2025-09-11T11:56:29,444 Created temporary directory: /tmp/pip-build-tracker-kn001db9 2025-09-11T11:56:29,444 Initialized build tracking at /tmp/pip-build-tracker-kn001db9 2025-09-11T11:56:29,444 Created build tracker: /tmp/pip-build-tracker-kn001db9 2025-09-11T11:56:29,444 Entered build tracker: /tmp/pip-build-tracker-kn001db9 2025-09-11T11:56:29,445 Created temporary directory: /tmp/pip-wheel-j55tsa1x 2025-09-11T11:56:29,448 Created temporary directory: /tmp/pip-ephem-wheel-cache-0x2r2ugz 2025-09-11T11:56:29,507 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-11T11:56:29,509 2 location(s) to search for versions of wwpdb-utils-align: 2025-09-11T11:56:29,509 * https://pypi.org/simple/wwpdb-utils-align/ 2025-09-11T11:56:29,509 * https://www.piwheels.org/simple/wwpdb-utils-align/ 2025-09-11T11:56:29,510 Fetching project page and analyzing links: https://pypi.org/simple/wwpdb-utils-align/ 2025-09-11T11:56:29,510 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) 2025-09-11T11:56:29,688 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) 2025-09-11T11:56:29,688 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) 2025-09-11T11:56:29,688 Skipping link: No binaries permitted for wwpdb-utils-align: https://files.pythonhosted.org/packages/a0/36/f5e9c37d027c3a00577e3da233ca9c914b2d21fd8d87b0ae75e820287562/wwpdb_utils_align-0.12.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/wwpdb-utils-align/) (requires-python:>=3.8) 2025-09-11T11:56:29,688 Skipping link: No binaries permitted for wwpdb-utils-align: https://files.pythonhosted.org/packages/ae/c7/863246bab293f3a63997b8e21fcb0f802fce73f72c1aa98e6c741225fd0f/wwpdb_utils_align-0.12.0-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/wwpdb-utils-align/) (requires-python:>=3.8) 2025-09-11T11:56:29,688 Skipping link: No binaries permitted for wwpdb-utils-align: https://files.pythonhosted.org/packages/6c/e5/a62d9571e229f82867d534b11e216cbf98a713754a2f82fac7c8899668de/wwpdb_utils_align-0.12.0-cp39-cp39-macosx_11_0_arm64.whl (from https://pypi.org/simple/wwpdb-utils-align/) (requires-python:>=3.8) 2025-09-11T11:56:29,688 Skipping link: No 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) 2025-09-11T11:56:29,688 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) 2025-09-11T11:56:29,689 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 2025-09-11T11:56:29,689 Fetching project page and analyzing links: https://www.piwheels.org/simple/wwpdb-utils-align/ 2025-09-11T11:56:29,690 Getting page https://www.piwheels.org/simple/wwpdb-utils-align/ 2025-09-11T11:56:29,690 Found index url https://www.piwheels.org/simple/ 2025-09-11T11:56:29,785 Fetched page https://www.piwheels.org/simple/wwpdb-utils-align/ as text/html 2025-09-11T11:56:29,797 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) 2025-09-11T11:56:29,797 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/) 2025-09-11T11:56:29,805 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/) 2025-09-11T11:56:29,805 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/) 2025-09-11T11:56:29,805 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/) 2025-09-11T11:56:29,805 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/) 2025-09-11T11:56:29,806 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/) 2025-09-11T11:56:29,806 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/) 2025-09-11T11:56:29,806 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/) 2025-09-11T11:56:29,806 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/) 2025-09-11T11:56:29,806 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/) 2025-09-11T11:56:29,806 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/) 2025-09-11T11:56:29,807 Skipping link: not a file: https://www.piwheels.org/simple/wwpdb-utils-align/ 2025-09-11T11:56:29,807 Skipping link: not a file: https://pypi.org/simple/wwpdb-utils-align/ 2025-09-11T11:56:29,831 Given no hashes to check 1 links for project 'wwpdb-utils-align': discarding no candidates 2025-09-11T11:56:29,832 Collecting wwpdb-utils-align==0.11.4 2025-09-11T11:56:29,833 Created temporary directory: /tmp/pip-unpack-8r7pe94z 2025-09-11T11:56:29,976 Downloading wwpdb.utils.align-0.11.4.tar.gz (608 kB) 2025-09-11T11:56:30,256 Added wwpdb-utils-align==0.11.4 from https://files.pythonhosted.org/packages/72/f1/dbf1d3d7ce579ebfe697e9bf39915fdad652cfef8f577ab473bbb18638a9/wwpdb.utils.align-0.11.4.tar.gz to build tracker '/tmp/pip-build-tracker-kn001db9' 2025-09-11T11:56:30,257 Running setup.py (path:/tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/setup.py) egg_info for package wwpdb-utils-align 2025-09-11T11:56:30,258 Created temporary directory: /tmp/pip-pip-egg-info-_lvz9xm2 2025-09-11T11:56:30,258 Preparing metadata (setup.py): started 2025-09-11T11:56:30,259 Running command python setup.py egg_info 2025-09-11T11:56:31,167 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-11T11:56:31,167 warnings.warn(msg) 2025-09-11T11:56:31,167 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-11T11:56:31,167 warnings.warn(msg) 2025-09-11T11:56:31,377 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-11T11:56:31,377 !! 2025-09-11T11:56:31,377 ******************************************************************************** 2025-09-11T11:56:31,377 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-11T11:56:31,378 License :: OSI Approved :: Apache Software License 2025-09-11T11:56:31,378 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-11T11:56:31,378 ******************************************************************************** 2025-09-11T11:56:31,378 !! 