2025-10-15T16:51:48,542 Created temporary directory: /tmp/pip-ephem-wheel-cache-8mlx8e6w
2025-10-15T16:51:48,544 Created temporary directory: /tmp/pip-build-tracker-cnc1hhnt
2025-10-15T16:51:48,545 Initialized build tracking at /tmp/pip-build-tracker-cnc1hhnt
2025-10-15T16:51:48,545 Created build tracker: /tmp/pip-build-tracker-cnc1hhnt
2025-10-15T16:51:48,546 Entered build tracker: /tmp/pip-build-tracker-cnc1hhnt
2025-10-15T16:51:48,547 Created temporary directory: /tmp/pip-wheel-vpqjujb9
2025-10-15T16:51:48,550 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
2025-10-15T16:51:48,552 Created temporary directory: /tmp/pip-ephem-wheel-cache-2eltui8c
2025-10-15T16:51:48,574 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-15T16:51:48,578 2 location(s) to search for versions of pcangsd:
2025-10-15T16:51:48,578 * https://pypi.org/simple/pcangsd/
2025-10-15T16:51:48,578 * https://www.piwheels.org/simple/pcangsd/
2025-10-15T16:51:48,578 Fetching project page and analyzing links: https://pypi.org/simple/pcangsd/
2025-10-15T16:51:48,579 Getting page https://pypi.org/simple/pcangsd/
2025-10-15T16:51:48,581 Found index url https://pypi.org/simple
2025-10-15T16:51:48,788 Fetched page https://pypi.org/simple/pcangsd/ as application/vnd.pypi.simple.v1+json
2025-10-15T16:51:48,790   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
2025-10-15T16:51:48,791   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
2025-10-15T16:51:48,792   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
2025-10-15T16:51:48,793   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
2025-10-15T16:51:48,794   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
2025-10-15T16:51:48,795 Fetching project page and analyzing links: https://www.piwheels.org/simple/pcangsd/
2025-10-15T16:51:48,796 Getting page https://www.piwheels.org/simple/pcangsd/
2025-10-15T16:51:48,797 Found index url https://www.piwheels.org/simple
2025-10-15T16:51:48,953 Fetched page https://www.piwheels.org/simple/pcangsd/ as text/html
2025-10-15T16:51:48,955   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)
2025-10-15T16:51:48,956   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)
2025-10-15T16:51:48,957   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)
2025-10-15T16:51:48,957   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)
2025-10-15T16:51:48,958 Skipping link: not a file: https://www.piwheels.org/simple/pcangsd/
2025-10-15T16:51:48,959 Skipping link: not a file: https://pypi.org/simple/pcangsd/
2025-10-15T16:51:48,978 Given no hashes to check 1 links for project 'pcangsd': discarding no candidates
2025-10-15T16:51:48,996 Collecting pcangsd==1.36.2
2025-10-15T16:51:48,999   Created temporary directory: /tmp/pip-unpack-_l2vtuj1
2025-10-15T16:51:49,213   Downloading pcangsd-1.36.2.tar.gz (971 kB)
2025-10-15T16:51:49,657   Added pcangsd==1.36.2 from https://files.pythonhosted.org/packages/47/bc/4ee519ccd62d64da95785ce2e65101b5fef3bade6b4ea3af145645320a76/pcangsd-1.36.2.tar.gz to build tracker '/tmp/pip-build-tracker-cnc1hhnt'
2025-10-15T16:51:49,663   Created temporary directory: /tmp/pip-build-env-wty_w1ja
2025-10-15T16:51:49,668   Installing build dependencies: started
2025-10-15T16:51:49,669   Running command pip subprocess to install build dependencies
2025-10-15T16:51:50,828   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2025-10-15T16:51:51,437   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
2025-10-15T16:51:51,460   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-15T16:51:53,369   Collecting setuptools>=0.61
2025-10-15T16:51:53,463     Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB)
2025-10-15T16:51:55,261   Collecting cython>3.0.0
2025-10-15T16:51:55,283     Using cached cython-3.1.4-py3-none-any.whl (1.2 MB)
