2025-09-08T14:17:13,702 Created temporary directory: /tmp/pip-build-tracker-1evtcbsg 2025-09-08T14:17:13,703 Initialized build tracking at /tmp/pip-build-tracker-1evtcbsg 2025-09-08T14:17:13,703 Created build tracker: /tmp/pip-build-tracker-1evtcbsg 2025-09-08T14:17:13,703 Entered build tracker: /tmp/pip-build-tracker-1evtcbsg 2025-09-08T14:17:13,704 Created temporary directory: /tmp/pip-wheel-51ty2iac 2025-09-08T14:17:13,707 Created temporary directory: /tmp/pip-ephem-wheel-cache-82vslncb 2025-09-08T14:17:13,762 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T14:17:13,765 2 location(s) to search for versions of wwpdb-utils-align: 2025-09-08T14:17:13,765 * https://pypi.org/simple/wwpdb-utils-align/ 2025-09-08T14:17:13,765 * https://www.piwheels.org/simple/wwpdb-utils-align/ 2025-09-08T14:17:13,765 Fetching project page and analyzing links: https://pypi.org/simple/wwpdb-utils-align/ 2025-09-08T14:17:13,765 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) 2025-09-08T14:17:14,022 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) 2025-09-08T14:17:14,022 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) 2025-09-08T14:17:14,022 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) 2025-09-08T14:17:14,023 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) 2025-09-08T14:17:14,023 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 2025-09-08T14:17:14,024 Fetching project page and analyzing links: 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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/) 2025-09-08T14:17:14,130 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/) 2025-09-08T14:17:14,130 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/) 2025-09-08T14:17:14,130 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/) 2025-09-08T14:17:14,130 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/) 2025-09-08T14:17:14,130 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/) 2025-09-08T14:17:14,130 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/) 2025-09-08T14:17:14,131 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/) 2025-09-08T14:17:14,131 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/) 2025-09-08T14:17:14,131 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/) 2025-09-08T14:17:14,131 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/) 2025-09-08T14:17:14,131 Skipping link: not a file: https://www.piwheels.org/simple/wwpdb-utils-align/ 2025-09-08T14:17:14,131 Skipping link: not a file: https://pypi.org/simple/wwpdb-utils-align/ 2025-09-08T14:17:14,156 Given no hashes to check 1 links for project 'wwpdb-utils-align': discarding no candidates 2025-09-08T14:17:14,157 Collecting wwpdb-utils-align==0.10 2025-09-08T14:17:14,158 Created temporary directory: /tmp/pip-unpack-l1m27t_l 2025-09-08T14:17:14,311 Downloading wwpdb.utils.align-0.10.tar.gz (600 kB) 2025-09-08T14:17:14,547 Added wwpdb-utils-align==0.10 from https://files.pythonhosted.org/packages/25/52/f224d04f128b12c37559d523f5e11dc561b28d4c1fec7853c94cd4377bb2/wwpdb.utils.align-0.10.tar.gz to build tracker '/tmp/pip-build-tracker-1evtcbsg' 2025-09-08T14:17:14,548 Running setup.py (path:/tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/setup.py) egg_info for package wwpdb-utils-align 2025-09-08T14:17:14,548 Created temporary directory: /tmp/pip-pip-egg-info-jfew_i73 2025-09-08T14:17:14,548 Preparing metadata (setup.py): started 2025-09-08T14:17:14,549 Running command python setup.py egg_info 2025-09-08T14:17:15,429 Warning: 'classifiers' should be a list, got type 'tuple' 2025-09-08T14:17:15,430 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T14:17:15,430 warnings.warn(msg) 2025-09-08T14:17:15,430 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-08T14:17:15,430 warnings.warn(msg) 2025-09-08T14:17:15,637 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T14:17:15,637 !! 2025-09-08T14:17:15,637 ******************************************************************************** 2025-09-08T14:17:15,637 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T14:17:15,637 License :: OSI Approved :: Apache Software License 2025-09-08T14:17:15,638 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T14:17:15,638 ******************************************************************************** 2025-09-08T14:17:15,638 !! 2025-09-08T14:17:15,638 self._finalize_license_expression() 2025-09-08T14:17:15,712 running egg_info 2025-09-08T14:17:15,787 creating /tmp/pip-pip-egg-info-jfew_i73/wwpdb.utils.align.egg-info 2025-09-08T14:17:15,787 writing /tmp/pip-pip-egg-info-jfew_i73/wwpdb.utils.align.egg-info/PKG-INFO 2025-09-08T14:17:15,789 writing dependency_links to /tmp/pip-pip-egg-info-jfew_i73/wwpdb.utils.align.egg-info/dependency_links.txt 2025-09-08T14:17:15,790 writing requirements to /tmp/pip-pip-egg-info-jfew_i73/wwpdb.utils.align.egg-info/requires.txt 2025-09-08T14:17:15,790 writing top-level names to /tmp/pip-pip-egg-info-jfew_i73/wwpdb.utils.align.egg-info/top_level.txt 2025-09-08T14:17:15,791 writing manifest file '/tmp/pip-pip-egg-info-jfew_i73/wwpdb.utils.align.egg-info/SOURCES.txt' 