2025-09-11T11:56:31,378 self._finalize_license_expression() 2025-09-11T11:56:31,452 running egg_info 2025-09-11T11:56:31,525 creating /tmp/pip-pip-egg-info-_lvz9xm2/wwpdb.utils.align.egg-info 2025-09-11T11:56:31,525 writing /tmp/pip-pip-egg-info-_lvz9xm2/wwpdb.utils.align.egg-info/PKG-INFO 2025-09-11T11:56:31,527 writing dependency_links to /tmp/pip-pip-egg-info-_lvz9xm2/wwpdb.utils.align.egg-info/dependency_links.txt 2025-09-11T11:56:31,528 writing requirements to /tmp/pip-pip-egg-info-_lvz9xm2/wwpdb.utils.align.egg-info/requires.txt 2025-09-11T11:56:31,529 writing top-level names to /tmp/pip-pip-egg-info-_lvz9xm2/wwpdb.utils.align.egg-info/top_level.txt 2025-09-11T11:56:31,529 writing manifest file '/tmp/pip-pip-egg-info-_lvz9xm2/wwpdb.utils.align.egg-info/SOURCES.txt' 2025-09-11T11:56:31,757 reading manifest file '/tmp/pip-pip-egg-info-_lvz9xm2/wwpdb.utils.align.egg-info/SOURCES.txt' 2025-09-11T11:56:31,758 reading manifest template 'MANIFEST.in' 2025-09-11T11:56:31,765 adding license file 'LICENSE' 2025-09-11T11:56:31,773 writing manifest file '/tmp/pip-pip-egg-info-_lvz9xm2/wwpdb.utils.align.egg-info/SOURCES.txt' 2025-09-11T11:56:31,887 Preparing metadata (setup.py): finished with status 'done' 2025-09-11T11:56:31,891 Source in /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c has version 0.11.4, which satisfies requirement wwpdb-utils-align==0.11.4 from https://files.pythonhosted.org/packages/72/f1/dbf1d3d7ce579ebfe697e9bf39915fdad652cfef8f577ab473bbb18638a9/wwpdb.utils.align-0.11.4.tar.gz 2025-09-11T11:56:31,892 Removed wwpdb-utils-align==0.11.4 from https://files.pythonhosted.org/packages/72/f1/dbf1d3d7ce579ebfe697e9bf39915fdad652cfef8f577ab473bbb18638a9/wwpdb.utils.align-0.11.4.tar.gz from build tracker '/tmp/pip-build-tracker-kn001db9' 2025-09-11T11:56:31,896 Created temporary directory: /tmp/pip-unpack-1fuhwemb 2025-09-11T11:56:31,896 Created temporary directory: /tmp/pip-unpack-4gup0k_a 2025-09-11T11:56:31,896 Building wheels for collected packages: wwpdb-utils-align 2025-09-11T11:56:31,897 Created temporary directory: /tmp/pip-wheel-s6a8sbuv 2025-09-11T11:56:31,898 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 2025-09-11T11:56:31,899 Building wheel for wwpdb-utils-align (setup.py): started 2025-09-11T11:56:31,899 Destination directory: /tmp/pip-wheel-s6a8sbuv 2025-09-11T11:56:31,900 Running command python setup.py bdist_wheel 2025-09-11T11:56:32,761 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-11T11:56:32,761 warnings.warn(msg) 2025-09-11T11:56:32,762 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-11T11:56:32,762 warnings.warn(msg) 2025-09-11T11:56:32,964 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-11T11:56:32,965 !! 2025-09-11T11:56:32,965 ******************************************************************************** 2025-09-11T11:56:32,965 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-11T11:56:32,965 License :: OSI Approved :: Apache Software License 2025-09-11T11:56:32,965 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-11T11:56:32,965 ******************************************************************************** 2025-09-11T11:56:32,966 !! 2025-09-11T11:56:32,966 self._finalize_license_expression() 2025-09-11T11:56:32,966 running bdist_wheel 2025-09-11T11:56:33,253 running build 2025-09-11T11:56:33,253 running build_py 2025-09-11T11:56:33,330 creating build/lib.linux-armv7l-cpython-313/wwpdb 2025-09-11T11:56:33,330 copying wwpdb/__init__.py -> build/lib.linux-armv7l-cpython-313/wwpdb 2025-09-11T11:56:33,331 creating build/lib.linux-armv7l-cpython-313/wwpdb/utils 2025-09-11T11:56:33,332 copying wwpdb/utils/__init__.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils 2025-09-11T11:56:33,332 creating build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-11T11:56:33,333 copying wwpdb/utils/align/__init__.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-11T11:56:33,333 copying wwpdb/utils/align/SequenceReferenceData.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-11T11:56:33,334 copying wwpdb/utils/align/SequenceExamples.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-11T11:56:33,339 running build_ext 2025-09-11T11:56:33,396 ------ WARNING could not locate python library 2025-09-11T11:56:33,398 ------------- setup.py ----------------- 2025-09-11T11:56:33,398 Extension source path /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c 2025-09-11T11:56:33,398 CMAKE_ARGS ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/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'] 2025-09-11T11:56:33,398 self.build_temp build/temp.linux-armv7l-cpython-313 2025-09-11T11:56:33,398 extdir /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-11T11:56:33,399 ext.name wwpdb.utils.align.alignlib 2025-09-11T11:56:33,399 sys.executable /usr/bin/python3 2025-09-11T11:56:33,399 sys.exec_prefix /usr 2025-09-11T11:56:33,399 CXXFLAGS -DVERSION_INFO=\"0.11.4\" 2025-09-11T11:56:33,452 CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): 2025-09-11T11:56:33,453 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T11:56:33,453 CMake. 