2025-10-16T05:50:54,619 Created temporary directory: /tmp/pip-ephem-wheel-cache-vh1hyov0
2025-10-16T05:50:54,621 Created temporary directory: /tmp/pip-build-tracker-yo0mdxd2
2025-10-16T05:50:54,622 Initialized build tracking at /tmp/pip-build-tracker-yo0mdxd2
2025-10-16T05:50:54,622 Created build tracker: /tmp/pip-build-tracker-yo0mdxd2
2025-10-16T05:50:54,622 Entered build tracker: /tmp/pip-build-tracker-yo0mdxd2
2025-10-16T05:50:54,623 Created temporary directory: /tmp/pip-wheel-i8lfjl7p
2025-10-16T05:50:54,626 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2025-10-16T05:50:54,628 Created temporary directory: /tmp/pip-ephem-wheel-cache-xf3hk9rn
2025-10-16T05:50:54,650 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-16T05:50:54,653 2 location(s) to search for versions of pcangsd:
2025-10-16T05:50:54,653 * https://pypi.org/simple/pcangsd/
2025-10-16T05:50:54,653 * https://www.piwheels.org/simple/pcangsd/
2025-10-16T05:50:54,654 Fetching project page and analyzing links: https://pypi.org/simple/pcangsd/
2025-10-16T05:50:54,655 Getting page https://pypi.org/simple/pcangsd/
2025-10-16T05:50:54,656 Found index url https://pypi.org/simple
2025-10-16T05:50:54,872 Fetched page https://pypi.org/simple/pcangsd/ as application/vnd.pypi.simple.v1+json
2025-10-16T05:50:54,894   Found link https://files.pythonhosted.org/packages/2e/1c/aea0770f4e20a0e0872e57c0d6b99a5e641c1ac119a6c6ca0cab05e73df4/pcangsd-1.36.0.tar.gz (from https://pypi.org/simple/pcangsd/) (requires-python:>=3.10), version: 1.36.0
2025-10-16T05:50:54,895   Found link https://files.pythonhosted.org/packages/fc/d3/f98deb573617e7b39c6422ed700c86e9decbb3ccd13ed38aea0d1b1f4e82/pcangsd-1.36.1.tar.gz (from https://pypi.org/simple/pcangsd/) (requires-python:>=3.10), version: 1.36.1
2025-10-16T05:50:54,896   Found link https://files.pythonhosted.org/packages/47/bc/4ee519ccd62d64da95785ce2e65101b5fef3bade6b4ea3af145645320a76/pcangsd-1.36.2.tar.gz (from https://pypi.org/simple/pcangsd/) (requires-python:>=3.10), version: 1.36.2
2025-10-16T05:50:54,898   Found link https://files.pythonhosted.org/packages/86/33/3e0e52bbe5f313f5ed3414364ddbcb590706ff56b52aca77c7219b3b0626/pcangsd-1.36.3.tar.gz (from https://pypi.org/simple/pcangsd/) (requires-python:>=3.10), version: 1.36.3
2025-10-16T05:50:54,899   Found link https://files.pythonhosted.org/packages/fd/3c/7be7b9fb3efe789f2202b0cbdb740c5a569d2254e661bba9fa2a5e189f3d/pcangsd-1.36.4.tar.gz (from https://pypi.org/simple/pcangsd/) (requires-python:>=3.10), version: 1.36.4
2025-10-16T05:50:54,900 Fetching project page and analyzing links: https://www.piwheels.org/simple/pcangsd/
2025-10-16T05:50:54,901 Getting page https://www.piwheels.org/simple/pcangsd/
2025-10-16T05:50:54,902 Found index url https://www.piwheels.org/simple
2025-10-16T05:50:55,065 Fetched page https://www.piwheels.org/simple/pcangsd/ as text/html
2025-10-16T05:50:55,069   Skipping link: No binaries permitted for pcangsd: https://www.piwheels.org/simple/pcangsd/pcangsd-1.36.3-cp311-cp311-linux_armv6l.whl#sha256=9bf1d663c72beafa0ee85dca06a4a94e19b238eed20e5dc12c6df03a69e7c60d (from https://www.piwheels.org/simple/pcangsd/) (requires-python:>=3.10)
2025-10-16T05:50:55,070   Skipping link: No binaries permitted for pcangsd: https://www.piwheels.org/simple/pcangsd/pcangsd-1.36.3-cp311-cp311-linux_armv7l.whl#sha256=9bf1d663c72beafa0ee85dca06a4a94e19b238eed20e5dc12c6df03a69e7c60d (from https://www.piwheels.org/simple/pcangsd/) (requires-python:>=3.10)
2025-10-16T05:50:55,070   Skipping link: No binaries permitted for pcangsd: https://www.piwheels.org/simple/pcangsd/pcangsd-1.36.2-cp311-cp311-linux_armv6l.whl#sha256=5f120afe8e78823a8b1c6ebdd7a6ccecc865f96e08fb904a26b672f2bd294333 (from https://www.piwheels.org/simple/pcangsd/) (requires-python:>=3.10)