2025-10-15T16:51:56,448     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)
2025-10-15T16:51:56,456     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)
2025-10-15T16:51:56,463     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)
2025-10-15T16:51:56,470     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)
2025-10-15T16:51:56,477     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)
2025-10-15T16:51:57,086   Collecting numpy>2.0.0
2025-10-15T16:51:57,524     Using cached https://www.piwheels.org/simple/numpy/numpy-2.3.3-cp311-cp311-linux_armv7l.whl (6.1 MB)
2025-10-15T16:51:58,237     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)
2025-10-15T16:51:58,242     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)
2025-10-15T16:51:58,247     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)
2025-10-15T16:51:58,253     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)
2025-10-15T16:51:58,259     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)
2025-10-15T16:51:58,266     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)
2025-10-15T16:51:58,272     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)
2025-10-15T16:51:58,278     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)
2025-10-15T16:51:58,284     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)
2025-10-15T16:51:58,289     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)
2025-10-15T16:51:58,295     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)
2025-10-15T16:51:58,301     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)
2025-10-15T16:51:58,699   Collecting scipy>1.14.0
2025-10-15T16:52:00,433     Using cached https://www.piwheels.org/simple/scipy/scipy-1.16.2-cp311-cp311-linux_armv7l.whl (22.9 MB)
2025-10-15T16:52:04,383   Installing collected packages: setuptools, numpy, cython, scipy
2025-10-15T16:52:16,731     Creating /tmp/pip-build-env-wty_w1ja/overlay/local/bin
2025-10-15T16:52:16,733     changing mode of /tmp/pip-build-env-wty_w1ja/overlay/local/bin/f2py to 755
2025-10-15T16:52:16,735     changing mode of /tmp/pip-build-env-wty_w1ja/overlay/local/bin/numpy-config to 755
2025-10-15T16:52:19,817     changing mode of /tmp/pip-build-env-wty_w1ja/overlay/local/bin/cygdb to 755
2025-10-15T16:52:19,819     changing mode of /tmp/pip-build-env-wty_w1ja/overlay/local/bin/cython to 755
2025-10-15T16:52:19,821     changing mode of /tmp/pip-build-env-wty_w1ja/overlay/local/bin/cythonize to 755
2025-10-15T16:52:37,568   Successfully installed cython-3.1.4 numpy-2.3.3 scipy-1.16.2 setuptools-80.9.0
2025-10-15T16:52:38,066   Installing build dependencies: finished with status 'done'
2025-10-15T16:52:38,073   Getting requirements to build wheel: started
2025-10-15T16:52:38,074   Running command Getting requirements to build wheel
2025-10-15T16:53:09,980   Compiling pcangsd/reader_cy.pyx because it changed.
2025-10-15T16:53:09,980   Compiling pcangsd/shared_cy.pyx because it changed.
2025-10-15T16:53:09,981   Compiling pcangsd/covariance_cy.pyx because it changed.
2025-10-15T16:53:09,981   Compiling pcangsd/inbreed_cy.pyx because it changed.
2025-10-15T16:53:09,982   Compiling pcangsd/admixture_cy.pyx because it changed.
2025-10-15T16:53:09,982   Compiling pcangsd/tree_cy.pyx because it changed.
2025-10-15T16:53:09,982   [1/6] Cythonizing pcangsd/admixture_cy.pyx
2025-10-15T16:53:09,983   [2/6] Cythonizing pcangsd/covariance_cy.pyx
2025-10-15T16:53:09,983   [3/6] Cythonizing pcangsd/inbreed_cy.pyx
2025-10-15T16:53:09,984   [4/6] Cythonizing pcangsd/reader_cy.pyx
2025-10-15T16:53:09,985   [5/6] Cythonizing pcangsd/shared_cy.pyx
2025-10-15T16:53:09,985   [6/6] Cythonizing pcangsd/tree_cy.pyx
2025-10-15T16:53:10,039   /tmp/pip-build-env-wty_w1ja/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T16:53:10,039   !!

