2025-09-11T14:32:52,162 Created temporary directory: /tmp/pip-build-tracker-_9227bf8 2025-09-11T14:32:52,163 Initialized build tracking at /tmp/pip-build-tracker-_9227bf8 2025-09-11T14:32:52,163 Created build tracker: /tmp/pip-build-tracker-_9227bf8 2025-09-11T14:32:52,163 Entered build tracker: /tmp/pip-build-tracker-_9227bf8 2025-09-11T14:32:52,164 Created temporary directory: /tmp/pip-wheel-p2m726rg 2025-09-11T14:32:52,167 Created temporary directory: /tmp/pip-ephem-wheel-cache-bet6vfus 2025-09-11T14:32:52,231 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-11T14:32:52,234 2 location(s) to search for versions of wwpdb-utils-align: 2025-09-11T14:32:52,234 * https://pypi.org/simple/wwpdb-utils-align/ 2025-09-11T14:32:52,234 * https://www.piwheels.org/simple/wwpdb-utils-align/ 2025-09-11T14:32:52,234 Fetching project page and analyzing links: https://pypi.org/simple/wwpdb-utils-align/ 2025-09-11T14:32:52,235 Getting page 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Skipping link: No binaries permitted for wwpdb-utils-align: https://files.pythonhosted.org/packages/82/47/3499f7b34613164ea04d251cd3a7585bb90b8e10992d5286cba6212d5ef0/wwpdb_utils_align-0.12.0-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/wwpdb-utils-align/) (requires-python:>=3.8) 2025-09-11T14:32:52,405 Skipping link: No binaries permitted for wwpdb-utils-align: https://files.pythonhosted.org/packages/e0/61/dc57428cc9efabaec80fe6785b61ba1070cdf8b622be0ac32ee1d2e87c66/wwpdb_utils_align-0.12.0-cp38-cp38-macosx_11_0_arm64.whl (from https://pypi.org/simple/wwpdb-utils-align/) (requires-python:>=3.8) 2025-09-11T14:32:52,405 Skipping link: No binaries permitted for wwpdb-utils-align: https://files.pythonhosted.org/packages/f2/8e/dd63a82fffdb19e44d658bb3db9a3f5a64fb49b36ffd2c0a61f81f03a8cd/wwpdb_utils_align-0.12.0-cp38-cp38-manylinux_2_17_i686.manylinux2014_i686.whl (from https://pypi.org/simple/wwpdb-utils-align/) (requires-python:>=3.8) 2025-09-11T14:32:52,405 Skipping 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binaries permitted for wwpdb-utils-align: https://files.pythonhosted.org/packages/d9/08/0ced2b87c63f9de50db297f5f08c496e69e84292b79f0e071dd00cd0dfb5/wwpdb_utils_align-0.12.0-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl (from https://pypi.org/simple/wwpdb-utils-align/) (requires-python:>=3.8) 2025-09-11T14:32:52,406 Skipping link: No binaries permitted for wwpdb-utils-align: https://files.pythonhosted.org/packages/11/b1/918bdcd7b72076bfb10ebd397ea0e74331b76ca46843849c9f22e66ce168/wwpdb_utils_align-0.12.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/wwpdb-utils-align/) (requires-python:>=3.8) 2025-09-11T14:32:52,406 Found link https://files.pythonhosted.org/packages/80/2d/34f040d635d0a6701f3f483816d1da05b8218ccbdf84fc6799e00526dadd/wwpdb_utils_align-0.12.0.tar.gz (from https://pypi.org/simple/wwpdb-utils-align/) (requires-python:>=3.8), version: 0.12.0 2025-09-11T14:32:52,407 Fetching project page and analyzing links: https://www.piwheels.org/simple/wwpdb-utils-align/ 2025-09-11T14:32:52,407 Getting page https://www.piwheels.org/simple/wwpdb-utils-align/ 2025-09-11T14:32:52,408 Found index url https://www.piwheels.org/simple/ 2025-09-11T14:32:52,498 Fetched page https://www.piwheels.org/simple/wwpdb-utils-align/ as text/html 2025-09-11T14:32:52,508 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb_utils_align-0.12.0-cp311-cp311-linux_armv6l.whl#sha256=080bc5e2404f1a8a996797dbd0150e91912fe9bb01ec2e615a85503d3486d27e (from https://www.piwheels.org/simple/wwpdb-utils-align/) (requires-python:>=3.8) 2025-09-11T14:32:52,508 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb_utils_align-0.12.0-cp311-cp311-linux_armv7l.whl#sha256=080bc5e2404f1a8a996797dbd0150e91912fe9bb01ec2e615a85503d3486d27e (from https://www.piwheels.org/simple/wwpdb-utils-align/) 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https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.11-cp37-cp37m-linux_armv7l.whl#sha256=e65ad4a6ad82d1e4905c284608c9732a727fcab01c38466a346e7c12dbc918d8 (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,515 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.11-cp39-cp39-linux_armv6l.whl#sha256=f7ddeb0afcfb089397aec18e9140691d3e575467e2a29f5e49bf1946143ea414 (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,515 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.11-cp39-cp39-linux_armv7l.whl#sha256=f7ddeb0afcfb089397aec18e9140691d3e575467e2a29f5e49bf1946143ea414 (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,515 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.10-cp39-cp39-linux_armv6l.whl#sha256=81c22f07ee157ac44dcbc45396a046cfe4bee4e9b83fe896db81a44207ac3652 (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,515 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.10-cp39-cp39-linux_armv7l.whl#sha256=81c22f07ee157ac44dcbc45396a046cfe4bee4e9b83fe896db81a44207ac3652 (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,516 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.10-cp34-cp34m-linux_armv7l.whl#sha256=187aa2cc62cb9fc33666664df45110a8a9ea22bbb45ae35aa7dab2c181846c3e (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,516 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.10-cp34-cp34m-linux_armv6l.whl#sha256=187aa2cc62cb9fc33666664df45110a8a9ea22bbb45ae35aa7dab2c181846c3e (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,516 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.10-cp35-cp35m-linux_armv6l.whl#sha256=f1b32225cb7d430e9fea4c6247fbe4fecf95a881104e4b4039b6ff343b28269c (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,516 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.10-cp35-cp35m-linux_armv7l.whl#sha256=f1b32225cb7d430e9fea4c6247fbe4fecf95a881104e4b4039b6ff343b28269c (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,516 