer3_core829shrinking /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/src/libprimer3/primer3_masker830checking for references to /build/ in /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1...831patching script interpreter paths in /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1832stripping (with command strip and flags -S -p) in /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib833shrinking RPATHs of ELF executables and libraries in /nix/store/8w01w50az5wzvxkyf542z6y8wgw1ab0l-python3.14-primer3-py-2.3.1-dist834checking for references to /build/ in /nix/store/8w01w50az5wzvxkyf542z6y8wgw1ab0l-python3.14-primer3-py-2.3.1-dist...835patching script interpreter paths in /nix/store/8w01w50az5wzvxkyf542z6y8wgw1ab0l-python3.14-primer3-py-2.3.1-dist836Executing pythonRemoveTestsDir837Finished executing pythonRemoveTestsDirinstallCheckPhase
838no Makefile or custom installCheckPhase, doing nothingpythonImportsCheckPhase
839Executing pythonImportsCheckPhase840Check whether the following modules can be imported: primer3 primer3.bindingspythonMetadataCheckPhase
841Executing pythonMetadataCheckPhasepytestCheckPhase
842Executing pytestCheckPhase843/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-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.844 warnings.warn(845/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-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.yml846 warnings.warn(847no windows848rm -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 ../*~849no windows850cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib primer3_boulder_main.c851cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o format_output.o format_output.c852cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o read_boulder.o read_boulder.c853cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o print_boulder.o print_boulder.c854cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -Wno-deprecated -o libprimer3.o libprimer3.c855cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o p3_seq_lib.o p3_seq_lib.c856ar rv libprimer3.a libprimer3.o p3_seq_lib.o857ar: creating libprimer3.a858a - libprimer3.o859a - p3_seq_lib.o860ranlib libprimer3.a861cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o dpal_primer.o dpal.c862ar rv libdpal.a dpal_primer.o863ar: creating libdpal.a864a - dpal_primer.o865ranlib libdpal.a866cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal_primer.o thal.c867ar rv libthal.a thal_primer.o868ar: creating libthal.a869a - thal_primer.o870ranlib libthal.a871cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal_parameters.o thal_parameters.c872ar rv libthalpara.a thal_parameters.o873ar: creating libthalpara.a874a - thal_parameters.o875ranlib libthalpara.a876cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -c -o oligotm.o oligotm.c877ar rv liboligotm.a oligotm.o878ar: creating liboligotm.a879a - oligotm.o880ranlib liboligotm.a881cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -c -o amplicontm.o amplicontm.c882ar rv libamplicontm.a amplicontm.o883ar: creating libamplicontm.a884a - amplicontm.o885ranlib libamplicontm.a886cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib masker.c887ar rv libmasker.a masker.o888ar: creating libmasker.a889a - masker.o890ranlib libmasker.a891cc -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 -lm892cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -o ntdpal_main.o ntdpal_main.c893cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o dpal.o dpal.c894cc -g -o ntdpal ntdpal_main.o dpal.o895cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o thal_main.o thal_main.c896cc -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -ffloat-store -o thal.o thal.c897cc -g -o ntthal thal_main.o thal.o thal_parameters.o -lm898cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o amplicon3_core amplicontm_main.c libamplicontm.a -lm899cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o oligotm oligotm_main.c liboligotm.a -lm900cc -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -I klib -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm901cc -g -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libamplicontm.a libmasker.a -lm902[1/2] Cythonizing primer3/p3helpers.pyx903warning: primer3/p3helpers.pyx:34:28: 'COMP_BASE_LUT' redeclared 904warning: primer3/p3helpers.pyx:35:27: 'SANITIZE_LUT' redeclared 905warning: primer3/p3helpers.pyx:36:29: 'ACGT_UPPER_LUT' redeclared 906warning: primer3/p3helpers.pyx:37:36: 'IS_UPPERCASE_ACGT_LUT' redeclared 907[2/2] Cythonizing primer3/thermoanalysis.pyx908warning: 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/4310909/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-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 deprecated910!!911912 ********************************************************************************913 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).914915 By 2027-Feb-18, you need to update your project and remove deprecated calls916 or your builds will no longer be supported.917918 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.919 ********************************************************************************920921!!922 corresp(dist, value, root_dir)923/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated.924!!925926 ********************************************************************************927 Please consider removing the following classifiers in favor of a SPDX license expression:928929 License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)930931 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.932 ********************************************************************************933934!!935 dist._finalize_license_expression()936/nix/store/3zlx10nf4db20nvmiyylvkk9wrsbb3as-python3.14-setuptools-83.0.0/lib/python3.14/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.937!!938939 ********************************************************************************940 Please consider removing the following