2025-09-08T14:17:16,019 reading manifest file '/tmp/pip-pip-egg-info-jfew_i73/wwpdb.utils.align.egg-info/SOURCES.txt' 2025-09-08T14:17:16,020 reading manifest template 'MANIFEST.in' 2025-09-08T14:17:16,035 writing manifest file '/tmp/pip-pip-egg-info-jfew_i73/wwpdb.utils.align.egg-info/SOURCES.txt' 2025-09-08T14:17:16,148 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T14:17:16,153 Source in /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938 has version 0.10, which satisfies requirement wwpdb-utils-align==0.10 from https://files.pythonhosted.org/packages/25/52/f224d04f128b12c37559d523f5e11dc561b28d4c1fec7853c94cd4377bb2/wwpdb.utils.align-0.10.tar.gz 2025-09-08T14:17:16,153 Removed wwpdb-utils-align==0.10 from https://files.pythonhosted.org/packages/25/52/f224d04f128b12c37559d523f5e11dc561b28d4c1fec7853c94cd4377bb2/wwpdb.utils.align-0.10.tar.gz from build tracker '/tmp/pip-build-tracker-1evtcbsg' 2025-09-08T14:17:16,158 Created temporary directory: /tmp/pip-unpack-wdqqn01t 2025-09-08T14:17:16,158 Created temporary directory: /tmp/pip-unpack-8rwx7z1y 2025-09-08T14:17:16,158 Building wheels for collected packages: wwpdb-utils-align 2025-09-08T14:17:16,160 Created temporary directory: /tmp/pip-wheel-2vgvn9nu 2025-09-08T14:17:16,160 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 2025-09-08T14:17:16,161 Building wheel for wwpdb-utils-align (setup.py): started 2025-09-08T14:17:16,162 Destination directory: /tmp/pip-wheel-2vgvn9nu 2025-09-08T14:17:16,162 Running command python setup.py bdist_wheel 2025-09-08T14:17:17,028 Warning: 'classifiers' should be a list, got type 'tuple' 2025-09-08T14:17:17,029 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T14:17:17,029 warnings.warn(msg) 2025-09-08T14:17:17,029 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-08T14:17:17,029 warnings.warn(msg) 2025-09-08T14:17:17,469 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T14:17:17,469 !! 2025-09-08T14:17:17,469 ******************************************************************************** 2025-09-08T14:17:17,469 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T14:17:17,470 License :: OSI Approved :: Apache Software License 2025-09-08T14:17:17,470 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T14:17:17,470 ******************************************************************************** 2025-09-08T14:17:17,470 !! 2025-09-08T14:17:17,470 self._finalize_license_expression() 2025-09-08T14:17:17,470 running bdist_wheel 2025-09-08T14:17:17,760 running build 2025-09-08T14:17:17,760 running build_py 2025-09-08T14:17:17,836 creating build/lib.linux-armv7l-cpython-313/wwpdb 2025-09-08T14:17:17,836 copying wwpdb/__init__.py -> build/lib.linux-armv7l-cpython-313/wwpdb 2025-09-08T14:17:17,837 creating build/lib.linux-armv7l-cpython-313/wwpdb/utils 2025-09-08T14:17:17,837 copying wwpdb/utils/__init__.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils 2025-09-08T14:17:17,838 creating build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-08T14:17:17,838 copying wwpdb/utils/align/__init__.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-08T14:17:17,839 copying wwpdb/utils/align/SequenceReferenceData.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-08T14:17:17,839 copying wwpdb/utils/align/SequenceExamples.py -> build/lib.linux-armv7l-cpython-313/wwpdb/utils/align 2025-09-08T14:17:17,845 running build_ext 2025-09-08T14:17:17,945 CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): 2025-09-08T14:17:17,945 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-08T14:17:17,945 CMake. 2025-09-08T14:17:17,946 Update the VERSION argument value. Or, use the ... syntax 2025-09-08T14:17:17,946 to tell CMake that the project requires at least but has been updated 2025-09-08T14:17:17,946 to work with policies introduced by or earlier. 2025-09-08T14:17:18,225 -- The C compiler identification is GNU 14.2.0 2025-09-08T14:17:18,561 -- The CXX compiler identification is GNU 14.2.0 2025-09-08T14:17:18,612 -- Detecting C compiler ABI info 2025-09-08T14:17:19,038 -- Detecting C compiler ABI info - done 2025-09-08T14:17:19,113 -- Check for working C compiler: /usr/bin/cc - skipped 2025-09-08T14:17:19,115 -- Detecting C compile features 2025-09-08T14:17:19,119 -- Detecting C compile features - done 2025-09-08T14:17:19,192 -- Detecting CXX compiler ABI info 2025-09-08T14:17:19,661 -- Detecting CXX compiler ABI info - done 2025-09-08T14:17:19,739 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2025-09-08T14:17:19,741 -- Detecting CXX compile features 2025-09-08T14:17:19,746 -- Detecting CXX compile features - done 2025-09-08T14:17:19,779 CMake Warning (dev) at CMakeLists.txt:17 (find_package): 2025-09-08T14:17:19,779 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-08T14:17:19,779 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-08T14:17:19,779 the cmake_policy command to set the policy and suppress this warning. 