2025-09-11T11:56:33,453 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T11:56:33,453 to tell CMake that the project requires at least but has been updated 2025-09-11T11:56:33,453 to work with policies introduced by or earlier. 2025-09-11T11:56:33,738 -- The C compiler identification is GNU 14.2.0 2025-09-11T11:56:34,075 -- The CXX compiler identification is GNU 14.2.0 2025-09-11T11:56:34,127 -- Detecting C compiler ABI info 2025-09-11T11:56:34,541 -- Detecting C compiler ABI info - done 2025-09-11T11:56:34,621 -- Check for working C compiler: /usr/bin/cc - skipped 2025-09-11T11:56:34,623 -- Detecting C compile features 2025-09-11T11:56:34,625 -- Detecting C compile features - done 2025-09-11T11:56:34,700 -- Detecting CXX compiler ABI info 2025-09-11T11:56:35,182 -- Detecting CXX compiler ABI info - done 2025-09-11T11:56:35,260 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2025-09-11T11:56:35,262 -- Detecting CXX compile features 2025-09-11T11:56:35,266 -- Detecting CXX compile features - done 2025-09-11T11:56:35,303 CMake Warning (dev) at CMakeLists.txt:17 (find_package): 2025-09-11T11:56:35,304 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-11T11:56:35,304 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-11T11:56:35,304 the cmake_policy command to set the policy and suppress this warning. 2025-09-11T11:56:35,304 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-11T11:56:35,374 -- Found PythonInterp: /usr/bin/python3 (found version "3.13.5") 2025-09-11T11:56:35,376 CMake Warning (dev) at CMakeLists.txt:18 (find_package): 2025-09-11T11:56:35,376 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-11T11:56:35,376 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-11T11:56:35,376 the cmake_policy command to set the policy and suppress this warning. 2025-09-11T11:56:35,376 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-11T11:56:35,401 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.13.so (found version "3.13.5") 2025-09-11T11:56:35,402 -- Python include path set to /usr/include/python3.13 2025-09-11T11:56:35,404 CMake Deprecation Warning at modules/pybind11/CMakeLists.txt:8 (cmake_minimum_required): 2025-09-11T11:56:35,405 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T11:56:35,405 CMake. 2025-09-11T11:56:35,405 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T11:56:35,405 to tell CMake that the project requires at least but has been updated 2025-09-11T11:56:35,405 to work with policies introduced by or earlier. 2025-09-11T11:56:35,406 CMake Deprecation Warning at modules/pybind11/tools/pybind11Tools.cmake:8 (cmake_minimum_required): 2025-09-11T11:56:35,406 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T11:56:35,407 CMake. 2025-09-11T11:56:35,407 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T11:56:35,407 to tell CMake that the project requires at least but has been updated 2025-09-11T11:56:35,407 to work with policies introduced by or earlier. 2025-09-11T11:56:35,407 Call Stack (most recent call first): 2025-09-11T11:56:35,407 modules/pybind11/CMakeLists.txt:33 (include) 2025-09-11T11:56:35,408 CMake Warning (dev) at modules/pybind11/tools/FindPythonLibsNew.cmake:60 (find_package): 2025-09-11T11:56:35,408 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-11T11:56:35,408 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-11T11:56:35,408 the cmake_policy command to set the policy and suppress this warning. 2025-09-11T11:56:35,409 Call Stack (most recent call first): 2025-09-11T11:56:35,409 modules/pybind11/tools/pybind11Tools.cmake:16 (find_package) 2025-09-11T11:56:35,409 modules/pybind11/CMakeLists.txt:33 (include) 2025-09-11T11:56:35,409 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-11T11:56:36,075 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.13.so 2025-09-11T11:56:36,084 -- Performing Test HAS_CPP14_FLAG 2025-09-11T11:56:36,565 -- Performing Test HAS_CPP14_FLAG - Success 2025-09-11T11:56:36,588 -- pybind11 v2.3.dev0 2025-09-11T11:56:36,589 -- 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 2025-09-11T11:56:36,589 -- ---CMAKE MODULE PATH - 2025-09-11T11:56:36,589 -- ---CMAKE SOURCE DIR - /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c 2025-09-11T11:56:36,589 -- ---CMAKE PROJECT DIR - /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c 2025-09-11T11:56:36,599 -- Performing Test HAS_FLTO 2025-09-11T11:56:37,505 -- Performing Test HAS_FLTO - Success 2025-09-11T11:56:37,505 -- LTO enabled 2025-09-11T11:56:37,506 STATUS,---ALL DONE WITH CMAKE 2025-09-11T11:56:37,507 -- Configuring done (4.1s) 2025-09-11T11:56:37,550 -- Generating done (0.0s) 2025-09-11T11:56:37,551 -- Build files have been written to: /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/build/temp.linux-armv7l-cpython-313 2025-09-11T11:56:37,836 [ 6%] Building CXX object CMakeFiles/align.dir/modules/PairwiseAlign/src/AlignUtil.C.o 2025-09-11T11:56:37,837 [ 12%] Building CXX object CMakeFiles/align.dir/modules/PairwiseAlign/src/PairwiseAlign.C.o 2025-09-11T11:56:39,061 [ 18%] Building CXX object CMakeFiles/align.dir/modules/PairwiseAlign/src/PseudoMultiAlign.C.o 2025-09-11T11:56:42,546 [ 18%] Built target align 2025-09-11T11:56:42,658 [ 25%] Linking CXX static library lib/libalign-all.a 2025-09-11T11:56:42,835 [ 25%] Built target align-all 2025-09-11T11:56:42,950 [ 37%] Building CXX object CMakeFiles/align_test_1.dir/modules/PairwiseAlign/test/testPairwiseAlign.C.o 2025-09-11T11:56:42,950 [ 37%] Building CXX