2025-09-08T23:53:27,673 Created temporary directory: /tmp/pip-build-tracker-onb9gozh 2025-09-08T23:53:27,673 Initialized build tracking at /tmp/pip-build-tracker-onb9gozh 2025-09-08T23:53:27,674 Created build tracker: /tmp/pip-build-tracker-onb9gozh 2025-09-08T23:53:27,674 Entered build tracker: /tmp/pip-build-tracker-onb9gozh 2025-09-08T23:53:27,674 Created temporary directory: /tmp/pip-wheel-ign7odae 2025-09-08T23:53:27,677 Created temporary directory: /tmp/pip-ephem-wheel-cache-88udydoc 2025-09-08T23:53:27,739 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T23:53:27,741 2 location(s) to search for versions of segmentation-phenix: 2025-09-08T23:53:27,741 * https://pypi.org/simple/segmentation-phenix/ 2025-09-08T23:53:27,741 * https://www.piwheels.org/simple/segmentation-phenix/ 2025-09-08T23:53:27,741 Fetching project page and analyzing links: https://pypi.org/simple/segmentation-phenix/ 2025-09-08T23:53:27,742 Getting page https://pypi.org/simple/segmentation-phenix/ 2025-09-08T23:53:27,743 Found index url https://pypi.org/simple/ 2025-09-08T23:53:27,815 Fetched page https://pypi.org/simple/segmentation-phenix/ as application/vnd.pypi.simple.v1+json 2025-09-08T23:53:27,816 Found link https://files.pythonhosted.org/packages/30/6c/d50d13cc8a0f6e83dfcf9ee1759ba9932bd77b4e9a9d78ba0f507744ac37/segmentation_phenix-0.1.0.tar.gz (from https://pypi.org/simple/segmentation-phenix/), version: 0.1.0 2025-09-08T23:53:27,817 Found link https://files.pythonhosted.org/packages/04/55/6543f51023a5dcad42a9b10db8073a826ec9fa0cf14cdca970836d65e317/segmentation_phenix-0.1.1.tar.gz (from https://pypi.org/simple/segmentation-phenix/), version: 0.1.1 2025-09-08T23:53:27,817 Found link https://files.pythonhosted.org/packages/74/d8/f0734acbe90d53afdc8d297676992794fe5c0042e84aef81f9e886fe2135/segmentation_phenix-0.1.2.tar.gz (from https://pypi.org/simple/segmentation-phenix/), version: 0.1.2 2025-09-08T23:53:27,817 Found link https://files.pythonhosted.org/packages/5a/a4/8bfee07573bd5378121f60da7a3936010cf0e75feee6c7f3eb7a2dd7b196/segmentation_phenix-0.1.3.tar.gz (from https://pypi.org/simple/segmentation-phenix/), version: 0.1.3 2025-09-08T23:53:27,817 Found link https://files.pythonhosted.org/packages/af/d6/b3e45deb822008b224bfc9d6c25c9794bf2b394b00d9d955e2ac2df55b58/segmentation_phenix-0.1.4.tar.gz (from https://pypi.org/simple/segmentation-phenix/), version: 0.1.4 2025-09-08T23:53:27,818 Found link https://files.pythonhosted.org/packages/94/64/afd02ce8113aa913e7ea13937756b9e66fdf1f9225b743acd83a6c4bac18/segmentation_phenix-0.1.5.tar.gz (from https://pypi.org/simple/segmentation-phenix/), version: 0.1.5 2025-09-08T23:53:27,818 Found link https://files.pythonhosted.org/packages/5c/7d/752c9955ea2135add62b018cf97e5ad8facde379b8b08e14fc2a41c5db98/segmentation_phenix-0.1.6.tar.gz (from https://pypi.org/simple/segmentation-phenix/), version: 0.1.6 2025-09-08T23:53:27,818 Found link https://files.pythonhosted.org/packages/4f/fc/2aaf44d9abeb1b31cef9507fca044750d3bca9621c7c80c4ec29548bf3b6/segmentation_phenix-0.1.7.tar.gz (from https://pypi.org/simple/segmentation-phenix/), version: 0.1.7 2025-09-08T23:53:27,818 Fetching project page and analyzing links: https://www.piwheels.org/simple/segmentation-phenix/ 2025-09-08T23:53:27,819 Getting page https://www.piwheels.org/simple/segmentation-phenix/ 2025-09-08T23:53:27,820 Found index url https://www.piwheels.org/simple/ 2025-09-08T23:53:27,912 Fetched page https://www.piwheels.org/simple/segmentation-phenix/ as text/html 2025-09-08T23:53:27,913 Skipping link: not a file: https://www.piwheels.org/simple/segmentation-phenix/ 2025-09-08T23:53:27,913 Skipping link: not a file: https://pypi.org/simple/segmentation-phenix/ 2025-09-08T23:53:27,936 Given no hashes to check 1 links for project 'segmentation-phenix': discarding no candidates 2025-09-08T23:53:27,937 Collecting segmentation-phenix==0.1.4 2025-09-08T23:53:27,939 Created temporary directory: /tmp/pip-unpack-urd8tfsd 2025-09-08T23:53:28,156 Downloading segmentation_phenix-0.1.4.tar.gz (17 kB) 2025-09-08T23:53:28,181 Added segmentation-phenix==0.1.4 from https://files.pythonhosted.org/packages/af/d6/b3e45deb822008b224bfc9d6c25c9794bf2b394b00d9d955e2ac2df55b58/segmentation_phenix-0.1.4.tar.gz to build tracker '/tmp/pip-build-tracker-onb9gozh' 2025-09-08T23:53:28,183 Running setup.py (path:/tmp/pip-wheel-ign7odae/segmentation-phenix_16bb87ce839e4ff694837e6c32108e1c/setup.py) egg_info for package segmentation-phenix 2025-09-08T23:53:28,183 Created temporary directory: /tmp/pip-pip-egg-info-cxmbztdr 2025-09-08T23:53:28,184 Preparing metadata (setup.py): started 2025-09-08T23:53:28,184 Running command python setup.py egg_info 2025-09-08T23:53:29,040 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. 