2025-10-16T05:50:55,071   Skipping link: No binaries permitted for pcangsd: https://www.piwheels.org/simple/pcangsd/pcangsd-1.36.2-cp311-cp311-linux_armv7l.whl#sha256=5f120afe8e78823a8b1c6ebdd7a6ccecc865f96e08fb904a26b672f2bd294333 (from https://www.piwheels.org/simple/pcangsd/) (requires-python:>=3.10)
2025-10-16T05:50:55,072   Skipping link: No binaries permitted for pcangsd: https://archive1.piwheels.org/simple/pcangsd/pcangsd-1.36.1-cp311-cp311-linux_armv6l.whl#sha256=18225e68fc573c467f1a5ef78d5d6b1f802b109b87052d5bfa640b4732f97668 (from https://www.piwheels.org/simple/pcangsd/) (requires-python:>=3.10)
2025-10-16T05:50:55,072   Skipping link: No binaries permitted for pcangsd: https://archive1.piwheels.org/simple/pcangsd/pcangsd-1.36.1-cp311-cp311-linux_armv7l.whl#sha256=18225e68fc573c467f1a5ef78d5d6b1f802b109b87052d5bfa640b4732f97668 (from https://www.piwheels.org/simple/pcangsd/) (requires-python:>=3.10)
2025-10-16T05:50:55,073   Skipping link: No binaries permitted for pcangsd: https://archive1.piwheels.org/simple/pcangsd/pcangsd-1.36.0-cp311-cp311-linux_armv6l.whl#sha256=1d366fc83d0d34359059dd2cfb3ad294dc6974221374753a11fbffa6a9852680 (from https://www.piwheels.org/simple/pcangsd/) (requires-python:>=3.10)
2025-10-16T05:50:55,073   Skipping link: No binaries permitted for pcangsd: https://archive1.piwheels.org/simple/pcangsd/pcangsd-1.36.0-cp311-cp311-linux_armv7l.whl#sha256=1d366fc83d0d34359059dd2cfb3ad294dc6974221374753a11fbffa6a9852680 (from https://www.piwheels.org/simple/pcangsd/) (requires-python:>=3.10)
2025-10-16T05:50:55,074 Skipping link: not a file: https://www.piwheels.org/simple/pcangsd/
2025-10-16T05:50:55,074 Skipping link: not a file: https://pypi.org/simple/pcangsd/
2025-10-16T05:50:55,094 Given no hashes to check 1 links for project 'pcangsd': discarding no candidates
2025-10-16T05:50:55,112 Collecting pcangsd==1.36.4
2025-10-16T05:50:55,114   Created temporary directory: /tmp/pip-unpack-4r_27_02
2025-10-16T05:50:55,263   Downloading pcangsd-1.36.4.tar.gz (1.0 MB)
2025-10-16T05:50:55,731   Added pcangsd==1.36.4 from https://files.pythonhosted.org/packages/fd/3c/7be7b9fb3efe789f2202b0cbdb740c5a569d2254e661bba9fa2a5e189f3d/pcangsd-1.36.4.tar.gz to build tracker '/tmp/pip-build-tracker-yo0mdxd2'
2025-10-16T05:50:55,738   Created temporary directory: /tmp/pip-build-env-2bkhbge0
2025-10-16T05:50:55,743   Installing build dependencies: started
2025-10-16T05:50:55,744   Running command pip subprocess to install build dependencies
2025-10-16T05:50:56,991   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2025-10-16T05:50:57,626   DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2025-10-16T05:50:57,652   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-16T05:50:59,541   Collecting setuptools>=0.61
2025-10-16T05:50:59,653     Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB)
2025-10-16T05:51:01,478   Collecting cython>3.0.0
2025-10-16T05:51:01,500     Using cached cython-3.1.4-py3-none-any.whl (1.2 MB)
2025-10-16T05:51:02,535     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
2025-10-16T05:51:02,543     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
2025-10-16T05:51:02,550     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
2025-10-16T05:51:02,557     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
2025-10-16T05:51:02,564     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
2025-10-16T05:51:03,174   Collecting numpy>2.0.0
2025-10-16T05:51:03,629     Using cached https://www.piwheels.org/simple/numpy/numpy-2.3.3-cp311-cp311-linux_armv7l.whl (6.1 MB)
2025-10-16T05:51:04,351     Link requires a different Python (3.11.2 not in: '>=3.7,<3.10'): https://files.pythonhosted.org/packages/99/f1/c00d6be56e1a718a3068079e3ec8ce044d7179345280f6a3f5066068af0d/scipy-1.6.2.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.10)
2025-10-16T05:51:04,356     Link requires a different Python (3.11.2 not in: '>=3.7,<3.10'): https://files.pythonhosted.org/packages/fe/fd/8704c7b7b34cdac850485e638346025ca57c5a859934b9aa1be5399b33b7/scipy-1.6.3.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.10)