2025-10-15T16:53:10,040           ********************************************************************************
2025-10-15T16:53:10,041           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T16:53:10,042           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2025-10-15T16:53:10,043           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T16:53:10,043           ********************************************************************************

2025-10-15T16:53:10,044   !!
2025-10-15T16:53:10,045     self._finalize_license_expression()
2025-10-15T16:53:10,066   running egg_info
2025-10-15T16:53:10,075   writing pcangsd.egg-info/PKG-INFO
2025-10-15T16:53:10,078   writing dependency_links to pcangsd.egg-info/dependency_links.txt
2025-10-15T16:53:10,080   writing entry points to pcangsd.egg-info/entry_points.txt
2025-10-15T16:53:10,082   writing requirements to pcangsd.egg-info/requires.txt
2025-10-15T16:53:10,083   writing top-level names to pcangsd.egg-info/top_level.txt
2025-10-15T16:53:10,127   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,128   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,128   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,129   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,130   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,130   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,131   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,131   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,132   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,133   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,134   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,134   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,135   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,135   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,136   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,136   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,137   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,138   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,138   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,139   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,139   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,140   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,140   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,141   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,141   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,142   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,143   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,143   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,144   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,144   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:10,185   reading manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-15T16:53:10,223   reading manifest template 'MANIFEST.in'
2025-10-15T16:53:10,254   adding license file 'LICENSE'
2025-10-15T16:53:10,279   writing manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-15T16:53:11,182   Getting requirements to build wheel: finished with status 'done'
2025-10-15T16:53:11,186   Created temporary directory: /tmp/pip-modern-metadata-49djgahw
2025-10-15T16:53:11,188   Preparing metadata (pyproject.toml): started
2025-10-15T16:53:11,189   Running command Preparing metadata (pyproject.toml)
2025-10-15T16:53:12,864   /tmp/pip-build-env-wty_w1ja/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T16:53:12,864   !!

2025-10-15T16:53:12,866           ********************************************************************************
2025-10-15T16:53:12,866           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T16:53:12,867           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2025-10-15T16:53:12,869           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T16:53:12,869           ********************************************************************************

2025-10-15T16:53:12,870   !!
2025-10-15T16:53:12,871     self._finalize_license_expression()
2025-10-15T16:53:12,894   running dist_info
2025-10-15T16:53:12,909   creating /tmp/pip-modern-metadata-49djgahw/pcangsd.egg-info
2025-10-15T16:53:12,910   writing /tmp/pip-modern-metadata-49djgahw/pcangsd.egg-info/PKG-INFO
2025-10-15T16:53:12,914   writing dependency_links to /tmp/pip-modern-metadata-49djgahw/pcangsd.egg-info/dependency_links.txt
2025-10-15T16:53:12,915   writing entry points to /tmp/pip-modern-metadata-49djgahw/pcangsd.egg-info/entry_points.txt
2025-10-15T16:53:12,917   writing requirements to /tmp/pip-modern-metadata-49djgahw/pcangsd.egg-info/requires.txt
2025-10-15T16:53:12,918   writing top-level names to /tmp/pip-modern-metadata-49djgahw/pcangsd.egg-info/top_level.txt
2025-10-15T16:53:12,919   writing manifest file '/tmp/pip-modern-metadata-49djgahw/pcangsd.egg-info/SOURCES.txt'