2025-09-08T23:53:29,040 !! 2025-09-08T23:53:29,040 ******************************************************************************** 2025-09-08T23:53:29,040 Usage of dash-separated 'description-file' will not be supported in future 2025-09-08T23:53:29,040 versions. Please use the underscore name 'description_file' instead. 2025-09-08T23:53:29,041 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T23:53:29,041 or your builds will no longer be supported. 2025-09-08T23:53:29,041 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T23:53:29,041 ******************************************************************************** 2025-09-08T23:53:29,041 !! 2025-09-08T23:53:29,041 opt = self._enforce_underscore(opt, section) 2025-09-08T23:53:29,485 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. 2025-09-08T23:53:29,485 !! 2025-09-08T23:53:29,485 ******************************************************************************** 2025-09-08T23:53:29,485 Usage of dash-separated 'description-file' will not be supported in future 2025-09-08T23:53:29,485 versions. Please use the underscore name 'description_file' instead. 2025-09-08T23:53:29,485 (Affected: segmentation_phenix). 2025-09-08T23:53:29,486 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T23:53:29,486 or your builds will no longer be supported. 2025-09-08T23:53:29,486 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T23:53:29,486 ******************************************************************************** 2025-09-08T23:53:29,486 !! 2025-09-08T23:53:29,486 opt = self._enforce_underscore(opt, section) 2025-09-08T23:53:29,560 running egg_info 2025-09-08T23:53:29,636 creating /tmp/pip-pip-egg-info-cxmbztdr/segmentation_phenix.egg-info 2025-09-08T23:53:29,636 writing /tmp/pip-pip-egg-info-cxmbztdr/segmentation_phenix.egg-info/PKG-INFO 2025-09-08T23:53:29,637 writing dependency_links to /tmp/pip-pip-egg-info-cxmbztdr/segmentation_phenix.egg-info/dependency_links.txt 2025-09-08T23:53:29,638 writing requirements to /tmp/pip-pip-egg-info-cxmbztdr/segmentation_phenix.egg-info/requires.txt 2025-09-08T23:53:29,638 writing top-level names to /tmp/pip-pip-egg-info-cxmbztdr/segmentation_phenix.egg-info/top_level.txt 2025-09-08T23:53:29,638 writing manifest file '/tmp/pip-pip-egg-info-cxmbztdr/segmentation_phenix.egg-info/SOURCES.txt' 2025-09-08T23:53:29,864 reading manifest file '/tmp/pip-pip-egg-info-cxmbztdr/segmentation_phenix.egg-info/SOURCES.txt' 2025-09-08T23:53:29,865 reading manifest template 'MANIFEST.in' 2025-09-08T23:53:29,866 warning: no files found matching '*' under directory 'data' 2025-09-08T23:53:29,867 adding license file 'LICENSE' 2025-09-08T23:53:29,870 writing manifest file '/tmp/pip-pip-egg-info-cxmbztdr/segmentation_phenix.egg-info/SOURCES.txt' 2025-09-08T23:53:30,007 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T23:53:30,011 Source in /tmp/pip-wheel-ign7odae/segmentation-phenix_16bb87ce839e4ff694837e6c32108e1c has version 0.1.4, which satisfies requirement segmentation-phenix==0.1.4 from https://files.pythonhosted.org/packages/af/d6/b3e45deb822008b224bfc9d6c25c9794bf2b394b00d9d955e2ac2df55b58/segmentation_phenix-0.1.4.tar.gz 2025-09-08T23:53:30,012 Removed segmentation-phenix==0.1.4 from https://files.pythonhosted.org/packages/af/d6/b3e45deb822008b224bfc9d6c25c9794bf2b394b00d9d955e2ac2df55b58/segmentation_phenix-0.1.4.tar.gz from build tracker '/tmp/pip-build-tracker-onb9gozh' 2025-09-08T23:53:30,015 Created temporary directory: /tmp/pip-unpack-eu753mm7 2025-09-08T23:53:30,015 Created temporary directory: /tmp/pip-unpack-0lmmgs46 2025-09-08T23:53:30,015 Building wheels for collected packages: segmentation-phenix 2025-09-08T23:53:30,017 Created temporary directory: /tmp/pip-wheel-01qq8ccb 2025-09-08T23:53:30,017 DEPRECATION: Building 'segmentation-phenix' 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 'segmentation-phenix'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T23:53:30,018 Building wheel for segmentation-phenix (setup.py): started 2025-09-08T23:53:30,019 Destination directory: /tmp/pip-wheel-01qq8ccb 2025-09-08T23:53:30,019 Running command python setup.py bdist_wheel 2025-09-08T23:53:30,858 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. 