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.10-cp37-cp37m-linux_armv6l.whl#sha256=dacd2265ff97e73728f1e856657fb1099e938b0a1ae4759ae0c7ba189b52f540 (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,516 Skipping link: No binaries permitted for wwpdb-utils-align: https://archive1.piwheels.org/simple/wwpdb-utils-align/wwpdb.utils.align-0.10-cp37-cp37m-linux_armv7l.whl#sha256=dacd2265ff97e73728f1e856657fb1099e938b0a1ae4759ae0c7ba189b52f540 (from https://www.piwheels.org/simple/wwpdb-utils-align/) 2025-09-11T14:32:52,516 Skipping link: not a file: https://www.piwheels.org/simple/wwpdb-utils-align/ 2025-09-11T14:32:52,517 Skipping link: not a file: https://pypi.org/simple/wwpdb-utils-align/ 2025-09-11T14:32:52,541 Given no hashes to check 1 links for project 'wwpdb-utils-align': discarding no candidates 2025-09-11T14:32:52,543 Collecting wwpdb-utils-align==0.11.7 2025-09-11T14:32:52,544 Created temporary directory: /tmp/pip-unpack-e4lb150m 2025-09-11T14:32:52,689 Downloading wwpdb.utils.align-0.11.7.tar.gz (610 kB) 2025-09-11T14:32:53,007 Added wwpdb-utils-align==0.11.7 from https://files.pythonhosted.org/packages/5f/08/24b0c37005525ec0e373dc7da32712f8f04ab3a46d56d5a19d49a7ba53bb/wwpdb.utils.align-0.11.7.tar.gz to build tracker '/tmp/pip-build-tracker-_9227bf8' 2025-09-11T14:32:53,008 Running setup.py (path:/tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/setup.py) egg_info for package wwpdb-utils-align 2025-09-11T14:32:53,008 Created temporary directory: /tmp/pip-pip-egg-info-zn7216d_ 2025-09-11T14:32:53,009 Preparing metadata (setup.py): started 2025-09-11T14:32:53,009 Running command python setup.py egg_info 2025-09-11T14:32:54,037 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-11T14:32:54,038 warnings.warn(msg) 2025-09-11T14:32:54,038 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-11T14:32:54,038 warnings.warn(msg) 2025-09-11T14:32:54,286 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-11T14:32:54,286 !! 2025-09-11T14:32:54,287 ******************************************************************************** 2025-09-11T14:32:54,287 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-11T14:32:54,287 License :: OSI Approved :: Apache Software License 2025-09-11T14:32:54,287 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-11T14:32:54,287 ******************************************************************************** 2025-09-11T14:32:54,287 !! 2025-09-11T14:32:54,288 self._finalize_license_expression() 2025-09-11T14:32:54,373 running egg_info 2025-09-11T14:32:54,460 creating /tmp/pip-pip-egg-info-zn7216d_/wwpdb.utils.align.egg-info 2025-09-11T14:32:54,461 writing /tmp/pip-pip-egg-info-zn7216d_/wwpdb.utils.align.egg-info/PKG-INFO 2025-09-11T14:32:54,463 writing dependency_links to /tmp/pip-pip-egg-info-zn7216d_/wwpdb.utils.align.egg-info/dependency_links.txt 2025-09-11T14:32:54,464 writing requirements to /tmp/pip-pip-egg-info-zn7216d_/wwpdb.utils.align.egg-info/requires.txt 2025-09-11T14:32:54,465 writing top-level names to /tmp/pip-pip-egg-info-zn7216d_/wwpdb.utils.align.egg-info/top_level.txt 2025-09-11T14:32:54,465 writing manifest file '/tmp/pip-pip-egg-info-zn7216d_/wwpdb.utils.align.egg-info/SOURCES.txt' 2025-09-11T14:32:54,733 reading manifest file '/tmp/pip-pip-egg-info-zn7216d_/wwpdb.utils.align.egg-info/SOURCES.txt' 2025-09-11T14:32:54,734 reading manifest template 'MANIFEST.in' 2025-09-11T14:32:54,742 adding license file 'LICENSE' 2025-09-11T14:32:54,750 writing manifest file '/tmp/pip-pip-egg-info-zn7216d_/wwpdb.utils.align.egg-info/SOURCES.txt' 2025-09-11T14:32:54,881 Preparing metadata (setup.py): finished with status 'done' 2025-09-11T14:32:54,886 Source in /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd has version 0.11.7, which satisfies requirement wwpdb-utils-align==0.11.7 from https://files.pythonhosted.org/packages/5f/08/24b0c37005525ec0e373dc7da32712f8f04ab3a46d56d5a19d49a7ba53bb/wwpdb.utils.align-0.11.7.tar.gz 2025-09-11T14:32:54,886 Removed wwpdb-utils-align==0.11.7 from https://files.pythonhosted.org/packages/5f/08/24b0c37005525ec0e373dc7da32712f8f04ab3a46d56d5a19d49a7ba53bb/wwpdb.utils.align-0.11.7.tar.gz from build tracker '/tmp/pip-build-tracker-_9227bf8' 2025-09-11T14:32:54,891 Created temporary directory: /tmp/pip-unpack-nulyvabp 2025-09-11T14:32:54,891 Created temporary directory: /tmp/pip-unpack-chut12fp 2025-09-11T14:32:54,892 Building wheels for collected packages: wwpdb-utils-align 2025-09-11T14:32:54,893 Created temporary directory: /tmp/pip-wheel-d0ropalt 2025-09-11T14:32:54,894 DEPRECATION: Building 'wwpdb-utils-align' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'wwpdb-utils-align'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-11T14:32:54,895 Building wheel for wwpdb-utils-align (setup.py): started 2025-09-11T14:32:54,896 Destination directory: /tmp/pip-wheel-d0ropalt 2025-09-11T14:32:54,896 Running command python setup.py bdist_wheel 2025-09-11T14:32:55,854 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-11T14:32:55,854 warnings.warn(msg) 2025-09-11T14:32:55,854 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-11T14:32:55,854 warnings.warn(msg) 2025-09-11T14:32:56,101 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-11T14:32:56,101 !! 2025-09-11T14:32:56,101 ******************************************************************************** 2025-09-11T14:32:56,101 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-11T14:32:56,102 License :: OSI Approved :: Apache Software License 2025-09-11T14:32:56,102 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-11T14:32:56,102 ******************************************************************************** 2025-09-11T14:32:56,102 !! 