2025-10-16T05:51:04,361     Link requires a different Python (3.11.2 not in: '>=3.7,<3.10'): https://files.pythonhosted.org/packages/bb/bb/944f559d554df6c9adf037aa9fc982a9706ee0e96c0d5beac701cb158900/scipy-1.7.0.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.10)
2025-10-16T05:51:04,365     Link requires a different Python (3.11.2 not in: '>=3.7,<3.10'): https://files.pythonhosted.org/packages/47/33/a24aec22b7be7fdb10ec117a95e1e4099890d8bbc6646902f443fc7719d1/scipy-1.7.1.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.10)
2025-10-16T05:51:04,371     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/0e/23/58c4f995475a2a97cb5f4a032aedaf881ad87cd976a7180c55118d105a1d/scipy-1.7.2.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.11)
2025-10-16T05:51:04,378     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/61/67/1a654b96309c991762ee9bc39c363fc618076b155fe52d295211cf2536c7/scipy-1.7.3.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.7,<3.11)
2025-10-16T05:51:04,384     Link requires a different Python (3.11.2 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/c0/ad/e3c052ed4e0027a8abef0a5e8441a044427d252d17d9aee06d56e62fc698/scipy-1.8.0rc1.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
2025-10-16T05:51:04,389     Link requires a different Python (3.11.2 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/29/d2/151a54944b333e465f98804dced31dab1284f3c37b752b9cefa710b64681/scipy-1.8.0rc2.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
2025-10-16T05:51:04,395     Link requires a different Python (3.11.2 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/e4/26/83dd1c6378513a6241d984bda9f08c512b6e35fff13fba3acc1b3c195f02/scipy-1.8.0rc3.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
2025-10-16T05:51:04,400     Link requires a different Python (3.11.2 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/22/78/056cc43e7737811b6f50886788a940f852773dd9804f5365952805db9648/scipy-1.8.0rc4.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
2025-10-16T05:51:04,406     Link requires a different Python (3.11.2 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/b4/a2/4faa34bf0cdbefd5c706625f1234987795f368eb4e97bde9d6f46860843e/scipy-1.8.0.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
2025-10-16T05:51:04,411     Link requires a different Python (3.11.2 not in: '>=3.8,<3.11'): https://files.pythonhosted.org/packages/26/b5/9330f004b9a3b2b6a31f59f46f1617ce9ca15c0e7fe64288c20385a05c9d/scipy-1.8.1.tar.gz (from https://pypi.org/simple/scipy/) (requires-python:>=3.8,<3.11)
2025-10-16T05:51:04,815   Collecting scipy>1.14.0
2025-10-16T05:51:06,437     Using cached https://www.piwheels.org/simple/scipy/scipy-1.16.2-cp311-cp311-linux_armv7l.whl (22.9 MB)
2025-10-16T05:51:10,458   Installing collected packages: setuptools, numpy, cython, scipy
2025-10-16T05:51:23,169     Creating /tmp/pip-build-env-2bkhbge0/overlay/local/bin
2025-10-16T05:51:23,171     changing mode of /tmp/pip-build-env-2bkhbge0/overlay/local/bin/f2py to 755
2025-10-16T05:51:23,173     changing mode of /tmp/pip-build-env-2bkhbge0/overlay/local/bin/numpy-config to 755
2025-10-16T05:51:26,094     changing mode of /tmp/pip-build-env-2bkhbge0/overlay/local/bin/cygdb to 755
2025-10-16T05:51:26,096     changing mode of /tmp/pip-build-env-2bkhbge0/overlay/local/bin/cython to 755
2025-10-16T05:51:26,098     changing mode of /tmp/pip-build-env-2bkhbge0/overlay/local/bin/cythonize to 755
2025-10-16T05:51:44,213   Successfully installed cython-3.1.4 numpy-2.3.3 scipy-1.16.2 setuptools-80.9.0
2025-10-16T05:51:44,704   Installing build dependencies: finished with status 'done'
2025-10-16T05:51:44,711   Getting requirements to build wheel: started
2025-10-16T05:51:44,713   Running command Getting requirements to build wheel
2025-10-16T05:52:16,827   Compiling pcangsd/reader_cy.pyx because it changed.