2025-10-15T16:53:12,956   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,957   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,957   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,958   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,959   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,959   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,960   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,960   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,960   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,961   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,961   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,962   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,962   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,963   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,963   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,964   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,964   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,965   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,966   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,966   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,967   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,967   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,968   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,969   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,969   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,970   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,970   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,970   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,971   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,971   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:53:12,972   reading manifest file '/tmp/pip-modern-metadata-49djgahw/pcangsd.egg-info/SOURCES.txt'
2025-10-15T16:53:12,973   reading manifest template 'MANIFEST.in'
2025-10-15T16:53:12,976   adding license file 'LICENSE'
2025-10-15T16:53:12,979   writing manifest file '/tmp/pip-modern-metadata-49djgahw/pcangsd.egg-info/SOURCES.txt'
2025-10-15T16:53:12,980   creating '/tmp/pip-modern-metadata-49djgahw/pcangsd-1.36.2.dist-info'
2025-10-15T16:53:13,194   Preparing metadata (pyproject.toml): finished with status 'done'
2025-10-15T16:53:13,199   Source in /tmp/pip-wheel-vpqjujb9/pcangsd_38237ca5322843e2b3b64dcdf5121b04 has version 1.36.2, which satisfies requirement pcangsd==1.36.2 from https://files.pythonhosted.org/packages/47/bc/4ee519ccd62d64da95785ce2e65101b5fef3bade6b4ea3af145645320a76/pcangsd-1.36.2.tar.gz
2025-10-15T16:53:13,200   Removed pcangsd==1.36.2 from https://files.pythonhosted.org/packages/47/bc/4ee519ccd62d64da95785ce2e65101b5fef3bade6b4ea3af145645320a76/pcangsd-1.36.2.tar.gz from build tracker '/tmp/pip-build-tracker-cnc1hhnt'
2025-10-15T16:53:13,206 Created temporary directory: /tmp/pip-unpack-jdzoegkg
2025-10-15T16:53:13,207 Building wheels for collected packages: pcangsd
2025-10-15T16:53:13,212   Created temporary directory: /tmp/pip-wheel-vesft4wi
2025-10-15T16:53:13,212   Destination directory: /tmp/pip-wheel-vesft4wi
2025-10-15T16:53:13,214   Building wheel for pcangsd (pyproject.toml): started
2025-10-15T16:53:13,216   Running command Building wheel for pcangsd (pyproject.toml)
2025-10-15T16:53:14,801   /tmp/pip-build-env-wty_w1ja/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T16:53:14,801   !!

2025-10-15T16:53:14,803           ********************************************************************************
2025-10-15T16:53:14,803           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T16:53:14,805           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2025-10-15T16:53:14,806           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T16:53:14,807           ********************************************************************************

2025-10-15T16:53:14,809   !!
2025-10-15T16:53:14,809     self._finalize_license_expression()
2025-10-15T16:53:14,831   running bdist_wheel
2025-10-15T16:53:14,868   running build
2025-10-15T16:53:14,869   running build_py
2025-10-15T16:53:14,880   creating build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T16:53:14,882   copying pcangsd/__init__.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T16:53:14,883   copying pcangsd/tree.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T16:53:14,885   copying pcangsd/main.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T16:53:14,888   copying pcangsd/shared.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T16:53:14,890   copying pcangsd/covariance.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T16:53:14,892   copying pcangsd/selection.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T16:53:14,894   copying pcangsd/admixture.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T16:53:14,896   copying pcangsd/inbreed.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T16:53:14,899   running build_ext
2025-10-15T16:53:14,907   building 'pcangsd.reader_cy' extension
2025-10-15T16:53:14,908   creating build/temp.linux-armv7l-cpython-311/pcangsd