2025-09-11T14:32:56,102 self._finalize_license_expression() 2025-09-11T14:32:56,103 running bdist_wheel 2025-09-11T14:32:56,456 running build 2025-09-11T14:32:56,457 running build_py 2025-09-11T14:32:56,548 creating build/lib.linux-armv7l-cpython-313/wwpdb 2025-09-11T14:32:56,548 copying wwpdb/__init__.py -> build/lib.linux-armv7l-cpython-313/wwpdb 2025-09-11T14:32:56,549 creating build/lib.linux-armv7l-cpython-313/wwpdb/utils 2025-09-11T14:32:56,550 copying wwpdb/utils/__init__.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils 2025-09-11T14:32:56,551 creating build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-11T14:32:56,551 copying wwpdb/utils/align/__init__.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-11T14:32:56,552 copying wwpdb/utils/align/SequenceReferenceData.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-11T14:32:56,552 copying wwpdb/utils/align/SequenceExamples.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-11T14:32:56,559 running build_ext 2025-09-11T14:32:56,617 ------ WARNING could not locate python library 2025-09-11T14:32:56,620 ------------- setup.py ----------------- 2025-09-11T14:32:56,620 Extension source path /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd 2025-09-11T14:32:56,620 CMAKE_ARGS ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/build/lib.linux-armv7l-cpython-313/wwpdb/utils/align', '-DPYTHON_EXECUTABLE=/usr/bin/python3', '-DPYTHON_INCLUDE_DIR=/usr/include/python3.13', '-DCMAKE_BUILD_TYPE=Release'] 2025-09-11T14:32:56,620 self.build_temp build/temp.linux-armv7l-cpython-313 2025-09-11T14:32:56,620 extdir /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-11T14:32:56,620 ext.name wwpdb.utils.align.alignlib 2025-09-11T14:32:56,620 sys.executable /usr/bin/python3 2025-09-11T14:32:56,620 sys.exec_prefix /usr 2025-09-11T14:32:56,621 CXXFLAGS -DVERSION_INFO=\"0.11.7\" 2025-09-11T14:32:56,669 CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): 2025-09-11T14:32:56,670 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T14:32:56,670 CMake. 2025-09-11T14:32:56,670 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T14:32:56,670 to tell CMake that the project requires at least but has been updated 2025-09-11T14:32:56,670 to work with policies introduced by or earlier. 2025-09-11T14:32:56,972 -- The C compiler identification is GNU 14.2.0 2025-09-11T14:32:57,326 -- The CXX compiler identification is GNU 14.2.0 2025-09-11T14:32:57,379 -- Detecting C compiler ABI info 2025-09-11T14:32:57,816 -- Detecting C compiler ABI info - done 2025-09-11T14:32:57,893 -- Check for working C compiler: /usr/bin/cc - skipped 2025-09-11T14:32:57,894 -- Detecting C compile features 2025-09-11T14:32:57,897 -- Detecting C compile features - done 2025-09-11T14:32:57,962 -- Detecting CXX compiler ABI info 2025-09-11T14:32:58,454 -- Detecting CXX compiler ABI info - done 2025-09-11T14:32:58,540 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2025-09-11T14:32:58,542 -- Detecting CXX compile features 2025-09-11T14:32:58,546 -- Detecting CXX compile features - done 2025-09-11T14:32:58,582 CMake Warning (dev) at CMakeLists.txt:17 (find_package): 2025-09-11T14:32:58,583 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-11T14:32:58,583 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-11T14:32:58,583 the cmake_policy command to set the policy and suppress this warning. 2025-09-11T14:32:58,583 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-11T14:32:58,658 -- Found PythonInterp: /usr/bin/python3 (found version "3.13.5") 2025-09-11T14:32:58,659 CMake Warning (dev) at CMakeLists.txt:18 (find_package): 2025-09-11T14:32:58,659 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-11T14:32:58,660 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-11T14:32:58,660 the cmake_policy command to set the policy and suppress this warning. 2025-09-11T14:32:58,660 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-11T14:32:58,686 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.13.so (found version "3.13.5") 2025-09-11T14:32:58,687 -- Python include path set to /usr/include/python3.13 2025-09-11T14:32:58,689 CMake Deprecation Warning at modules/pybind11/CMakeLists.txt:8 (cmake_minimum_required): 2025-09-11T14:32:58,689 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T14:32:58,690 CMake. 2025-09-11T14:32:58,690 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T14:32:58,690 to tell CMake that the project requires at least but has been updated 2025-09-11T14:32:58,690 to work with policies introduced by or earlier. 2025-09-11T14:32:58,692 CMake Deprecation Warning at modules/pybind11/tools/pybind11Tools.cmake:8 (cmake_minimum_required): 2025-09-11T14:32:58,692 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T14:32:58,692 CMake. 2025-09-11T14:32:58,693 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T14:32:58,693 to tell CMake that the project requires at least but has been updated 2025-09-11T14:32:58,693 to work with policies introduced by or earlier. 2025-09-11T14:32:58,693 Call Stack (most recent call first): 2025-09-11T14:32:58,693 modules/pybind11/CMakeLists.txt:33 (include) 2025-09-11T14:32:58,694 CMake Warning (dev) at modules/pybind11/tools/FindPythonLibsNew.cmake:60 (find_package): 2025-09-11T14:32:58,694 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-11T14:32:58,694 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-11T14:32:58,694 the cmake_policy command to set the policy and suppress this warning. 