2025-10-16T05:52:16,829   Compiling pcangsd/shared_cy.pyx because it changed.
2025-10-16T05:52:16,830   Compiling pcangsd/covariance_cy.pyx because it changed.
2025-10-16T05:52:16,831   Compiling pcangsd/inbreed_cy.pyx because it changed.
2025-10-16T05:52:16,831   Compiling pcangsd/admixture_cy.pyx because it changed.
2025-10-16T05:52:16,832   Compiling pcangsd/tree_cy.pyx because it changed.
2025-10-16T05:52:16,833   [1/6] Cythonizing pcangsd/admixture_cy.pyx
2025-10-16T05:52:16,833   [2/6] Cythonizing pcangsd/covariance_cy.pyx
2025-10-16T05:52:16,834   [3/6] Cythonizing pcangsd/inbreed_cy.pyx
2025-10-16T05:52:16,834   [4/6] Cythonizing pcangsd/reader_cy.pyx
2025-10-16T05:52:16,835   [5/6] Cythonizing pcangsd/shared_cy.pyx
2025-10-16T05:52:16,835   [6/6] Cythonizing pcangsd/tree_cy.pyx
2025-10-16T05:52:16,887   /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-16T05:52:16,888   !!

2025-10-16T05:52:16,889           ********************************************************************************
2025-10-16T05:52:16,889           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-16T05:52:16,891           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2025-10-16T05:52:16,892           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-16T05:52:16,892           ********************************************************************************

2025-10-16T05:52:16,893   !!
2025-10-16T05:52:16,894     self._finalize_license_expression()
2025-10-16T05:52:16,916   running egg_info
2025-10-16T05:52:16,924   writing pcangsd.egg-info/PKG-INFO
2025-10-16T05:52:16,927   writing dependency_links to pcangsd.egg-info/dependency_links.txt
2025-10-16T05:52:16,929   writing entry points to pcangsd.egg-info/entry_points.txt
2025-10-16T05:52:16,930   writing requirements to pcangsd.egg-info/requires.txt
2025-10-16T05:52:16,931   writing top-level names to pcangsd.egg-info/top_level.txt
2025-10-16T05:52:16,974   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,975   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,976   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,976   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,977   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,977   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,978   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,978   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,979   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,983   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,985   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,990   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,991   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,992   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,993   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,993   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,994   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,994   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,995   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,996   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,996   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,997   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,998   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,998   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,998   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,999   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:16,999   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:17,000   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:17,000   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:17,001   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:17,001   reading manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-16T05:52:17,005   reading manifest template 'MANIFEST.in'
2025-10-16T05:52:17,009   adding license file 'LICENSE'
2025-10-16T05:52:17,013   writing manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-16T05:52:17,902   Getting requirements to build wheel: finished with status 'done'
2025-10-16T05:52:17,906   Created temporary directory: /tmp/pip-modern-metadata-11c6j4r5
2025-10-16T05:52:17,908   Preparing metadata (pyproject.toml): started
2025-10-16T05:52:17,910   Running command Preparing metadata (pyproject.toml)
2025-10-16T05:52:19,577   /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-16T05:52:19,578   !!