2025-09-08T14:17:19,780 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-08T14:17:19,851 -- Found PythonInterp: /usr/bin/python3 (found version "3.13.5") 2025-09-08T14:17:19,852 CMake Warning (dev) at CMakeLists.txt:18 (find_package): 2025-09-08T14:17:19,852 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-08T14:17:19,853 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-08T14:17:19,853 the cmake_policy command to set the policy and suppress this warning. 2025-09-08T14:17:19,853 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-08T14:17:19,880 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.13.so (found version "3.13.5") 2025-09-08T14:17:19,880 -- Python include path set to /usr/include/python3.13 2025-09-08T14:17:19,883 CMake Deprecation Warning at modules/pybind11/CMakeLists.txt:8 (cmake_minimum_required): 2025-09-08T14:17:19,883 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-08T14:17:19,883 CMake. 2025-09-08T14:17:19,884 Update the VERSION argument value. Or, use the ... syntax 2025-09-08T14:17:19,884 to tell CMake that the project requires at least but has been updated 2025-09-08T14:17:19,884 to work with policies introduced by or earlier. 2025-09-08T14:17:19,886 CMake Deprecation Warning at modules/pybind11/tools/pybind11Tools.cmake:8 (cmake_minimum_required): 2025-09-08T14:17:19,886 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-08T14:17:19,886 CMake. 2025-09-08T14:17:19,886 Update the VERSION argument value. Or, use the ... syntax 2025-09-08T14:17:19,887 to tell CMake that the project requires at least but has been updated 2025-09-08T14:17:19,887 to work with policies introduced by or earlier. 2025-09-08T14:17:19,887 Call Stack (most recent call first): 2025-09-08T14:17:19,887 modules/pybind11/CMakeLists.txt:33 (include) 2025-09-08T14:17:19,889 CMake Warning (dev) at modules/pybind11/tools/FindPythonLibsNew.cmake:60 (find_package): 2025-09-08T14:17:19,889 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-08T14:17:19,889 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-08T14:17:19,889 the cmake_policy command to set the policy and suppress this warning. 2025-09-08T14:17:19,889 Call Stack (most recent call first): 2025-09-08T14:17:19,889 modules/pybind11/tools/pybind11Tools.cmake:16 (find_package) 2025-09-08T14:17:19,889 modules/pybind11/CMakeLists.txt:33 (include) 2025-09-08T14:17:19,890 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-08T14:17:20,558 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.13.so 2025-09-08T14:17:20,569 -- Performing Test HAS_CPP14_FLAG 2025-09-08T14:17:21,052 -- Performing Test HAS_CPP14_FLAG - Success 2025-09-08T14:17:21,073 -- pybind11 v2.3.dev0 2025-09-08T14:17:21,075 -- 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 2025-09-08T14:17:21,075 -- ---CMAKE MODULE PATH - 2025-09-08T14:17:21,075 -- ---CMAKE SOURCE DIR - /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938 2025-09-08T14:17:21,075 -- ---CMAKE PROJECT DIR - /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938 2025-09-08T14:17:21,087 -- Performing Test HAS_FLTO 2025-09-08T14:17:21,746 -- Performing Test HAS_FLTO - Success 2025-09-08T14:17:21,747 -- LTO enabled 2025-09-08T14:17:21,748 STATUS,---ALL DONE WITH CMAKE 2025-09-08T14:17:21,749 -- Configuring done (3.8s) 2025-09-08T14:17:21,783 -- Generating done (0.0s) 2025-09-08T14:17:21,785 -- Build files have been written to: /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/build/temp.linux-armv7l-cpython-313 2025-09-08T14:17:22,069 [ 16%] Building CXX object CMakeFiles/align.dir/modules/PairwiseAlign/src/AlignUtil.C.o 2025-09-08T14:17:22,069 [ 16%] Building CXX object CMakeFiles/align.dir/modules/PairwiseAlign/src/PairwiseAlign.C.o 2025-09-08T14:17:23,296 [ 25%] Building CXX object CMakeFiles/align.dir/modules/PairwiseAlign/src/PseudoMultiAlign.C.o 2025-09-08T14:17:26,748 [ 25%] Built target align 2025-09-08T14:17:26,863 [ 33%] Linking CXX static library lib/libalign-all.a 2025-09-08T14:17:27,036 [ 33%] Built target align-all 2025-09-08T14:17:27,148 [ 50%] Building CXX object CMakeFiles/align_test_1.dir/modules/PairwiseAlign/test/testPairwiseAlign.C.o 2025-09-08T14:17:27,148 [ 50%] Building CXX object CMakeFiles/align_test_2.dir/modules/PairwiseAlign/test/testPairwiseAlignZF.C.o 2025-09-08T14:17:29,389 [ 58%] Linking CXX executable bin/align_test_2 2025-09-08T14:17:29,509 [ 66%] Linking CXX executable bin/align_test_1 2025-09-08T14:17:34,499 [ 66%] Built target align_test_2 2025-09-08T14:17:34,611 [ 75%] Building CXX object CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPairwiseAlign.cpp.o 2025-09-08T14:17:37,095 [ 75%] Built target align_test_1 2025-09-08T14:17:37,144 [ 83%] Building CXX object CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPseudoMultiAlign.cpp.o 2025-09-08T14:17:37,235 In file included from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h:13, 2025-09-08T14:17:37,235 from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:43, 2025-09-08T14:17:37,235 from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/cpp-alignlib-wrapper/src/wrapPairwiseAlign.cpp:5: 2025-09-08T14:17:37,235 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h: In function ‘std::string pybind11::detail::error_string()’: 2025-09-08T14:17:37,236 