2025-09-11T14:32:58,694 Call Stack (most recent call first): 2025-09-11T14:32:58,694 modules/pybind11/tools/pybind11Tools.cmake:16 (find_package) 2025-09-11T14:32:58,694 modules/pybind11/CMakeLists.txt:33 (include) 2025-09-11T14:32:58,695 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-11T14:32:59,432 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.13.so 2025-09-11T14:32:59,443 -- Performing Test HAS_CPP14_FLAG 2025-09-11T14:32:59,959 -- Performing Test HAS_CPP14_FLAG - Success 2025-09-11T14:32:59,978 -- pybind11 v2.3.dev0 2025-09-11T14:32:59,979 -- Compiler flags -Wall -Wno-unused-variable -Wno-unused-value -Wno-unused-but-set-variable -Wno-deprecated-declarations -DBIG_ENDIAN_PLATFORM -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -fno-common -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11 -flto 2025-09-11T14:32:59,979 -- ---CMAKE MODULE PATH - 2025-09-11T14:32:59,980 -- ---CMAKE SOURCE DIR - /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd 2025-09-11T14:32:59,980 -- ---CMAKE PROJECT DIR - /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd 2025-09-11T14:32:59,992 -- Performing Test HAS_FLTO 2025-09-11T14:33:00,674 -- Performing Test HAS_FLTO - Success 2025-09-11T14:33:00,674 -- LTO enabled 2025-09-11T14:33:00,675 STATUS,---ALL DONE WITH CMAKE 2025-09-11T14:33:00,676 -- Configuring done (4.0s) 2025-09-11T14:33:00,722 -- Generating done (0.0s) 2025-09-11T14:33:00,723 -- Build files have been written to: /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/build/temp.linux-armv7l-cpython-313 2025-09-11T14:33:01,007 [ 12%] Building CXX object CMakeFiles/align.dir/modules/PairwiseAlign/src/PairwiseAlign.C.o 2025-09-11T14:33:01,008 [ 12%] Building CXX object CMakeFiles/align.dir/modules/PairwiseAlign/src/AlignUtil.C.o 2025-09-11T14:33:02,427 [ 18%] Building CXX object CMakeFiles/align.dir/modules/PairwiseAlign/src/PseudoMultiAlign.C.o 2025-09-11T14:33:06,691 [ 18%] Built target align 2025-09-11T14:33:06,805 [ 25%] Linking CXX static library lib/libalign-all.a 2025-09-11T14:33:06,983 [ 25%] Built target align-all 2025-09-11T14:33:07,107 [ 37%] Building CXX object CMakeFiles/align_test_1.dir/modules/PairwiseAlign/test/testPairwiseAlign.C.o 2025-09-11T14:33:07,107 [ 37%] Building CXX object CMakeFiles/align_test_2.dir/modules/PairwiseAlign/test/testPairwiseAlignZF.C.o 2025-09-11T14:33:09,761 [ 43%] Linking CXX executable bin/align_test_2 2025-09-11T14:33:10,250 [ 50%] Linking CXX executable bin/align_test_1 2025-09-11T14:33:15,864 [ 50%] Built target align_test_2 2025-09-11T14:33:15,999 [ 56%] Building CXX object CMakeFiles/align_test_3.dir/modules/PairwiseAlign/test/testPseudoMultiAlign.C.o 2025-09-11T14:33:17,799 [ 62%] Linking CXX executable bin/align_test_3 2025-09-11T14:33:18,796 [ 62%] Built target align_test_1 2025-09-11T14:33:18,919 [ 68%] Building CXX object CMakeFiles/align_test_4.dir/modules/PairwiseAlign/test/testRefSeqAlign.C.o 2025-09-11T14:33:21,027 [ 75%] Linking CXX executable bin/align_test_4 2025-09-11T14:33:24,431 [ 75%] Built target align_test_3 2025-09-11T14:33:24,569 [ 81%] Building CXX object CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPairwiseAlign.cpp.o 2025-09-11T14:33:27,694 In file included from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h:13, 2025-09-11T14:33:27,694 from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:43, 2025-09-11T14:33:27,695 from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/cpp-alignlib-wrapper/src/wrapPairwiseAlign.cpp:5: 2025-09-11T14:33:27,695 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h: In function ‘std::string pybind11::detail::error_string()’: 2025-09-11T14:33:27,695 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:442:36: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:27,696 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T14:33:27,696 | ^~ 2025-09-11T14:33:27,697 In file included from /usr/include/python3.13/Python.h:67, 2025-09-11T14:33:27,697 from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/detail/common.h:112, 2025-09-11T14:33:27,698 from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pytypes.h:12, 2025-09-11T14:33:27,698 from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:13: 2025-09-11T14:33:27,698 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:27,698 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:27,698 | ^~~~~~ 2025-09-11T14:33:27,698 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:442:75: error: expected primary-expression before ‘>’ token 2025-09-11T14:33:27,699 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T14:33:27,699 | ^ 2025-09-11T14:33:27,699 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:442:77: error: expected primary-expression before ‘)’ token 2025-09-11T14:33:27,699 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T14:33:27,700 | ^ 2025-09-11T14:33:27,700 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:444:29: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:27,701 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T14:33:27,701 | ^~ 2025-09-11T14:33:27,701 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:27,701 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:27,702 | ^~~~~~ 2025-09-11T14:33:27,702 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:444:64: error: expected primary-expression before ‘>’ token 2025-09-11T14:33:27,702 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T14:33:27,703 | ^ 2025-09-11T14:33:27,703 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:444:66: error: expected primary-expression before ‘)’ token 2025-09-11T14:33:27,703 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T14:33:27,703 | ^ 2025-09-11T14:33:27,703 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:445:26: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:27,704 445 | frame = frame->f_back; 2025-09-11T14:33:27,704 | ^~ 2025-09-11T14:33:27,704 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:27,704 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:27,705 | ^~~~~~ 2025-09-11T14:33:27,923 [ 81%] Built target align_test_4 2025-09-11T14:33:27,930 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h: At global scope: 2025-09-11T14:33:27,930 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h:185:10: error: ‘uint16_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’? 