2025-10-16T05:52:19,579           ********************************************************************************
2025-10-16T05:52:19,579           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-16T05:52:19,580           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2025-10-16T05:52:19,582           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-16T05:52:19,582           ********************************************************************************

2025-10-16T05:52:19,583   !!
2025-10-16T05:52:19,584     self._finalize_license_expression()
2025-10-16T05:52:19,606   running dist_info
2025-10-16T05:52:19,621   creating /tmp/pip-modern-metadata-11c6j4r5/pcangsd.egg-info
2025-10-16T05:52:19,622   writing /tmp/pip-modern-metadata-11c6j4r5/pcangsd.egg-info/PKG-INFO
2025-10-16T05:52:19,625   writing dependency_links to /tmp/pip-modern-metadata-11c6j4r5/pcangsd.egg-info/dependency_links.txt
2025-10-16T05:52:19,627   writing entry points to /tmp/pip-modern-metadata-11c6j4r5/pcangsd.egg-info/entry_points.txt
2025-10-16T05:52:19,628   writing requirements to /tmp/pip-modern-metadata-11c6j4r5/pcangsd.egg-info/requires.txt
2025-10-16T05:52:19,629   writing top-level names to /tmp/pip-modern-metadata-11c6j4r5/pcangsd.egg-info/top_level.txt
2025-10-16T05:52:19,631   writing manifest file '/tmp/pip-modern-metadata-11c6j4r5/pcangsd.egg-info/SOURCES.txt'
2025-10-16T05:52:19,668   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,668   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,669   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,669   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,670   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,670   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,670   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,671   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,672   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,672   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,673   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,674   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,674   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,675   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,676   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,676   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,677   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,678   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,678   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,678   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,679   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,679   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,680   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,680   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,681   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,681   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,682   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,683   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,683   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,684   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:52:19,684   reading manifest file '/tmp/pip-modern-metadata-11c6j4r5/pcangsd.egg-info/SOURCES.txt'
2025-10-16T05:52:19,685   reading manifest template 'MANIFEST.in'
2025-10-16T05:52:19,689   adding license file 'LICENSE'
2025-10-16T05:52:19,693   writing manifest file '/tmp/pip-modern-metadata-11c6j4r5/pcangsd.egg-info/SOURCES.txt'
2025-10-16T05:52:19,694   creating '/tmp/pip-modern-metadata-11c6j4r5/pcangsd-1.36.4.dist-info'
2025-10-16T05:52:19,905   Preparing metadata (pyproject.toml): finished with status 'done'
2025-10-16T05:52:20,127   Source in /tmp/pip-wheel-i8lfjl7p/pcangsd_f8674e7aca8a48ce849c0740fec9e129 has version 1.36.4, which satisfies requirement pcangsd==1.36.4 from https://files.pythonhosted.org/packages/fd/3c/7be7b9fb3efe789f2202b0cbdb740c5a569d2254e661bba9fa2a5e189f3d/pcangsd-1.36.4.tar.gz
2025-10-16T05:52:20,128   Removed pcangsd==1.36.4 from https://files.pythonhosted.org/packages/fd/3c/7be7b9fb3efe789f2202b0cbdb740c5a569d2254e661bba9fa2a5e189f3d/pcangsd-1.36.4.tar.gz from build tracker '/tmp/pip-build-tracker-yo0mdxd2'
2025-10-16T05:52:20,134 Created temporary directory: /tmp/pip-unpack-2ygiy2sk
2025-10-16T05:52:20,135 Building wheels for collected packages: pcangsd
2025-10-16T05:52:20,139   Created temporary directory: /tmp/pip-wheel-rt84xxt2
2025-10-16T05:52:20,140   Destination directory: /tmp/pip-wheel-rt84xxt2
2025-10-16T05:52:20,142   Building wheel for pcangsd (pyproject.toml): started
2025-10-16T05:52:20,143   Running command Building wheel for pcangsd (pyproject.toml)
2025-10-16T05:52:21,729   /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-16T05:52:21,730   !!

2025-10-16T05:52:21,731           ********************************************************************************
2025-10-16T05:52:21,731           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-16T05:52:21,732           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2025-10-16T05:52:21,733           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-16T05:52:21,733           ********************************************************************************

2025-10-16T05:52:21,734   !!