object CMakeFiles/align_test_2.dir/modules/PairwiseAlign/test/testPairwiseAlignZF.C.o 2025-09-11T11:56:45,198 [ 43%] Linking CXX executable bin/align_test_2 2025-09-11T11:56:45,328 [ 50%] Linking CXX executable bin/align_test_1 2025-09-11T11:56:50,418 [ 50%] Built target align_test_2 2025-09-11T11:56:50,531 [ 56%] Building CXX object CMakeFiles/align_test_3.dir/modules/PairwiseAlign/test/testPseudoMultiAlign.C.o 2025-09-11T11:56:51,838 [ 62%] Linking CXX executable bin/align_test_3 2025-09-11T11:56:52,884 [ 62%] Built target align_test_1 2025-09-11T11:56:53,219 [ 68%] Building CXX object CMakeFiles/align_test_4.dir/modules/PairwiseAlign/test/testRefSeqAlign.C.o 2025-09-11T11:56:55,011 [ 75%] Linking CXX executable bin/align_test_4 2025-09-11T11:56:57,783 [ 75%] Built target align_test_3 2025-09-11T11:56:57,897 [ 81%] Building CXX object CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPairwiseAlign.cpp.o 2025-09-11T11:57:00,542 In file included from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h:13, 2025-09-11T11:57:00,542 from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:43, 2025-09-11T11:57:00,542 from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/cpp-alignlib-wrapper/src/wrapPairwiseAlign.cpp:5: 2025-09-11T11:57:00,542 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h: In function ‘std::string pybind11::detail::error_string()’: 2025-09-11T11:57:00,543 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:442:36: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:00,543 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T11:57:00,543 | ^~ 2025-09-11T11:57:00,543 In file included from /usr/include/python3.13/Python.h:67, 2025-09-11T11:57:00,543 from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/detail/common.h:112, 2025-09-11T11:57:00,543 from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pytypes.h:12, 2025-09-11T11:57:00,544 from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:13: 2025-09-11T11:57:00,544 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:00,544 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:00,544 | ^~~~~~ 2025-09-11T11:57:00,544 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:442:75: error: expected primary-expression before ‘>’ token 2025-09-11T11:57:00,544 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T11:57:00,545 | ^ 2025-09-11T11:57:00,545 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:442:77: error: expected primary-expression before ‘)’ token 2025-09-11T11:57:00,545 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T11:57:00,545 | ^ 2025-09-11T11:57:00,545 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:444:29: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:00,545 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T11:57:00,545 | ^~ 2025-09-11T11:57:00,546 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:00,546 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:00,546 | ^~~~~~ 2025-09-11T11:57:00,546 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:444:64: error: expected primary-expression before ‘>’ token 2025-09-11T11:57:00,546 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T11:57:00,546 | ^ 2025-09-11T11:57:00,546 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:444:66: error: expected primary-expression before ‘)’ token 2025-09-11T11:57:00,547 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T11:57:00,547 | ^ 2025-09-11T11:57:00,547 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:445:26: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:00,547 445 | frame = frame->f_back; 2025-09-11T11:57:00,547 | ^~ 2025-09-11T11:57:00,547 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:00,547 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:00,548 | ^~~~~~ 2025-09-11T11:57:00,727 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h: At global scope: 2025-09-11T11:57:00,727 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h:185:10: error: ‘uint16_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’? 2025-09-11T11:57:00,727 185 | std::uint16_t nargs; 2025-09-11T11:57:00,727 | ^~~~~~~~ 2025-09-11T11:57:00,727 | wint_t 2025-09-11T11:57:00,741 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h: In constructor ‘pybind11::detail::function_call::function_call(const pybind11::detail::function_record&, pybind11::handle)’: 2025-09-11T11:57:00,741 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h:283:20: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T11:57:00,741 283 | args.reserve(f.nargs); 2025-09-11T11:57:00,741 | ^~~~~ 2025-09-11T11:57:00,741 | args 2025-09-11T11:57:00,741 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h:284:28: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T11:57:00,742 284 | args_convert.reserve(f.nargs); 2025-09-11T11:57:00,742 | ^~~~~ 2025-09-11T11:57:00,742 | args 2025-09-11T11:57:00,832 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/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)’: 2025-09-11T11:57:00,832 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:283:14: error: ‘struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T11:57:00,832 283 | rec->nargs = (std::uint16_t) args; 2025-09-11T11:57:00,832 | ^~~~~ 2025-09-11T11:57:00,833 | args 2025-09-11T11:57:00,834 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:283:28: error: ‘uint16_t’ is not a member of ‘std’; did you mean ‘wint_t’? 