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:442:36: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,236 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-08T14:17:37,236 | ^~ 2025-09-08T14:17:37,236 In file included from /usr/include/python3.13/Python.h:67, 2025-09-08T14:17:37,236 from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/detail/common.h:112, 2025-09-08T14:17:37,236 from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pytypes.h:12, 2025-09-08T14:17:37,236 from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:13: 2025-09-08T14:17:37,237 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,237 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:37,237 | ^~~~~~ 2025-09-08T14:17:37,237 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:442:75: error: expected primary-expression before ‘>’ token 2025-09-08T14:17:37,237 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-08T14:17:37,237 | ^ 2025-09-08T14:17:37,237 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:442:77: error: expected primary-expression before ‘)’ token 2025-09-08T14:17:37,237 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-08T14:17:37,238 | ^ 2025-09-08T14:17:37,238 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:444:29: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,238 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-08T14:17:37,238 | ^~ 2025-09-08T14:17:37,238 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,238 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:37,238 | ^~~~~~ 2025-09-08T14:17:37,238 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:444:64: error: expected primary-expression before ‘>’ token 2025-09-08T14:17:37,239 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-08T14:17:37,239 | ^ 2025-09-08T14:17:37,239 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:444:66: error: expected primary-expression before ‘)’ token 2025-09-08T14:17:37,239 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-08T14:17:37,239 | ^ 2025-09-08T14:17:37,239 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:445:26: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,239 445 | frame = frame->f_back; 2025-09-08T14:17:37,239 | ^~ 2025-09-08T14:17:37,240 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,240 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:37,240 | ^~~~~~ 2025-09-08T14:17:37,415 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h: At global scope: 2025-09-08T14:17:37,415 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h:185:10: error: ‘uint16_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’? 2025-09-08T14:17:37,415 185 | std::uint16_t nargs; 2025-09-08T14:17:37,415 | ^~~~~~~~ 2025-09-08T14:17:37,416 | wint_t 2025-09-08T14:17:37,431 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h: In constructor ‘pybind11::detail::function_call::function_call(const pybind11::detail::function_record&, pybind11::handle)’: 2025-09-08T14:17:37,431 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h:283:20: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-08T14:17:37,431 283 | args.reserve(f.nargs); 2025-09-08T14:17:37,431 | ^~~~~ 2025-09-08T14:17:37,431 | args 2025-09-08T14:17:37,432 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h:284:28: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-08T14:17:37,432 284 | args_convert.reserve(f.nargs); 2025-09-08T14:17:37,432 | ^~~~~ 2025-09-08T14:17:37,432 | args 2025-09-08T14:17:37,524 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/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)’: 2025-09-08T14:17:37,524 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:283:14: error: ‘struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-08T14:17:37,524 283 | rec->nargs = (std::uint16_t) args; 2025-09-08T14:17:37,524 | ^~~~~ 2025-09-08T14:17:37,525 | args 2025-09-08T14:17:37,526 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:283:28: error: ‘uint16_t’ is not a member of ‘std’; did you mean ‘wint_t’? 2025-09-08T14:17:37,526 283 | rec->nargs = (std::uint16_t) args; 2025-09-08T14:17:37,526 | ^~~~~~~~ 2025-09-08T14:17:37,527 | wint_t 2025-09-08T14:17:37,550 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h: In static member function ‘static PyObject* pybind11::cpp_function::dispatcher(PyObject*, PyObject*, PyObject*)’: 2025-09-08T14:17:37,550 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:481:40: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-08T14:17:37,550 481 | size_t pos_args = func.nargs; // Number of positional arguments that we need 2025-09-08T14:17:37,550 | ^~~~~ 2025-09-08T14:17:37,551 | args 2025-09-08T14:17:37,559 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:612:53: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-08T14:17:37,559 612 | second_pass_convert.resize(func.nargs, false); 2025-09-08T14:17:37,559 | ^~~~~ 2025-09-08T14:17:37,559 | args 2025-09-08T14:17:37,765 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h: In function ‘pybind11::function pybind11::get_type_overload(const void*, const detail::type_info*, const