2025-10-16T05:52:21,734     self._finalize_license_expression()
2025-10-16T05:52:21,757   running bdist_wheel
2025-10-16T05:52:21,794   running build
2025-10-16T05:52:21,794   running build_py
2025-10-16T05:52:21,805   creating build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-16T05:52:21,807   copying pcangsd/__init__.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-16T05:52:21,809   copying pcangsd/tree.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-16T05:52:21,811   copying pcangsd/main.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-16T05:52:21,813   copying pcangsd/shared.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-16T05:52:21,815   copying pcangsd/covariance.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-16T05:52:21,817   copying pcangsd/selection.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-16T05:52:21,819   copying pcangsd/admixture.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-16T05:52:21,821   copying pcangsd/inbreed.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-16T05:52:21,825   running build_ext
2025-10-16T05:52:21,833   building 'pcangsd.reader_cy' extension
2025-10-16T05:52:21,834   creating build/temp.linux-armv7l-cpython-311/pcangsd
2025-10-16T05:52:21,835   arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c pcangsd/reader_cy.cpp -o build/temp.linux-armv7l-cpython-311/pcangsd/reader_cy.o -fopenmp -O3 -g0 -Wno-unreachable-code
2025-10-16T05:52:45,203   In function ‘PyArrayObject* __pyx_f_7pcangsd_9reader_cy_readBeagle(PyObject*, int)’,
2025-10-16T05:52:45,204       inlined from ‘PyObject* __pyx_pf_7pcangsd_9reader_cy_readBeagle(PyObject*, PyObject*)’ at pcangsd/reader_cy.cpp:20328:66,
2025-10-16T05:52:45,205       inlined from ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_1readBeagle(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at pcangsd/reader_cy.cpp:20300:52:
2025-10-16T05:52:45,205   pcangsd/reader_cy.cpp:20039:52: warning: ‘__pyx_v_N’ may be used uninitialized [-Wmaybe-uninitialized]
2025-10-16T05:52:45,206   20039 |   __pyx_t_18 = __Pyx_PyLong_FromSize_t(((__pyx_v_N / 3) * 2)); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 53, __pyx_L1_error)
2025-10-16T05:52:45,206         |                                         ~~~~~~~~~~~^~~~
2025-10-16T05:52:45,207   pcangsd/reader_cy.cpp: In function ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_1readBeagle(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’:
2025-10-16T05:52:45,208   pcangsd/reader_cy.cpp:19495:10: note: ‘__pyx_v_N’ was declared here
2025-10-16T05:52:45,209   19495 |   size_t __pyx_v_N;
2025-10-16T05:52:45,209         |          ^~~~~~~~~
2025-10-16T05:52:47,913   In function ‘PyArrayObject* __pyx_f_7pcangsd_9reader_cy_readBeagleFilterSites(PyObject*, __Pyx_memviewslice, int)’,
2025-10-16T05:52:47,914       inlined from ‘PyObject* __pyx_pf_7pcangsd_9reader_cy_2readBeagleFilterSites(PyObject*, PyObject*, __Pyx_memviewslice)’ at pcangsd/reader_cy.cpp:21246:77,
2025-10-16T05:52:47,914       inlined from ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_3readBeagleFilterSites(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at pcangsd/reader_cy.cpp:21217:64:
2025-10-16T05:52:47,915   pcangsd/reader_cy.cpp:20947:52: warning: ‘__pyx_v_N’ may be used uninitialized [-Wmaybe-uninitialized]
2025-10-16T05:52:47,915   20947 |   __pyx_t_18 = __Pyx_PyLong_FromSize_t(((__pyx_v_N / 3) * 2)); if (unlikely(!__pyx_t_18)) __PYX_ERR(0, 102, __pyx_L1_error)
2025-10-16T05:52:47,916         |                                         ~~~~~~~~~~~^~~~
2025-10-16T05:52:47,917   pcangsd/reader_cy.cpp: In function ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_3readBeagleFilterSites(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’:
2025-10-16T05:52:47,917   pcangsd/reader_cy.cpp:20365:10: note: ‘__pyx_v_N’ was declared here
2025-10-16T05:52:47,918   20365 |   size_t __pyx_v_N;
2025-10-16T05:52:47,919         |          ^~~~~~~~~
2025-10-16T05:52:48,906   arm-linux-gnueabihf-g++ -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-armv7l-cpython-311/pcangsd/reader_cy.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pcangsd/reader_cy.cpython-311-arm-linux-gnueabihf.so -fopenmp
2025-10-16T05:52:49,175   building 'pcangsd.shared_cy' extension
2025-10-16T05:52:49,176   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c pcangsd/shared_cy.c -o build/temp.linux-armv7l-cpython-311/pcangsd/shared_cy.o -fopenmp -O3 -g0 -Wno-unreachable-code
2025-10-16T05:53:10,165   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pcangsd/shared_cy.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pcangsd/shared_cy.cpython-311-arm-linux-gnueabihf.so -fopenmp