2025-09-08T23:53:30,858 !! 2025-09-08T23:53:30,858 ******************************************************************************** 2025-09-08T23:53:30,858 Usage of dash-separated 'description-file' will not be supported in future 2025-09-08T23:53:30,858 versions. Please use the underscore name 'description_file' instead. 2025-09-08T23:53:30,859 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T23:53:30,859 or your builds will no longer be supported. 2025-09-08T23:53:30,859 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T23:53:30,859 ******************************************************************************** 2025-09-08T23:53:30,859 !! 2025-09-08T23:53:30,859 opt = self._enforce_underscore(opt, section) 2025-09-08T23:53:31,300 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. 2025-09-08T23:53:31,300 !! 2025-09-08T23:53:31,300 ******************************************************************************** 2025-09-08T23:53:31,300 Usage of dash-separated 'description-file' will not be supported in future 2025-09-08T23:53:31,300 versions. Please use the underscore name 'description_file' instead. 2025-09-08T23:53:31,300 (Affected: segmentation_phenix). 2025-09-08T23:53:31,300 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T23:53:31,301 or your builds will no longer be supported. 2025-09-08T23:53:31,301 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T23:53:31,301 ******************************************************************************** 2025-09-08T23:53:31,301 !! 2025-09-08T23:53:31,301 opt = self._enforce_underscore(opt, section) 2025-09-08T23:53:31,302 running bdist_wheel 2025-09-08T23:53:31,594 running build 2025-09-08T23:53:31,594 running build_py 2025-09-08T23:53:31,671 creating build/lib.linux-armv7l-cpython-313/segmentation_phenix 2025-09-08T23:53:31,671 copying segmentation_phenix/__init__.py -> build/lib.linux-armv7l-cpython-313/segmentation_phenix 2025-09-08T23:53:31,673 running build_ext 2025-09-08T23:53:32,108 Compiling segmentation_phenix/segmentation.pyx because it changed. 2025-09-08T23:53:32,109 [1/1] Cythonizing segmentation_phenix/segmentation.pyx 2025-09-08T23:53:35,218 building 'segmentation_phenix.segmentation' extension 2025-09-08T23:53:35,218 creating build/temp.linux-armv7l-cpython-313/segmentation_phenix 2025-09-08T23:53:35,219 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include -I/usr/include/python3.13 -c segmentation_phenix/segmentation.cpp -o build/temp.linux-armv7l-cpython-313/segmentation_phenix/segmentation.o -march=native -std=c++11 -DNDEBUG -Ofast -Wcpp 2025-09-08T23:53:35,534 In file included from segmentation_phenix/segmentation.cpp:1179: 2025-09-08T23:53:35,535 segmentation_phenix/fastmm.cpp:1:10: fatal error: boost/multi_array.hpp: No such file or directory 2025-09-08T23:53:35,535 1 | #include 2025-09-08T23:53:35,535 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T23:53:35,535 compilation terminated. 2025-09-08T23:53:35,538 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-08T23:53:36,063 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T23:53:36,075 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T23:53:36,075 exec(compile('"'"''"'"''"'"' 2025-09-08T23:53:36,075 # This is -- a caller that pip uses to run setup.py 2025-09-08T23:53:36,075 # 2025-09-08T23:53:36,075 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T23:53:36,075 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T23:53:36,075 # - It provides a clear error message when setuptools is not installed. 