classifiers in favor of a SPDX license expression:941942 License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)943944 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.945 ********************************************************************************946947!!948 self._finalize_license_expression()949running build_ext950building 'primer3.p3helpers' extension951gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall -fPIC -Iprimer3 -I/build/source/primer3 -I/nix/store/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function952gcc -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-2.42.2-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-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/p0ff33dca0fbkskqwrl3spvxcn5974h0-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-2.42.2-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-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/p0ff33dca0fbkskqwrl3spvxcn5974h0-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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/primer3/p3helpers.cpython-314-x86_64-linux-gnu.so953building 'primer3.thermoanalysis' extension954gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function955gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function956gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function957gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function958gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function959gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function960gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function961gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function962In file included from /nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/string.h:548,963 from primer3/src/libprimer3/thalflex.c:66:964In function ‘strcpy’,965 inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5,966 inlined from ‘calc_hairpin’ at primer3/src/libprimer3/thalflex.c:1842:18:967/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-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]968 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));969 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~970/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’971In function ‘strcpy’,972 inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5,973 inlined from ‘calc_bulge_internal.constprop’ at primer3/src/libprimer3/thalflex.c:1946:18:974/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-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]975 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));976 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~977/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’978In function ‘strcpy’,979 inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5,980 inlined from ‘maxTM’ at primer3/src/libprimer3/thalflex.h:752:18,981 inlined from ‘fillMatrix.constprop’ at primer3/src/libprimer3/thalflex.c:1701:11:982/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-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]983 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));984 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~985/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’986In function ‘strcpy’,987 inlined from ‘safe_malloc’ at primer3/src/libprimer3/thalflex.c:916:5,988 inlined from ‘calc_bulge_internal’ at primer3/src/libprimer3/thalflex.c:1946:18,989 inlined from ‘fillMatrix.constprop’ at primer3/src/libprimer3/thalflex.c:1721:17:990/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-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]991 81 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest));992 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~993/nix/store/qwi863qp79xkdm2yw3xzjh73dpg9qh67-glibc-2.42-84-dev/include/bits/string_fortified.h:81:10: note: in a call to built-in function ‘__builtin___memcpy_chk’994gcc -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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-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-function995gcc -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-2.42.2-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-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/p0ff33dca0fbkskqwrl3spvxcn5974h0-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-2.42.2-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-3.6.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.53.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-mpdecimal-4.0.1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.8.3/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zstd-1.5.7/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bluez-headers-5.87/lib -L/nix/store/p0ff33dca0fbkskqwrl3spvxcn5974h0-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/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-python3-3.14.7/lib -o build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so996copying build/lib.linux-x86_64-cpython-314/primer3/p3helpers.cpython-314-x86_64-linux-gnu.so -> primer3997copying build/lib.linux-x86_64-cpython-314/primer3/thermoanalysis.cpython-314-x86_64-linux-gnu.so -> primer3998pytest flags: -m pytest tests999============================= test session starts ==============================1000platform linux -- Python 3.14.7, pytest-9.1.1, pluggy-1.6.01001rootdir: /build/source1002configfile: pyproject.toml1003plugins: typeguard-4.5.21004collected 45 items 10051006tests/test_argdefaults.py ... [ 6%]1007tests/test_ntthal_io.py . [ 8%]1008tests/test_p3helpers.py ....... [ 24%]1009tests/test_primerdesign.py ......... [ 44%]1010tests/test_sequences.py .......... [ 66%]1011tests/test_str_rep_ifc_compat.py .. [ 71%]1012tests/test_thermoanalysis.py ........... [ 95%]1013tests/test_threadsafe.py .. [100%]10141015============================= 45 passed in 19.20s ==============================1016Finished executing pytestCheckPhase1017pytestCheckPhase completed in 48 seconds