2025-10-16T05:53:10,300   building 'pcangsd.covariance_cy' extension
2025-10-16T05:53:10,300   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c pcangsd/covariance_cy.c -o build/temp.linux-armv7l-cpython-311/pcangsd/covariance_cy.o -fopenmp -O3 -g0 -Wno-unreachable-code
2025-10-16T05:53:29,283   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pcangsd/covariance_cy.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pcangsd/covariance_cy.cpython-311-arm-linux-gnueabihf.so -fopenmp
2025-10-16T05:53:29,397   building 'pcangsd.inbreed_cy' extension
2025-10-16T05:53:29,398   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c pcangsd/inbreed_cy.c -o build/temp.linux-armv7l-cpython-311/pcangsd/inbreed_cy.o -fopenmp -O3 -g0 -Wno-unreachable-code
2025-10-16T05:53:48,506   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pcangsd/inbreed_cy.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pcangsd/inbreed_cy.cpython-311-arm-linux-gnueabihf.so -fopenmp
2025-10-16T05:53:48,621   building 'pcangsd.admixture_cy' extension
2025-10-16T05:53:48,621   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c pcangsd/admixture_cy.c -o build/temp.linux-armv7l-cpython-311/pcangsd/admixture_cy.o -fopenmp -O3 -g0 -Wno-unreachable-code
2025-10-16T05:54:06,261   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pcangsd/admixture_cy.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pcangsd/admixture_cy.cpython-311-arm-linux-gnueabihf.so -fopenmp
2025-10-16T05:54:06,377   building 'pcangsd.tree_cy' extension
2025-10-16T05:54:06,377   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include -I/usr/include/python3.11 -c pcangsd/tree_cy.c -o build/temp.linux-armv7l-cpython-311/pcangsd/tree_cy.o -fopenmp -O3 -g0 -Wno-unreachable-code
2025-10-16T05:54:24,248   arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pcangsd/tree_cy.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pcangsd/tree_cy.cpython-311-arm-linux-gnueabihf.so -fopenmp
2025-10-16T05:54:24,384   installing to build/bdist.linux-armv7l/wheel
2025-10-16T05:54:24,385   running install
2025-10-16T05:54:24,408   running install_lib
2025-10-16T05:54:24,419   creating build/bdist.linux-armv7l/wheel
2025-10-16T05:54:24,421   creating build/bdist.linux-armv7l/wheel/pcangsd
2025-10-16T05:54:24,422   copying build/lib.linux-armv7l-cpython-311/pcangsd/covariance_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,429   copying build/lib.linux-armv7l-cpython-311/pcangsd/__init__.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,431   copying build/lib.linux-armv7l-cpython-311/pcangsd/admixture_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,436   copying build/lib.linux-armv7l-cpython-311/pcangsd/shared_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,442   copying build/lib.linux-armv7l-cpython-311/pcangsd/tree.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,444   copying build/lib.linux-armv7l-cpython-311/pcangsd/main.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,446   copying build/lib.linux-armv7l-cpython-311/pcangsd/reader_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,452   copying build/lib.linux-armv7l-cpython-311/pcangsd/shared.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,454   copying build/lib.linux-armv7l-cpython-311/pcangsd/inbreed_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,459   copying build/lib.linux-armv7l-cpython-311/pcangsd/covariance.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,461   copying build/lib.linux-armv7l-cpython-311/pcangsd/tree_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,466   copying build/lib.linux-armv7l-cpython-311/pcangsd/selection.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,468   copying build/lib.linux-armv7l-cpython-311/pcangsd/admixture.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,470   copying build/lib.linux-armv7l-cpython-311/pcangsd/inbreed.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-16T05:54:24,472   running install_egg_info
2025-10-16T05:54:24,494   running egg_info
2025-10-16T05:54:24,501   writing pcangsd.egg-info/PKG-INFO
2025-10-16T05:54:24,505   writing dependency_links to pcangsd.egg-info/dependency_links.txt
2025-10-16T05:54:24,506   writing entry points to pcangsd.egg-info/entry_points.txt
2025-10-16T05:54:24,507   writing requirements to pcangsd.egg-info/requires.txt
2025-10-16T05:54:24,514   writing top-level names to pcangsd.egg-info/top_level.txt