2025-10-15T16:53:14,909   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-wty_w1ja/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
2025-10-15T16:53:38,295   In function ‘PyArrayObject* __pyx_f_7pcangsd_9reader_cy_readBeagle(PyObject*, int)’,
2025-10-15T16:53:38,296       inlined from ‘PyObject* __pyx_pf_7pcangsd_9reader_cy_readBeagle(PyObject*, PyObject*)’ at pcangsd/reader_cy.cpp:20328:66,
2025-10-15T16:53:38,297       inlined from ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_1readBeagle(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at pcangsd/reader_cy.cpp:20300:52:
2025-10-15T16:53:38,297   pcangsd/reader_cy.cpp:20039:52: warning: ‘__pyx_v_N’ may be used uninitialized [-Wmaybe-uninitialized]
2025-10-15T16:53:38,298   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)
2025-10-15T16:53:38,299         |                                         ~~~~~~~~~~~^~~~
2025-10-15T16:53:38,300   pcangsd/reader_cy.cpp: In function ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_1readBeagle(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’:
2025-10-15T16:53:38,301   pcangsd/reader_cy.cpp:19495:10: note: ‘__pyx_v_N’ was declared here
2025-10-15T16:53:38,302   19495 |   size_t __pyx_v_N;
2025-10-15T16:53:38,302         |          ^~~~~~~~~
2025-10-15T16:53:40,997   In function ‘PyArrayObject* __pyx_f_7pcangsd_9reader_cy_readBeagleFilterSites(PyObject*, __Pyx_memviewslice, int)’,
2025-10-15T16:53:40,997       inlined from ‘PyObject* __pyx_pf_7pcangsd_9reader_cy_2readBeagleFilterSites(PyObject*, PyObject*, __Pyx_memviewslice)’ at pcangsd/reader_cy.cpp:21246:77,
2025-10-15T16:53:40,998       inlined from ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_3readBeagleFilterSites(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at pcangsd/reader_cy.cpp:21217:64:
2025-10-15T16:53:40,999   pcangsd/reader_cy.cpp:20947:52: warning: ‘__pyx_v_N’ may be used uninitialized [-Wmaybe-uninitialized]
2025-10-15T16:53:40,999   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)
2025-10-15T16:53:41,000         |                                         ~~~~~~~~~~~^~~~
2025-10-15T16:53:41,001   pcangsd/reader_cy.cpp: In function ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_3readBeagleFilterSites(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’:
2025-10-15T16:53:41,002   pcangsd/reader_cy.cpp:20365:10: note: ‘__pyx_v_N’ was declared here
2025-10-15T16:53:41,003   20365 |   size_t __pyx_v_N;
2025-10-15T16:53:41,003         |          ^~~~~~~~~
2025-10-15T16:53:41,981   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
2025-10-15T16:53:42,242   building 'pcangsd.shared_cy' extension
2025-10-15T16:53:42,243   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-wty_w1ja/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
2025-10-15T16:54:03,207   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
2025-10-15T16:54:03,323   building 'pcangsd.covariance_cy' extension
2025-10-15T16:54:03,323   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-wty_w1ja/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
2025-10-15T16:54:22,371   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
2025-10-15T16:54:22,488   building 'pcangsd.inbreed_cy' extension
2025-10-15T16:54:22,488   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-wty_w1ja/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
2025-10-15T16:54:41,499   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
2025-10-15T16:54:41,616   building 'pcangsd.admixture_cy' extension
2025-10-15T16:54:41,617   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-wty_w1ja/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
2025-10-15T16:54:59,314   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
2025-10-15T16:54:59,432   building 'pcangsd.tree_cy' extension
2025-10-15T16:54:59,433   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-wty_w1ja/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
2025-10-15T16:55:17,407   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
2025-10-15T16:55:17,548   installing to build/bdist.linux-armv7l/wheel
2025-10-15T16:55:17,548   running install
2025-10-15T16:55:17,572   running install_lib
2025-10-15T16:55:17,581   creating build/bdist.linux-armv7l/wheel
2025-10-15T16:55:17,584   creating build/bdist.linux-armv7l/wheel/pcangsd
2025-10-15T16:55:17,585   copying build/lib.linux-armv7l-cpython-311/pcangsd/covariance_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,591   copying build/lib.linux-armv7l-cpython-311/pcangsd/__init__.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,592   copying build/lib.linux-armv7l-cpython-311/pcangsd/admixture_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,597   copying build/lib.linux-armv7l-cpython-311/pcangsd/shared_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,603   copying build/lib.linux-armv7l-cpython-311/pcangsd/tree.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,605   copying build/lib.linux-armv7l-cpython-311/pcangsd/main.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,608   copying build/lib.linux-armv7l-cpython-311/pcangsd/reader_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,616   copying build/lib.linux-armv7l-cpython-311/pcangsd/shared.