2025-09-11T14:33:27,930 185 | std::uint16_t nargs; 2025-09-11T14:33:27,930 | ^~~~~~~~ 2025-09-11T14:33:27,931 | wint_t 2025-09-11T14:33:27,949 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h: In constructor ‘pybind11::detail::function_call::function_call(const pybind11::detail::function_record&, pybind11::handle)’: 2025-09-11T14:33:27,949 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h:283:20: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T14:33:27,949 283 | args.reserve(f.nargs); 2025-09-11T14:33:27,950 | ^~~~~ 2025-09-11T14:33:27,950 | args 2025-09-11T14:33:27,950 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h:284:28: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T14:33:27,950 284 | args_convert.reserve(f.nargs); 2025-09-11T14:33:27,951 | ^~~~~ 2025-09-11T14:33:27,951 | args 2025-09-11T14:33:27,991 [ 87%] Building CXX object CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPseudoMultiAlign.cpp.o 2025-09-11T14:33:28,061 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h: In member function ‘void pybind11::cpp_function::initialize_generic(pybind11::detail::function_record*, const char*, const std::type_info* const*, pybind11::size_t)’: 2025-09-11T14:33:28,061 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:283:14: error: ‘struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T14:33:28,061 283 | rec->nargs = (std::uint16_t) args; 2025-09-11T14:33:28,061 | ^~~~~ 2025-09-11T14:33:28,062 | args 2025-09-11T14:33:28,063 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:283:28: error: ‘uint16_t’ is not a member of ‘std’; did you mean ‘wint_t’? 2025-09-11T14:33:28,063 283 | rec->nargs = (std::uint16_t) args; 2025-09-11T14:33:28,063 | ^~~~~~~~ 2025-09-11T14:33:28,064 | wint_t 2025-09-11T14:33:28,091 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h: In static member function ‘static PyObject* pybind11::cpp_function::dispatcher(PyObject*, PyObject*, PyObject*)’: 2025-09-11T14:33:28,091 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:481:40: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T14:33:28,092 481 | size_t pos_args = func.nargs; // Number of positional arguments that we need 2025-09-11T14:33:28,092 | ^~~~~ 2025-09-11T14:33:28,092 | args 2025-09-11T14:33:28,101 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:612:53: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T14:33:28,101 612 | second_pass_convert.resize(func.nargs, false); 2025-09-11T14:33:28,101 | ^~~~~ 2025-09-11T14:33:28,101 | args 2025-09-11T14:33:28,351 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h: In function ‘pybind11::function pybind11::get_type_overload(const void*, const detail::type_info*, const char*)’: 2025-09-11T14:33:28,351 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1994:49: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-11T14:33:28,351 1994 | PyFrameObject *frame = PyThreadState_Get()->frame; 2025-09-11T14:33:28,351 | ^~~~~ 2025-09-11T14:33:28,351 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1995:41: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:28,352 1995 | if (frame && (std::string) str(frame->f_code->co_name) == name && 2025-09-11T14:33:28,352 | ^~ 2025-09-11T14:33:28,352 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:28,352 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:28,352 | ^~~~~~ 2025-09-11T14:33:28,353 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1996:14: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:28,353 1996 | frame->f_code->co_argcount > 0) { 2025-09-11T14:33:28,353 | ^~ 2025-09-11T14:33:28,353 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:28,353 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:28,353 | ^~~~~~ 2025-09-11T14:33:28,353 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1999:18: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:28,354 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T14:33:28,354 | ^~ 2025-09-11T14:33:28,354 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:28,354 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:28,354 | ^~~~~~ 2025-09-11T14:33:28,355 In file included from /usr/include/python3.13/Python.h:63: 2025-09-11T14:33:28,355 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1999:52: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:28,355 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T14:33:28,355 | ^~ 2025-09-11T14:33:28,355 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-11T14:33:28,356 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-11T14:33:28,356 | ^~~~ 2025-09-11T14:33:28,356 /usr/include/python3.13/cpython/tupleobject.h:27:38: note: in expansion of macro ‘_PyTuple_CAST’ 2025-09-11T14:33:28,356 27 | #define PyTuple_GET_ITEM(op, index) (_PyTuple_CAST(op)->ob_item[(index)]) 2025-09-11T14:33:28,356 | ^~~~~~~~~~~~~ 2025-09-11T14:33:28,356 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1999:30: note: in expansion of macro ‘PyTuple_GET_ITEM’ 2025-09-11T14:33:28,357 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T14:33:28,357 | ^~~~~~~~~~~~~~~~ 2025-09-11T14:33:28,357 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:28,357 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:28,358 | ^~~~~~ 2025-09-11T14:33:30,984 In file included from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h:13, 2025-09-11T14:33:30,984 from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:43, 2025-09-11T14:33:30,985 from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/cpp-alignlib-wrapper/src/wrapPseudoMultiAlign.cpp:5: 2025-09-11T14:33:30,985 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h: In function ‘std::string