2025-09-08T23:53:36,075 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T23:53:36,075 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T23:53:36,075 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T23:53:36,075 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T23:53:36,075 import os, sys, tokenize, traceback 2025-09-08T23:53:36,075 2025-09-08T23:53:36,075 try: 2025-09-08T23:53:36,075 import setuptools 2025-09-08T23:53:36,075 except ImportError: 2025-09-08T23:53:36,075 print( 2025-09-08T23:53:36,075 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T23:53:36,075 "the build environment with exception:", 2025-09-08T23:53:36,075 file=sys.stderr, 2025-09-08T23:53:36,075 ) 2025-09-08T23:53:36,075 traceback.print_exc() 2025-09-08T23:53:36,075 sys.exit(1) 2025-09-08T23:53:36,075 2025-09-08T23:53:36,075 __file__ = %r 2025-09-08T23:53:36,075 sys.argv[0] = __file__ 2025-09-08T23:53:36,075 2025-09-08T23:53:36,075 if os.path.exists(__file__): 2025-09-08T23:53:36,075 filename = __file__ 2025-09-08T23:53:36,075 with tokenize.open(__file__) as f: 2025-09-08T23:53:36,075 setup_py_code = f.read() 2025-09-08T23:53:36,075 else: 2025-09-08T23:53:36,075 filename = "" 2025-09-08T23:53:36,075 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T23:53:36,075 2025-09-08T23:53:36,075 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T23:53:36,075 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-ign7odae/segmentation-phenix_16bb87ce839e4ff694837e6c32108e1c/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-01qq8ccb[/] 2025-09-08T23:53:36,075 [bold magenta]cwd[/]: /tmp/pip-wheel-ign7odae/segmentation-phenix_16bb87ce839e4ff694837e6c32108e1c/ 2025-09-08T23:53:36,075 Building wheel for segmentation-phenix (setup.py): finished with status 'error' 2025-09-08T23:53:36,076 ERROR: Failed building wheel for segmentation-phenix 2025-09-08T23:53:36,077 Running setup.py clean for segmentation-phenix 2025-09-08T23:53:36,077 Running command python setup.py clean 2025-09-08T23:53:36,917 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. 2025-09-08T23:53:36,917 !! 2025-09-08T23:53:36,917 ******************************************************************************** 2025-09-08T23:53:36,917 Usage of dash-separated 'description-file' will not be supported in future 2025-09-08T23:53:36,917 versions. Please use the underscore name 'description_file' instead. 2025-09-08T23:53:36,917 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T23:53:36,918 or your builds will no longer be supported. 2025-09-08T23:53:36,918 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T23:53:36,918 ******************************************************************************** 2025-09-08T23:53:36,918 !! 2025-09-08T23:53:36,918 opt = self._enforce_underscore(opt, section) 2025-09-08T23:53:37,368 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. 2025-09-08T23:53:37,368 !! 2025-09-08T23:53:37,369 ******************************************************************************** 2025-09-08T23:53:37,369 Usage of dash-separated 'description-file' will not be supported in future 2025-09-08T23:53:37,369 versions. Please use the underscore name 'description_file' instead. 2025-09-08T23:53:37,369 (Affected: segmentation_phenix). 2025-09-08T23:53:37,369 By 2026-Mar-03, you need to update your project and remove deprecated calls 2025-09-08T23:53:37,369 or your builds will no longer be supported. 2025-09-08T23:53:37,369 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2025-09-08T23:53:37,369 ******************************************************************************** 2025-09-08T23:53:37,370 !! 2025-09-08T23:53:37,370 opt = self._enforce_underscore(opt, section) 2025-09-08T23:53:37,445 running clean 2025-09-08T23:53:37,590 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T23:53:37,590 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T23:53:37,590 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T23:53:37,590 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T23:53:37,590 removing 'build' 2025-09-08T23:53:37,726 Failed to build segmentation-phenix 2025-09-08T23:53:37,727 ERROR: Failed to build one or more wheels 2025-09-08T23:53:37,728 Exception information: 2025-09-08T23:53:37,728 Traceback (most recent call last): 2025-09-08T23:53:37,728 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T23:53:37,728 status = _inner_run() 2025-09-08T23:53:37,728 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T23:53:37,728 return self.run(options, args) 2025-09-08T23:53:37,728 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T23:53:37,728 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T23:53:37,728 return func(self, options, args) 2025-09-08T23:53:37,728 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T23:53:37,728 raise CommandError("Failed to build one or more wheels") 2025-09-08T23:53:37,728 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T23:53:37,732 Removed build tracker: '/tmp/pip-build-tracker-onb9gozh'