char*)’: 2025-09-08T14:17:37,765 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1994:49: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T14:17:37,765 1994 | PyFrameObject *frame = PyThreadState_Get()->frame; 2025-09-08T14:17:37,766 | ^~~~~ 2025-09-08T14:17:37,766 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1995:41: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,766 1995 | if (frame && (std::string) str(frame->f_code->co_name) == name && 2025-09-08T14:17:37,766 | ^~ 2025-09-08T14:17:37,766 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,766 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:37,766 | ^~~~~~ 2025-09-08T14:17:37,767 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1996:14: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,767 1996 | frame->f_code->co_argcount > 0) { 2025-09-08T14:17:37,767 | ^~ 2025-09-08T14:17:37,767 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,767 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:37,767 | ^~~~~~ 2025-09-08T14:17:37,767 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1999:18: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,767 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-08T14:17:37,768 | ^~ 2025-09-08T14:17:37,768 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,768 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:37,768 | ^~~~~~ 2025-09-08T14:17:37,768 In file included from /usr/include/python3.13/Python.h:63: 2025-09-08T14:17:37,768 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1999:52: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,769 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-08T14:17:37,769 | ^~ 2025-09-08T14:17:37,769 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-08T14:17:37,769 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-08T14:17:37,769 | ^~~~ 2025-09-08T14:17:37,769 /usr/include/python3.13/cpython/tupleobject.h:27:38: note: in expansion of macro ‘_PyTuple_CAST’ 2025-09-08T14:17:37,769 27 | #define PyTuple_GET_ITEM(op, index) (_PyTuple_CAST(op)->ob_item[(index)]) 2025-09-08T14:17:37,769 | ^~~~~~~~~~~~~ 2025-09-08T14:17:37,770 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1999:30: note: in expansion of macro ‘PyTuple_GET_ITEM’ 2025-09-08T14:17:37,770 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-08T14:17:37,770 | ^~~~~~~~~~~~~~~~ 2025-09-08T14:17:37,770 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:37,770 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:37,770 | ^~~~~~ 2025-09-08T14:17:39,705 In file included from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h:13, 2025-09-08T14:17:39,705 from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:43, 2025-09-08T14:17:39,705 from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/cpp-alignlib-wrapper/src/wrapPseudoMultiAlign.cpp:5: 2025-09-08T14:17:39,706 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h: In function ‘std::string pybind11::detail::error_string()’: 2025-09-08T14:17:39,706 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:442:36: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:39,706 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-08T14:17:39,706 | ^~ 2025-09-08T14:17:39,706 In file included from /usr/include/python3.13/Python.h:67, 2025-09-08T14:17:39,706 from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/detail/common.h:112, 2025-09-08T14:17:39,706 from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pytypes.h:12, 2025-09-08T14:17:39,707 from /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:13: 2025-09-08T14:17:39,707 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:39,707 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:39,707 | ^~~~~~ 2025-09-08T14:17:39,707 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:442:75: error: expected primary-expression before ‘>’ token 2025-09-08T14:17:39,707 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-08T14:17:39,707 | ^ 2025-09-08T14:17:39,708 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:442:77: error: expected primary-expression before ‘)’ token 2025-09-08T14:17:39,708 442 | " " + handle(frame->f_code->co_filename).cast() + 2025-09-08T14:17:39,708 | ^ 2025-09-08T14:17:39,708 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:444:29: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:39,708 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-08T14:17:39,708 | ^~ 2025-09-08T14:17:39,708 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:39,709 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:39,709 | ^~~~~~ 2025-09-08T14:17:39,709 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:444:64: error: expected primary-expression before ‘>’ token 2025-09-08T14:17:39,709 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-08T14:17:39,709 | ^ 2025-09-08T14:17:39,709 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:444:66: error: expected primary-expression before ‘)’ token 2025-09-08T14:17:39,709 444 | handle(frame->f_code->co_name).cast() + "\n"; 2025-09-08T14:17:39,710 | ^ 2025-09-08T14:17:39,710 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/cast.h:445:26: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:39,710 445 | frame = frame->f_back; 2025-09-08T14:17:39,710 | ^~ 2025-09-08T14:17:39,710 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:39,710 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:39,710 | ^~~~~~ 2025-09-08T14:17:39,873 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h: At global scope: 2025-09-08T14:17:39,873 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h:185:10: error: ‘uint16_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’? 