pybind11::detail::error_string()’: 2025-09-11T14:33:30,985 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:442:36: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:30,985 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T14:33:30,985 | ^~ 2025-09-11T14:33:30,986 In file included from /usr/include/python3.13/Python.h:67, 2025-09-11T14:33:30,986 from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/detail/common.h:112, 2025-09-11T14:33:30,986 from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pytypes.h:12, 2025-09-11T14:33:30,987 from /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:13: 2025-09-11T14:33:30,987 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:30,987 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:30,987 | ^~~~~~ 2025-09-11T14:33:30,988 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:442:75: error: expected primary-expression before ‘>’ token 2025-09-11T14:33:30,988 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T14:33:30,988 | ^ 2025-09-11T14:33:30,988 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:442:77: error: expected primary-expression before ‘)’ token 2025-09-11T14:33:30,989 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T14:33:30,989 | ^ 2025-09-11T14:33:30,989 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:444:29: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:30,990 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T14:33:30,990 | ^~ 2025-09-11T14:33:30,990 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:30,990 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:30,991 | ^~~~~~ 2025-09-11T14:33:30,991 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:444:64: error: expected primary-expression before ‘>’ token 2025-09-11T14:33:30,991 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T14:33:30,991 | ^ 2025-09-11T14:33:30,992 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:444:66: error: expected primary-expression before ‘)’ token 2025-09-11T14:33:30,992 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T14:33:30,992 | ^ 2025-09-11T14:33:30,993 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/cast.h:445:26: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:30,993 445 | frame = frame->f_back; 2025-09-11T14:33:30,993 | ^~ 2025-09-11T14:33:30,993 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:30,994 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:30,994 | ^~~~~~ 2025-09-11T14:33:31,193 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h: At global scope: 2025-09-11T14:33:31,193 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h:185:10: error: ‘uint16_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’? 2025-09-11T14:33:31,194 185 | std::uint16_t nargs; 2025-09-11T14:33:31,194 | ^~~~~~~~ 2025-09-11T14:33:31,194 | wint_t 2025-09-11T14:33:31,212 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h: In constructor ‘pybind11::detail::function_call::function_call(const pybind11::detail::function_record&, pybind11::handle)’: 2025-09-11T14:33:31,212 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h:283:20: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T14:33:31,212 283 | args.reserve(f.nargs); 2025-09-11T14:33:31,212 | ^~~~~ 2025-09-11T14:33:31,212 | args 2025-09-11T14:33:31,213 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/attr.h:284:28: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T14:33:31,213 284 | args_convert.reserve(f.nargs); 2025-09-11T14:33:31,213 | ^~~~~ 2025-09-11T14:33:31,214 | args 2025-09-11T14:33:31,320 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h: In member function ‘void pybind11::cpp_function::initialize_generic(pybind11::detail::function_record*, const char*, const std::type_info* const*, pybind11::size_t)’: 2025-09-11T14:33:31,321 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:283:14: error: ‘struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T14:33:31,321 283 | rec->nargs = (std::uint16_t) args; 2025-09-11T14:33:31,321 | ^~~~~ 2025-09-11T14:33:31,321 | args 2025-09-11T14:33:31,323 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:283:28: error: ‘uint16_t’ is not a member of ‘std’; did you mean ‘wint_t’? 2025-09-11T14:33:31,324 283 | rec->nargs = (std::uint16_t) args; 2025-09-11T14:33:31,324 | ^~~~~~~~ 2025-09-11T14:33:31,324 | wint_t 2025-09-11T14:33:31,351 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h: In static member function ‘static PyObject* pybind11::cpp_function::dispatcher(PyObject*, PyObject*, PyObject*)’: 2025-09-11T14:33:31,351 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:481:40: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T14:33:31,351 481 | size_t pos_args = func.nargs; // Number of positional arguments that we need 2025-09-11T14:33:31,352 | ^~~~~ 2025-09-11T14:33:31,352 | args 2025-09-11T14:33:31,361 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:612:53: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T14:33:31,361 612 | second_pass_convert.resize(func.nargs, false); 2025-09-11T14:33:31,362 | ^~~~~ 2025-09-11T14:33:31,362 | args 2025-09-11T14:33:31,608 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h: In function ‘pybind11::function pybind11::get_type_overload(const void*, const detail::type_info*, const char*)’: 2025-09-11T14:33:31,608 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1994:49: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-11T14:33:31,608 1994 | PyFrameObject *frame = PyThreadState_Get()->frame; 2025-09-11T14:33:31,608 | ^~~~~ 2025-09-11T14:33:31,609 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1995:41: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:31,609 1995 | if (frame && (std::string) str(frame->f_code->co_name) == name && 2025-09-11T14:33:31,609 | ^~ 2025-09-11T14:33:31,609 