2025-09-11T11:57:00,834 283 | rec->nargs = (std::uint16_t) args; 2025-09-11T11:57:00,834 | ^~~~~~~~ 2025-09-11T11:57:00,835 | wint_t 2025-09-11T11:57:00,860 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h: In static member function ‘static PyObject* pybind11::cpp_function::dispatcher(PyObject*, PyObject*, PyObject*)’: 2025-09-11T11:57:00,860 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:481:40: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T11:57:00,860 481 | size_t pos_args = func.nargs; // Number of positional arguments that we need 2025-09-11T11:57:00,860 | ^~~~~ 2025-09-11T11:57:00,860 | args 2025-09-11T11:57:00,868 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:612:53: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T11:57:00,868 612 | second_pass_convert.resize(func.nargs, false); 2025-09-11T11:57:00,868 | ^~~~~ 2025-09-11T11:57:00,868 | args 2025-09-11T11:57:01,112 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h: In function ‘pybind11::function pybind11::get_type_overload(const void*, const detail::type_info*, const char*)’: 2025-09-11T11:57:01,113 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1994:49: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-11T11:57:01,113 1994 | PyFrameObject *frame = PyThreadState_Get()->frame; 2025-09-11T11:57:01,113 | ^~~~~ 2025-09-11T11:57:01,113 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1995:41: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:01,113 1995 | if (frame && (std::string) str(frame->f_code->co_name) == name && 2025-09-11T11:57:01,113 | ^~ 2025-09-11T11:57:01,113 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:01,113 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:01,114 | ^~~~~~ 2025-09-11T11:57:01,114 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1996:14: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:01,114 1996 | frame->f_code->co_argcount > 0) { 2025-09-11T11:57:01,114 | ^~ 2025-09-11T11:57:01,114 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:01,114 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:01,114 | ^~~~~~ 2025-09-11T11:57:01,114 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1999:18: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:01,114 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T11:57:01,114 | ^~ 2025-09-11T11:57:01,114 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:01,115 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:01,115 | ^~~~~~ 2025-09-11T11:57:01,121 In file included from /usr/include/python3.13/Python.h:63: 2025-09-11T11:57:01,122 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1999:52: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:01,122 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T11:57:01,122 | ^~ 2025-09-11T11:57:01,122 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-11T11:57:01,122 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-11T11:57:01,122 | ^~~~ 2025-09-11T11:57:01,123 /usr/include/python3.13/cpython/tupleobject.h:27:38: note: in expansion of macro ‘_PyTuple_CAST’ 2025-09-11T11:57:01,123 27 | #define PyTuple_GET_ITEM(op, index) (_PyTuple_CAST(op)->ob_item[(index)]) 2025-09-11T11:57:01,123 | ^~~~~~~~~~~~~ 2025-09-11T11:57:01,123 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1999:30: note: in expansion of macro ‘PyTuple_GET_ITEM’ 2025-09-11T11:57:01,123 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T11:57:01,123 | ^~~~~~~~~~~~~~~~ 2025-09-11T11:57:01,124 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:01,124 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:01,124 | ^~~~~~ 2025-09-11T11:57:01,126 [ 81%] Built target align_test_4 2025-09-11T11:57:01,176 [ 87%] Building CXX object CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPseudoMultiAlign.cpp.o 2025-09-11T11:57:03,715 In file included from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h:13, 2025-09-11T11:57:03,716 from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:43, 2025-09-11T11:57:03,716 from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/cpp-alignlib-wrapper/src/wrapPseudoMultiAlign.cpp:5: 2025-09-11T11:57:03,716 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h: In function ‘std::string pybind11::detail::error_string()’: 2025-09-11T11:57:03,716 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:442:36: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:03,716 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T11:57:03,716 | ^~ 2025-09-11T11:57:03,717 In file included from /usr/include/python3.13/Python.h:67, 2025-09-11T11:57:03,717 from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/detail/common.h:112, 2025-09-11T11:57:03,717 from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pytypes.h:12, 2025-09-11T11:57:03,717 from /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:13: 2025-09-11T11:57:03,717 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:03,717 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:03,717 | ^~~~~~ 2025-09-11T11:57:03,718 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:442:75: error: expected primary-expression before ‘>’ token 2025-09-11T11:57:03,718 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T11:57:03,718 | ^ 2025-09-11T11:57:03,718 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:442:77: error: expected primary-expression before ‘)’ token 