2025-10-16T05:54:24,519   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,519   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,520   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,520   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,521   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,521   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,522   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,523   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,523   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,524   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,524   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,525   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,525   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,526   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,527   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,527   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,528   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,529   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,529   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,529   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,530   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,530   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,531   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,531   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,532   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,532   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,533   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,533   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,534   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,534   dependency /tmp/pip-build-env-2bkhbge0/overlay/local/lib/python3.11/dist-packages/numpy/_core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative
2025-10-16T05:54:24,535   reading manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-16T05:54:24,536   reading manifest template 'MANIFEST.in'
2025-10-16T05:54:24,546   adding license file 'LICENSE'
2025-10-16T05:54:24,550   writing manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-16T05:54:24,551   Copying pcangsd.egg-info to build/bdist.linux-armv7l/wheel/./pcangsd-1.36.4-py3.11.egg-info
2025-10-16T05:54:24,562   running install_scripts
2025-10-16T05:54:24,610   creating build/bdist.linux-armv7l/wheel/pcangsd-1.36.4.dist-info/WHEEL
2025-10-16T05:54:24,614   creating '/tmp/pip-wheel-rt84xxt2/.tmp-rwra8mhx/pcangsd-1.36.4-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-10-16T05:54:24,616   adding 'pcangsd/__init__.py'
2025-10-16T05:54:24,618   adding 'pcangsd/admixture.py'
2025-10-16T05:54:24,663   adding 'pcangsd/admixture_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-16T05:54:24,666   adding 'pcangsd/covariance.py'
2025-10-16T05:54:24,715   adding 'pcangsd/covariance_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-16T05:54:24,718   adding 'pcangsd/inbreed.py'
2025-10-16T05:54:24,766   adding 'pcangsd/inbreed_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-16T05:54:24,770   adding 'pcangsd/main.py'
2025-10-16T05:54:24,832   adding 'pcangsd/reader_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-16T05:54:24,835   adding 'pcangsd/selection.py'
2025-10-16T05:54:24,836   adding 'pcangsd/shared.py'
2025-10-16T05:54:24,888   adding 'pcangsd/shared_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-16T05:54:24,891   adding 'pcangsd/tree.py'
2025-10-16T05:54:24,938   adding 'pcangsd/tree_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-16T05:54:24,946   adding 'pcangsd-1.36.4.dist-info/licenses/LICENSE'
2025-10-16T05:54:24,948   adding 'pcangsd-1.36.4.dist-info/METADATA'
2025-10-16T05:54:24,949   adding 'pcangsd-1.36.4.dist-info/WHEEL'
2025-10-16T05:54:24,950   adding 'pcangsd-1.36.4.dist-info/entry_points.txt'
2025-10-16T05:54:24,950   adding 'pcangsd-1.36.4.dist-info/top_level.txt'
2025-10-16T05:54:24,951   adding 'pcangsd-1.36.4.dist-info/RECORD'
2025-10-16T05:54:24,958   removing build/bdist.linux-armv7l/wheel
2025-10-16T05:54:25,135   Building wheel for pcangsd (pyproject.toml): finished with status 'done'
2025-10-16T05:54:25,157   Created wheel for pcangsd: filename=pcangsd-1.36.4-cp311-cp311-linux_armv7l.whl size=619133 sha256=509947e597a18d9020bc34517abae456b3f53630db3905b8e8c33d45e3b7a30f
2025-10-16T05:54:25,158   Stored in directory: /tmp/pip-ephem-wheel-cache-xf3hk9rn/wheels/38/41/42/c9ee68e2ed2ff117af9f3add1189c2388506313cb2a7ecff4a
2025-10-16T05:54:25,170 Successfully built pcangsd
2025-10-16T05:54:25,196 Removed build tracker: '/tmp/pip-build-tracker-yo0mdxd2'