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:31,610 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:31,610 | ^~~~~~ 2025-09-11T14:33:31,610 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1996:14: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:31,610 1996 | frame->f_code->co_argcount > 0) { 2025-09-11T14:33:31,611 | ^~ 2025-09-11T14:33:31,611 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:31,611 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:31,611 | ^~~~~~ 2025-09-11T14:33:31,612 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1999:18: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:31,612 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T14:33:31,612 | ^~ 2025-09-11T14:33:31,613 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:31,613 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:31,613 | ^~~~~~ 2025-09-11T14:33:31,615 In file included from /usr/include/python3.13/Python.h:63: 2025-09-11T14:33:31,615 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1999:52: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:31,615 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T14:33:31,615 | ^~ 2025-09-11T14:33:31,615 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-11T14:33:31,616 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-11T14:33:31,616 | ^~~~ 2025-09-11T14:33:31,616 /usr/include/python3.13/cpython/tupleobject.h:27:38: note: in expansion of macro ‘_PyTuple_CAST’ 2025-09-11T14:33:31,616 27 | #define PyTuple_GET_ITEM(op, index) (_PyTuple_CAST(op)->ob_item[(index)]) 2025-09-11T14:33:31,616 | ^~~~~~~~~~~~~ 2025-09-11T14:33:31,616 /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/modules/pybind11/include/pybind11/pybind11.h:1999:30: note: in expansion of macro ‘PyTuple_GET_ITEM’ 2025-09-11T14:33:31,616 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T14:33:31,616 | ^~~~~~~~~~~~~~~~ 2025-09-11T14:33:31,617 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T14:33:31,617 22 | typedef struct _frame PyFrameObject; 2025-09-11T14:33:31,617 | ^~~~~~ 2025-09-11T14:33:32,885 gmake[2]: *** [CMakeFiles/alignlib.dir/build.make:79: CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPairwiseAlign.cpp.o] Error 1 2025-09-11T14:33:32,885 gmake[2]: *** Waiting for unfinished jobs.... 2025-09-11T14:33:35,466 gmake[2]: *** [CMakeFiles/alignlib.dir/build.make:93: CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPseudoMultiAlign.cpp.o] Error 1 2025-09-11T14:33:35,467 gmake[1]: *** [CMakeFiles/Makefile2:319: CMakeFiles/alignlib.dir/all] Error 2 2025-09-11T14:33:35,467 gmake: *** [Makefile:136: all] Error 2 2025-09-11T14:33:35,480 Traceback (most recent call last): 2025-09-11T14:33:35,489 File "", line 2, in 2025-09-11T14:33:35,489 exec(compile(''' 2025-09-11T14:33:35,489 ~~~~^^^^^^^^^^^^ 2025-09-11T14:33:35,489 # This is -- a caller that pip uses to run setup.py 2025-09-11T14:33:35,489 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T14:33:35,490 ...<32 lines>... 2025-09-11T14:33:35,490 exec(compile(setup_py_code, filename, "exec")) 2025-09-11T14:33:35,490 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T14:33:35,490 ''' % ('/tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/setup.py',), "", "exec")) 2025-09-11T14:33:35,490 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T14:33:35,490 File "", line 35, in 2025-09-11T14:33:35,490 File "/tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/setup.py", line 127, in 2025-09-11T14:33:35,491 setup( 2025-09-11T14:33:35,491 ~~~~~^ 2025-09-11T14:33:35,491 name=thisPackage, 2025-09-11T14:33:35,491 ^^^^^^^^^^^^^^^^^ 2025-09-11T14:33:35,491 ...<47 lines>... 2025-09-11T14:33:35,491 zip_safe=False, 2025-09-11T14:33:35,491 ^^^^^^^^^^^^^^^ 2025-09-11T14:33:35,491 ) 2025-09-11T14:33:35,491 ^ 2025-09-11T14:33:35,492 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-11T14:33:35,492 return distutils.core.setup(**attrs) 2025-09-11T14:33:35,492 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T14:33:35,492 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-11T14:33:35,493 return run_commands(dist) 2025-09-11T14:33:35,493 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-11T14:33:35,493 dist.run_commands() 2025-09-11T14:33:35,493 ~~~~~~~~~~~~~~~~~^^ 2025-09-11T14:33:35,493 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-11T14:33:35,493 self.run_command(cmd) 2025-09-11T14:33:35,494 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-11T14:33:35,494 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-11T14:33:35,494 super().run_command(command) 2025-09-11T14:33:35,494 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T14:33:35,494 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-11T14:33:35,494 cmd_obj.run() 2025-09-11T14:33:35,495 ~~~~~~~~~~~^^ 2025-09-11T14:33:35,495 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-11T14:33:35,495 self.run_command("build") 2025-09-11T14:33:35,495 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T14:33:35,495 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-11T14:33:35,496 self.distribution.run_command(command) 2025-09-11T14:33:35,496 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T14:33:35,496 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-11T14:33:35,496 super().run_command(command) 2025-09-11T14:33:35,496 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T14:33:35,496 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-11T14:33:35,497 cmd_obj.run() 2025-09-11T14:33:35,497 ~~~~~~~~~~~^^ 2025-09-11T14:33:35,497 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-11T14:33:35,497 self.run_command(cmd_name) 2025-09-11T14:33:35,497 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-11T14:33:35,497 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-11T14:33:35,498 self.distribution.run_command(command) 