2025-09-11T11:57:03,718 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-11T11:57:03,718 | ^ 2025-09-11T11:57:03,718 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:444:29: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:03,719 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T11:57:03,719 | ^~ 2025-09-11T11:57:03,719 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:03,719 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:03,719 | ^~~~~~ 2025-09-11T11:57:03,719 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:444:64: error: expected primary-expression before ‘>’ token 2025-09-11T11:57:03,719 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T11:57:03,720 | ^ 2025-09-11T11:57:03,720 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:444:66: error: expected primary-expression before ‘)’ token 2025-09-11T11:57:03,720 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-11T11:57:03,720 | ^ 2025-09-11T11:57:03,720 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/cast.h:445:26: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:03,720 445 | frame = frame->f_back; 2025-09-11T11:57:03,720 | ^~ 2025-09-11T11:57:03,720 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:03,721 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:03,721 | ^~~~~~ 2025-09-11T11:57:03,884 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h: At global scope: 2025-09-11T11:57:03,884 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h:185:10: error: ‘uint16_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’? 2025-09-11T11:57:03,884 185 | std::uint16_t nargs; 2025-09-11T11:57:03,884 | ^~~~~~~~ 2025-09-11T11:57:03,884 | wint_t 2025-09-11T11:57:03,897 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h: In constructor ‘pybind11::detail::function_call::function_call(const pybind11::detail::function_record&, pybind11::handle)’: 2025-09-11T11:57:03,898 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h:283:20: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T11:57:03,898 283 | args.reserve(f.nargs); 2025-09-11T11:57:03,898 | ^~~~~ 2025-09-11T11:57:03,898 | args 2025-09-11T11:57:03,898 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/attr.h:284:28: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T11:57:03,899 284 | args_convert.reserve(f.nargs); 2025-09-11T11:57:03,899 | ^~~~~ 2025-09-11T11:57:03,899 | args 2025-09-11T11:57:03,985 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/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)’: 2025-09-11T11:57:03,986 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:283:14: error: ‘struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T11:57:03,986 283 | rec->nargs = (std::uint16_t) args; 2025-09-11T11:57:03,986 | ^~~~~ 2025-09-11T11:57:03,986 | args 2025-09-11T11:57:03,987 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:283:28: error: ‘uint16_t’ is not a member of ‘std’; did you mean ‘wint_t’? 2025-09-11T11:57:03,988 283 | rec->nargs = (std::uint16_t) args; 2025-09-11T11:57:03,988 | ^~~~~~~~ 2025-09-11T11:57:03,988 | wint_t 2025-09-11T11:57:04,011 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h: In static member function ‘static PyObject* pybind11::cpp_function::dispatcher(PyObject*, PyObject*, PyObject*)’: 2025-09-11T11:57:04,011 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:481:40: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T11:57:04,011 481 | size_t pos_args = func.nargs; // Number of positional arguments that we need 2025-09-11T11:57:04,011 | ^~~~~ 2025-09-11T11:57:04,011 | args 2025-09-11T11:57:04,018 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:612:53: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-11T11:57:04,019 612 | second_pass_convert.resize(func.nargs, false); 2025-09-11T11:57:04,019 | ^~~~~ 2025-09-11T11:57:04,019 | args 2025-09-11T11:57:04,223 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h: In function ‘pybind11::function pybind11::get_type_overload(const void*, const detail::type_info*, const char*)’: 2025-09-11T11:57:04,223 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1994:49: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-11T11:57:04,223 1994 | PyFrameObject *frame = PyThreadState_Get()->frame; 2025-09-11T11:57:04,224 | ^~~~~ 2025-09-11T11:57:04,224 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1995:41: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:04,224 1995 | if (frame && (std::string) str(frame->f_code->co_name) == name && 2025-09-11T11:57:04,224 | ^~ 2025-09-11T11:57:04,224 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:04,224 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:04,225 | ^~~~~~ 2025-09-11T11:57:04,225 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1996:14: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:04,225 1996 | frame->f_code->co_argcount > 0) { 2025-09-11T11:57:04,225 | ^~ 2025-09-11T11:57:04,225 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:04,225 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:04,225 | ^~~~~~ 2025-09-11T11:57:04,226 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1999:18: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:04,226 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T11:57:04,226 | ^~ 2025-09-11T11:57:04,226 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:04,226 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:04,226 | ^~~~~~ 2025-09-11T11:57:04,227 In file included from /usr/include/python3.13/Python.h:63: 2025-09-11T11:57:04,227 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1999:52: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:04,227 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T11:57:04,227 | ^~ 2025-09-11T11:57:04,227 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-11T11:57:04,227 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-11T11:57:04,227 | ^~~~ 2025-09-11T11:57:04,228 /usr/include/python3.13/cpython/tupleobject.h:27:38: note: in expansion of macro ‘_PyTuple_CAST’ 2025-09-11T11:57:04,228 27 | #define PyTuple_GET_ITEM(op, index) (_PyTuple_CAST(op)->ob_item[(index)]) 2025-09-11T11:57:04,228 | ^~~~~~~~~~~~~ 2025-09-11T11:57:04,228 /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/modules/pybind11/include/pybind11/pybind11.h:1999:30: note: in expansion of macro ‘PyTuple_GET_ITEM’ 2025-09-11T11:57:04,228 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-11T11:57:04,228 | ^~~~~~~~~~~~~~~~ 2025-09-11T11:57:04,228 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-11T11:57:04,229 22 | typedef struct _frame PyFrameObject; 2025-09-11T11:57:04,229 | ^~~~~~ 2025-09-11T11:57:04,874 gmake[2]: *** [CMakeFiles/alignlib.dir/build.make:79: CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPairwiseAlign.cpp.o] Error 1 2025-09-11T11:57:04,875 gmake[2]: *** Waiting for unfinished jobs.... 2025-09-11T11:57:07,363 gmake[2]: *** [CMakeFiles/alignlib.dir/build.make:93: CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPseudoMultiAlign.cpp.o] Error 1 2025-09-11T11:57:07,363 gmake[1]: *** [CMakeFiles/Makefile2:319: CMakeFiles/alignlib.dir/all] Error 2 2025-09-11T11:57:07,363 gmake: *** [Makefile:136: all] Error 2 2025-09-11T11:57:07,374 Traceback (most recent call last): 2025-09-11T11:57:07,382 File "", line 2, in 2025-09-11T11:57:07,382 exec(compile(''' 2025-09-11T11:57:07,382 ~~~~^^^^^^^^^^^^ 2025-09-11T11:57:07,382 # This is -- a caller that pip uses to run setup.py 2025-09-11T11:57:07,383 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T11:57:07,383 ...<32 lines>... 2025-09-11T11:57:07,383 exec(compile(setup_py_code, filename, "exec")) 2025-09-11T11:57:07,383 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T11:57:07,383 ''' % ('/tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/setup.py',), "", "exec")) 2025-09-11T11:57:07,383 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T11:57:07,383 File "", line 35, in 2025-09-11T11:57:07,383 File "/tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/setup.py", line 126, in 2025-09-11T11:57:07,384 setup( 2025-09-11T11:57:07,384 ~~~~~^ 2025-09-11T11:57:07,384 name=thisPackage, 2025-09-11T11:57:07,384 ^^^^^^^^^^^^^^^^^ 2025-09-11T11:57:07,384 ...<47 lines>... 2025-09-11T11:57:07,384 zip_safe=False, 2025-09-11T11:57:07,384 ^^^^^^^^^^^^^^^ 2025-09-11T11:57:07,385 ) 2025-09-11T11:57:07,385 ^ 2025-09-11T11:57:07,385 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-11T11:57:07,385 return distutils.core.setup(**attrs) 2025-09-11T11:57:07,385 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T11:57:07,385 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-11T11:57:07,386 return run_commands(dist) 2025-09-11T11:57:07,386 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-11T11:57:07,386 dist.run_commands() 2025-09-11T11:57:07,386 ~~~~~~~~~~~~~~~~~^^ 2025-09-11T11:57:07,386 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-11T11:57:07,386 self.run_command(cmd) 2025-09-11T11:57:07,386 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-11T11:57:07,387 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-11T11:57:07,387 super().run_command(command) 2025-09-11T11:57:07,387 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T11:57:07,387 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-11T11:57:07,387 cmd_obj.run() 2025-09-11T11:57:07,387 ~~~~~~~~~~~^^ 2025-09-11T11:57:07,387 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-11T11:57:07,388 self.run_command("build") 2025-09-11T11:57:07,388 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T11:57:07,388 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-11T11:57:07,388 self.distribution.run_command(command) 2025-09-11T11:57:07,388 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T11:57:07,388 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-11T11:57:07,389 super().run_command(command) 2025-09-11T11:57:07,389 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T11:57:07,389 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-11T11:57:07,389 cmd_obj.run() 2025-09-11T11:57:07,389 ~~~~~~~~~~~^^ 2025-09-11T11:57:07,389 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-11T11:57:07,389 self.run_command(cmd_name) 2025-09-11T11:57:07,389 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-11T11:57:07,390 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-11T11:57:07,390 self.distribution.run_command(command) 2025-09-11T11:57:07,390 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T11:57:07,390 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-11T11:57:07,390 super().run_command(command) 2025-09-11T11:57:07,390 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-11T11:57:07,390 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-11T11:57:07,391 cmd_obj.run() 2025-09-11T11:57:07,391 ~~~~~~~~~~~^^ 2025-09-11T11:57:07,391 File "/tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/setup.py", line 39, in run 2025-09-11T11:57:07,391 self.build_extension(ext) 2025-09-11T11:57:07,391 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-11T11:57:07,392 File "/tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/setup.py", line 112, in build_extension 2025-09-11T11:57:07,392 subprocess.check_call(["cmake", "--build", "."] + buildArgs, cwd=self.build_temp) 2025-09-11T11:57:07,392 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-11T11:57:07,392 File "/usr/lib/python3.13/subprocess.py", line 419, in check_call 2025-09-11T11:57:07,392 raise CalledProcessError(retcode, cmd) 2025-09-11T11:57:07,392 subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2. 