2025-09-08T14:17:39,874 185 | std::uint16_t nargs; 2025-09-08T14:17:39,874 | ^~~~~~~~ 2025-09-08T14:17:39,874 | wint_t 2025-09-08T14:17:39,887 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h: In constructor ‘pybind11::detail::function_call::function_call(const pybind11::detail::function_record&, pybind11::handle)’: 2025-09-08T14:17:39,888 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h:283:20: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-08T14:17:39,888 283 | args.reserve(f.nargs); 2025-09-08T14:17:39,888 | ^~~~~ 2025-09-08T14:17:39,888 | args 2025-09-08T14:17:39,888 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/attr.h:284:28: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-08T14:17:39,889 284 | args_convert.reserve(f.nargs); 2025-09-08T14:17:39,889 | ^~~~~ 2025-09-08T14:17:39,889 | args 2025-09-08T14:17:39,976 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/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)’: 2025-09-08T14:17:39,977 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:283:14: error: ‘struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-08T14:17:39,977 283 | rec->nargs = (std::uint16_t) args; 2025-09-08T14:17:39,977 | ^~~~~ 2025-09-08T14:17:39,977 | args 2025-09-08T14:17:39,978 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:283:28: error: ‘uint16_t’ is not a member of ‘std’; did you mean ‘wint_t’? 2025-09-08T14:17:39,979 283 | rec->nargs = (std::uint16_t) args; 2025-09-08T14:17:39,979 | ^~~~~~~~ 2025-09-08T14:17:39,979 | wint_t 2025-09-08T14:17:40,002 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h: In static member function ‘static PyObject* pybind11::cpp_function::dispatcher(PyObject*, PyObject*, PyObject*)’: 2025-09-08T14:17:40,002 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:481:40: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-08T14:17:40,002 481 | size_t pos_args = func.nargs; // Number of positional arguments that we need 2025-09-08T14:17:40,002 | ^~~~~ 2025-09-08T14:17:40,003 | args 2025-09-08T14:17:40,009 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:612:53: error: ‘const struct pybind11::detail::function_record’ has no member named ‘nargs’; did you mean ‘args’? 2025-09-08T14:17:40,010 612 | second_pass_convert.resize(func.nargs, false); 2025-09-08T14:17:40,010 | ^~~~~ 2025-09-08T14:17:40,010 | args 2025-09-08T14:17:40,219 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h: In function ‘pybind11::function pybind11::get_type_overload(const void*, const detail::type_info*, const char*)’: 2025-09-08T14:17:40,219 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1994:49: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T14:17:40,219 1994 | PyFrameObject *frame = PyThreadState_Get()->frame; 2025-09-08T14:17:40,220 | ^~~~~ 2025-09-08T14:17:40,220 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1995:41: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:40,220 1995 | if (frame && (std::string) str(frame->f_code->co_name) == name && 2025-09-08T14:17:40,220 | ^~ 2025-09-08T14:17:40,220 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:40,220 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:40,221 | ^~~~~~ 2025-09-08T14:17:40,221 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1996:14: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:40,221 1996 | frame->f_code->co_argcount > 0) { 2025-09-08T14:17:40,221 | ^~ 2025-09-08T14:17:40,221 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:40,221 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:40,221 | ^~~~~~ 2025-09-08T14:17:40,222 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1999:18: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:40,222 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-08T14:17:40,222 | ^~ 2025-09-08T14:17:40,222 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:40,222 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:40,222 | ^~~~~~ 2025-09-08T14:17:40,223 In file included from /usr/include/python3.13/Python.h:63: 2025-09-08T14:17:40,223 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1999:52: error: invalid use of incomplete type ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:40,223 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-08T14:17:40,223 | ^~ 2025-09-08T14:17:40,223 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-08T14:17:40,223 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-08T14:17:40,224 | ^~~~ 2025-09-08T14:17:40,224 /usr/include/python3.13/cpython/tupleobject.h:27:38: note: in expansion of macro ‘_PyTuple_CAST’ 2025-09-08T14:17:40,224 27 | #define PyTuple_GET_ITEM(op, index) (_PyTuple_CAST(op)->ob_item[(index)]) 2025-09-08T14:17:40,224 | ^~~~~~~~~~~~~ 2025-09-08T14:17:40,224 /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/modules/pybind11/include/pybind11/pybind11.h:1999:30: note: in expansion of macro ‘PyTuple_GET_ITEM’ 2025-09-08T14:17:40,224 1999 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0)); 2025-09-08T14:17:40,224 | ^~~~~~~~~~~~~~~~ 2025-09-08T14:17:40,225 /usr/include/python3.13/pytypedefs.h:22:16: note: forward declaration of ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T14:17:40,225 22 | typedef struct _frame PyFrameObject; 2025-09-08T14:17:40,225 | ^~~~~~ 2025-09-08T14:17:41,498 gmake[2]: *** [CMakeFiles/alignlib.dir/build.make:79: CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPairwiseAlign.cpp.o] Error 1 2025-09-08T14:17:41,499 gmake[2]: *** Waiting for unfinished jobs.... 2025-09-08T14:17:43,430 gmake[2]: *** [CMakeFiles/alignlib.dir/build.make:93: CMakeFiles/alignlib.dir/modules/cpp-alignlib-wrapper/src/wrapPseudoMultiAlign.cpp.o] Error 1 2025-09-08T14:17:43,430 gmake[1]: *** [CMakeFiles/Makefile2:249: CMakeFiles/alignlib.dir/all] Error 2 2025-09-08T14:17:43,431 gmake: *** [Makefile:136: all] Error 2 2025-09-08T14:17:43,442 Traceback (most recent call last): 2025-09-08T14:17:43,450 File "", line 2, in 2025-09-08T14:17:43,450 exec(compile(''' 2025-09-08T14:17:43,450 ~~~~^^^^^^^^^^^^ 2025-09-08T14:17:43,450 # This is -- a caller that pip uses to run setup.py 2025-09-08T14:17:43,451 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:17:43,451 ...<32 lines>... 2025-09-08T14:17:43,451 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T14:17:43,451 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:17:43,451 ''' % ('/tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/setup.py',), "", "exec")) 2025-09-08T14:17:43,451 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:17:43,451 File "", line 35, in 2025-09-08T14:17:43,452 File "/tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/setup.py", line 116, in 2025-09-08T14:17:43,452 setup( 2025-09-08T14:17:43,452 ~~~~~^ 2025-09-08T14:17:43,452 name=thisPackage, 2025-09-08T14:17:43,452 ^^^^^^^^^^^^^^^^^ 2025-09-08T14:17:43,452 ...<54 lines>... 2025-09-08T14:17:43,452 zip_safe=False, 2025-09-08T14:17:43,452 ^^^^^^^^^^^^^^^ 2025-09-08T14:17:43,452 ) 2025-09-08T14:17:43,453 ^ 2025-09-08T14:17:43,453 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-08T14:17:43,453 return distutils.core.setup(**attrs) 2025-09-08T14:17:43,453 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T14:17:43,453 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-08T14:17:43,453 return run_commands(dist) 2025-09-08T14:17:43,453 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-08T14:17:43,453 dist.run_commands() 2025-09-08T14:17:43,454 ~~~~~~~~~~~~~~~~~^^ 2025-09-08T14:17:43,454 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-08T14:17:43,454 self.run_command(cmd) 2025-09-08T14:17:43,454 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T14:17:43,454 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T14:17:43,454 super().run_command(command) 2025-09-08T14:17:43,454 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T14:17:43,454 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T14:17:43,455 cmd_obj.run() 2025-09-08T14:17:43,455 ~~~~~~~~~~~^^ 2025-09-08T14:17:43,455 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-08T14:17:43,455 self.run_command("build") 2025-09-08T14:17:43,455 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T14:17:43,455 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T14:17:43,455 self.distribution.run_command(command) 2025-09-08T14:17:43,455 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T14:17:43,456 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T14:17:43,456 super().run_command(command) 2025-09-08T14:17:43,456 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T14:17:43,456 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T14:17:43,456 cmd_obj.run() 2025-09-08T14:17:43,456 ~~~~~~~~~~~^^ 2025-09-08T14:17:43,456 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-08T14:17:43,456 self.run_command(cmd_name) 2025-09-08T14:17:43,457 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-08T14:17:43,457 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T14:17:43,457 self.distribution.run_command(command) 2025-09-08T14:17:43,457 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T14:17:43,457 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T14:17:43,457 super().run_command(command) 2025-09-08T14:17:43,457 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T14:17:43,457 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T14:17:43,458 cmd_obj.run() 2025-09-08T14:17:43,458 ~~~~~~~~~~~^^ 2025-09-08T14:17:43,458 File "/tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/setup.py", line 40, in run 2025-09-08T14:17:43,458 self.build_extension(ext) 2025-09-08T14:17:43,458 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T14:17:43,458 File "/tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/setup.py", line 100, in build_extension 2025-09-08T14:17:43,458 subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp) 2025-09-08T14:17:43,458 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:17:43,459 File "/usr/lib/python3.13/subprocess.py", line 419, in check_call 2025-09-08T14:17:43,459 raise CalledProcessError(retcode, cmd) 2025-09-08T14:17:43,459 subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2. 