2025-09-11T14:33:35,498 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T14:33:35,498 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-11T14:33:35,498 super().run_command(command) 2025-09-11T14:33:35,499 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T14:33:35,499 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-11T14:33:35,499 cmd_obj.run() 2025-09-11T14:33:35,499 ~~~~~~~~~~~^^ 2025-09-11T14:33:35,499 File "/tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/setup.py", line 40, in run 2025-09-11T14:33:35,500 self.build_extension(ext) 2025-09-11T14:33:35,500 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-11T14:33:35,500 File "/tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/setup.py", line 113, in build_extension 2025-09-11T14:33:35,500 subprocess.check_call(["cmake", "--build", "."] + buildArgs, cwd=self.build_temp) 2025-09-11T14:33:35,500 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T14:33:35,500 File "/usr/lib/python3.13/subprocess.py", line 419, in check_call 2025-09-11T14:33:35,501 raise CalledProcessError(retcode, cmd) 2025-09-11T14:33:35,501 subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2. 2025-09-11T14:33:35,624 ERROR: python setup.py bdist_wheel exited with 1 2025-09-11T14:33:35,638 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-11T14:33:35,638 exec(compile('"'"''"'"''"'"' 2025-09-11T14:33:35,638 # This is -- a caller that pip uses to run setup.py 2025-09-11T14:33:35,638 # 2025-09-11T14:33:35,638 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-11T14:33:35,638 # import from `distutils.core` to work with newer packaging standards. 2025-09-11T14:33:35,638 # - It provides a clear error message when setuptools is not installed. 2025-09-11T14:33:35,638 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-11T14:33:35,638 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-11T14:33:35,638 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-11T14:33:35,638 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-11T14:33:35,638 import os, sys, tokenize, traceback 2025-09-11T14:33:35,638 2025-09-11T14:33:35,638 try: 2025-09-11T14:33:35,638 import setuptools 2025-09-11T14:33:35,638 except ImportError: 2025-09-11T14:33:35,638 print( 2025-09-11T14:33:35,638 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-11T14:33:35,638 "the build environment with exception:", 2025-09-11T14:33:35,638 file=sys.stderr, 2025-09-11T14:33:35,638 ) 2025-09-11T14:33:35,638 traceback.print_exc() 2025-09-11T14:33:35,638 sys.exit(1) 2025-09-11T14:33:35,638 2025-09-11T14:33:35,638 __file__ = %r 2025-09-11T14:33:35,638 sys.argv[0] = __file__ 2025-09-11T14:33:35,638 2025-09-11T14:33:35,638 if os.path.exists(__file__): 2025-09-11T14:33:35,638 filename = __file__ 2025-09-11T14:33:35,638 with tokenize.open(__file__) as f: 2025-09-11T14:33:35,638 setup_py_code = f.read() 2025-09-11T14:33:35,638 else: 2025-09-11T14:33:35,638 filename = "" 2025-09-11T14:33:35,638 setup_py_code = "from setuptools import setup; setup()" 2025-09-11T14:33:35,638 2025-09-11T14:33:35,638 exec(compile(setup_py_code, filename, "exec")) 2025-09-11T14:33:35,638 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-d0ropalt[/] 2025-09-11T14:33:35,638 [bold magenta]cwd[/]: /tmp/pip-wheel-p2m726rg/wwpdb-utils-align_810c318ddc1b43d4ba8ebeaa7d62e5cd/ 2025-09-11T14:33:35,638 Building wheel for wwpdb-utils-align (setup.py): finished with status 'error' 2025-09-11T14:33:35,639 ERROR: Failed building wheel for wwpdb-utils-align 2025-09-11T14:33:35,640 Running setup.py clean for wwpdb-utils-align 2025-09-11T14:33:35,641 Running command python setup.py clean 2025-09-11T14:33:36,697 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-11T14:33:36,697 warnings.warn(msg) 2025-09-11T14:33:36,698 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-11T14:33:36,698 warnings.warn(msg) 2025-09-11T14:33:36,937 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-11T14:33:36,937 !! 2025-09-11T14:33:36,938 ******************************************************************************** 2025-09-11T14:33:36,938 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-11T14:33:36,938 License :: OSI Approved :: Apache Software License 2025-09-11T14:33:36,938 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-11T14:33:36,938 ******************************************************************************** 2025-09-11T14:33:36,938 !! 2025-09-11T14:33:36,938 self._finalize_license_expression() 2025-09-11T14:33:37,029 running clean 2025-09-11T14:33:37,205 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-11T14:33:37,213 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-11T14:33:37,214 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-11T14:33:37,214 'build/scripts-3.13' does not exist -- can't clean it 2025-09-11T14:33:37,214 removing 'build' 2025-09-11T14:33:37,345 Failed to build wwpdb-utils-align 2025-09-11T14:33:37,346 ERROR: Failed to build one or more wheels 2025-09-11T14:33:37,347 Exception information: 2025-09-11T14:33:37,347 Traceback (most recent call last): 2025-09-11T14:33:37,347 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-11T14:33:37,347 status = _inner_run() 2025-09-11T14:33:37,347 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-11T14:33:37,347 return self.run(options, args) 2025-09-11T14:33:37,347 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-11T14:33:37,347 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-11T14:33:37,347 return func(self, options, args) 2025-09-11T14:33:37,347 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-11T14:33:37,347 raise CommandError("Failed to build one or more wheels") 2025-09-11T14:33:37,347 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-11T14:33:37,351 Removed build tracker: '/tmp/pip-build-tracker-_9227bf8'