2025-09-11T11:57:07,502 ERROR: python setup.py bdist_wheel exited with 1 2025-09-11T11:57:07,515 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-11T11:57:07,515 exec(compile('"'"''"'"''"'"' 2025-09-11T11:57:07,515 # This is -- a caller that pip uses to run setup.py 2025-09-11T11:57:07,515 # 2025-09-11T11:57:07,515 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-11T11:57:07,515 # import from `distutils.core` to work with newer packaging standards. 2025-09-11T11:57:07,515 # - It provides a clear error message when setuptools is not installed. 2025-09-11T11:57:07,515 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-11T11:57:07,515 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-11T11:57:07,515 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-11T11:57:07,515 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-11T11:57:07,515 import os, sys, tokenize, traceback 2025-09-11T11:57:07,515 2025-09-11T11:57:07,515 try: 2025-09-11T11:57:07,515 import setuptools 2025-09-11T11:57:07,515 except ImportError: 2025-09-11T11:57:07,515 print( 2025-09-11T11:57:07,515 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-11T11:57:07,515 "the build environment with exception:", 2025-09-11T11:57:07,515 file=sys.stderr, 2025-09-11T11:57:07,515 ) 2025-09-11T11:57:07,515 traceback.print_exc() 2025-09-11T11:57:07,515 sys.exit(1) 2025-09-11T11:57:07,515 2025-09-11T11:57:07,515 __file__ = %r 2025-09-11T11:57:07,515 sys.argv[0] = __file__ 2025-09-11T11:57:07,515 2025-09-11T11:57:07,515 if os.path.exists(__file__): 2025-09-11T11:57:07,515 filename = __file__ 2025-09-11T11:57:07,515 with tokenize.open(__file__) as f: 2025-09-11T11:57:07,515 setup_py_code = f.read() 2025-09-11T11:57:07,515 else: 2025-09-11T11:57:07,515 filename = "" 2025-09-11T11:57:07,515 setup_py_code = "from setuptools import setup; setup()" 2025-09-11T11:57:07,515 2025-09-11T11:57:07,515 exec(compile(setup_py_code, filename, "exec")) 2025-09-11T11:57:07,515 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-s6a8sbuv[/] 2025-09-11T11:57:07,515 [bold magenta]cwd[/]: /tmp/pip-wheel-j55tsa1x/wwpdb-utils-align_83871acfa59a49228eba0a123e6edc1c/ 2025-09-11T11:57:07,515 Building wheel for wwpdb-utils-align (setup.py): finished with status 'error' 2025-09-11T11:57:07,516 ERROR: Failed building wheel for wwpdb-utils-align 2025-09-11T11:57:07,516 Running setup.py clean for wwpdb-utils-align 2025-09-11T11:57:07,517 Running command python setup.py clean 2025-09-11T11:57:08,400 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-11T11:57:08,400 warnings.warn(msg) 2025-09-11T11:57:08,400 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-11T11:57:08,401 warnings.warn(msg) 2025-09-11T11:57:08,606 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-11T11:57:08,606 !! 2025-09-11T11:57:08,606 ******************************************************************************** 2025-09-11T11:57:08,606 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-11T11:57:08,607 License :: OSI Approved :: Apache Software License 2025-09-11T11:57:08,607 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-11T11:57:08,607 ******************************************************************************** 2025-09-11T11:57:08,607 !! 2025-09-11T11:57:08,607 self._finalize_license_expression() 2025-09-11T11:57:08,681 running clean 2025-09-11T11:57:08,826 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-11T11:57:08,833 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-11T11:57:08,834 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-11T11:57:08,834 'build/scripts-3.13' does not exist -- can't clean it 2025-09-11T11:57:08,834 removing 'build' 2025-09-11T11:57:08,947 Failed to build wwpdb-utils-align 2025-09-11T11:57:08,948 ERROR: Failed to build one or more wheels 2025-09-11T11:57:08,949 Exception information: 2025-09-11T11:57:08,949 Traceback (most recent call last): 2025-09-11T11:57:08,949 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-11T11:57:08,949 status = _inner_run() 2025-09-11T11:57:08,949 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-11T11:57:08,949 return self.run(options, args) 2025-09-11T11:57:08,949 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-11T11:57:08,949 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-11T11:57:08,949 return func(self, options, args) 2025-09-11T11:57:08,949 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-11T11:57:08,949 raise CommandError("Failed to build one or more wheels") 2025-09-11T11:57:08,949 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-11T11:57:08,953 Removed build tracker: '/tmp/pip-build-tracker-kn001db9'