2025-09-08T14:17:43,568 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T14:17:43,581 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T14:17:43,581 exec(compile('"'"''"'"''"'"' 2025-09-08T14:17:43,581 # This is -- a caller that pip uses to run setup.py 2025-09-08T14:17:43,581 # 2025-09-08T14:17:43,581 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T14:17:43,581 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T14:17:43,581 # - It provides a clear error message when setuptools is not installed. 2025-09-08T14:17:43,581 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T14:17:43,581 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T14:17:43,581 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T14:17:43,581 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T14:17:43,581 import os, sys, tokenize, traceback 2025-09-08T14:17:43,581 2025-09-08T14:17:43,581 try: 2025-09-08T14:17:43,581 import setuptools 2025-09-08T14:17:43,581 except ImportError: 2025-09-08T14:17:43,581 print( 2025-09-08T14:17:43,581 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T14:17:43,581 "the build environment with exception:", 2025-09-08T14:17:43,581 file=sys.stderr, 2025-09-08T14:17:43,581 ) 2025-09-08T14:17:43,581 traceback.print_exc() 2025-09-08T14:17:43,581 sys.exit(1) 2025-09-08T14:17:43,581 2025-09-08T14:17:43,581 __file__ = %r 2025-09-08T14:17:43,581 sys.argv[0] = __file__ 2025-09-08T14:17:43,581 2025-09-08T14:17:43,581 if os.path.exists(__file__): 2025-09-08T14:17:43,581 filename = __file__ 2025-09-08T14:17:43,581 with tokenize.open(__file__) as f: 2025-09-08T14:17:43,581 setup_py_code = f.read() 2025-09-08T14:17:43,581 else: 2025-09-08T14:17:43,581 filename = "" 2025-09-08T14:17:43,581 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T14:17:43,581 2025-09-08T14:17:43,581 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T14:17:43,581 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-2vgvn9nu[/] 2025-09-08T14:17:43,582 [bold magenta]cwd[/]: /tmp/pip-wheel-51ty2iac/wwpdb-utils-align_ac8080bc3bd74615b5dad1044920c938/ 2025-09-08T14:17:43,582 Building wheel for wwpdb-utils-align (setup.py): finished with status 'error' 2025-09-08T14:17:43,583 ERROR: Failed building wheel for wwpdb-utils-align 2025-09-08T14:17:43,583 Running setup.py clean for wwpdb-utils-align 2025-09-08T14:17:43,584 Running command python setup.py clean 2025-09-08T14:17:44,519 Warning: 'classifiers' should be a list, got type 'tuple' 2025-09-08T14:17:44,520 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T14:17:44,520 warnings.warn(msg) 2025-09-08T14:17:44,520 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-08T14:17:44,520 warnings.warn(msg) 2025-09-08T14:17:44,727 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T14:17:44,727 !! 2025-09-08T14:17:44,727 ******************************************************************************** 2025-09-08T14:17:44,727 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T14:17:44,727 License :: OSI Approved :: Apache Software License 2025-09-08T14:17:44,727 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T14:17:44,728 ******************************************************************************** 2025-09-08T14:17:44,728 !! 2025-09-08T14:17:44,728 self._finalize_license_expression() 2025-09-08T14:17:44,802 running clean 2025-09-08T14:17:44,946 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T14:17:44,952 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T14:17:44,952 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T14:17:44,953 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T14:17:44,953 removing 'build' 2025-09-08T14:17:45,066 Failed to build wwpdb-utils-align 2025-09-08T14:17:45,067 ERROR: Failed to build one or more wheels 2025-09-08T14:17:45,068 Exception information: 2025-09-08T14:17:45,068 Traceback (most recent call last): 2025-09-08T14:17:45,068 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T14:17:45,068 status = _inner_run() 2025-09-08T14:17:45,068 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T14:17:45,068 return self.run(options, args) 2025-09-08T14:17:45,068 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T14:17:45,068 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T14:17:45,068 return func(self, options, args) 2025-09-08T14:17:45,068 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T14:17:45,068 raise CommandError("Failed to build one or more wheels") 2025-09-08T14:17:45,068 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T14:17:45,072 Removed build tracker: '/tmp/pip-build-tracker-1evtcbsg'