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,618   copying build/lib.linux-armv7l-cpython-311/pcangsd/inbreed_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,625   copying build/lib.linux-armv7l-cpython-311/pcangsd/covariance.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,627   copying build/lib.linux-armv7l-cpython-311/pcangsd/tree_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,633   copying build/lib.linux-armv7l-cpython-311/pcangsd/selection.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,635   copying build/lib.linux-armv7l-cpython-311/pcangsd/admixture.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,637   copying build/lib.linux-armv7l-cpython-311/pcangsd/inbreed.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T16:55:17,639   running install_egg_info
2025-10-15T16:55:17,662   running egg_info
2025-10-15T16:55:17,669   writing pcangsd.egg-info/PKG-INFO
2025-10-15T16:55:17,672   writing dependency_links to pcangsd.egg-info/dependency_links.txt
2025-10-15T16:55:17,673   writing entry points to pcangsd.egg-info/entry_points.txt
2025-10-15T16:55:17,674   writing requirements to pcangsd.egg-info/requires.txt
2025-10-15T16:55:17,676   writing top-level names to pcangsd.egg-info/top_level.txt
2025-10-15T16:55:17,681   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,682   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,683   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,683   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,684   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,684   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,685   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,685   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,686   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,686   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,687   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,687   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,687   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,688   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,689   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,689   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,690   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,690   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,691   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,692   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,692   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,693   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,694   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,694   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,695   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,696   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,696   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,697   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,697   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,698   dependency /tmp/pip-build-env-wty_w1ja/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
2025-10-15T16:55:17,698   reading manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-15T16:55:17,702   reading manifest template 'MANIFEST.in'
2025-10-15T16:55:17,713   adding license file 'LICENSE'
2025-10-15T16:55:17,717   writing manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-15T16:55:17,719   Copying pcangsd.egg-info to build/bdist.linux-armv7l/wheel/./pcangsd-1.36.2-py3.11.egg-info
2025-10-15T16:55:17,734   running install_scripts
2025-10-15T16:55:17,783   creating build/bdist.linux-armv7l/wheel/pcangsd-1.36.2.dist-info/WHEEL
2025-10-15T16:55:17,787   creating '/tmp/pip-wheel-vesft4wi/.tmp-6dum51wp/pcangsd-1.36.2-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-10-15T16:55:17,789   adding 'pcangsd/__init__.py'
2025-10-15T16:55:17,790   adding 'pcangsd/admixture.py'
2025-10-15T16:55:17,837   adding 'pcangsd/admixture_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T16:55:17,840   adding 'pcangsd/covariance.py'
2025-10-15T16:55:17,888   adding 'pcangsd/covariance_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T16:55:17,891   adding 'pcangsd/inbreed.py'
2025-10-15T16:55:17,939   adding 'pcangsd/inbreed_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T16:55:17,943   adding 'pcangsd/main.py'
2025-10-15T16:55:18,005   adding 'pcangsd/reader_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T16:55:18,008   adding 'pcangsd/selection.py'
2025-10-15T16:55:18,010   adding 'pcangsd/shared.py'
2025-10-15T16:55:18,062   adding 'pcangsd/shared_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T16:55:18,065   adding 'pcangsd/tree.py'
2025-10-15T16:55:18,112   adding 'pcangsd/tree_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T16:55:18,121   adding 'pcangsd-1.36.2.dist-info/licenses/LICENSE'
2025-10-15T16:55:18,123   adding 'pcangsd-1.36.2.dist-info/METADATA'
2025-10-15T16:55:18,124   adding 'pcangsd-1.36.2.dist-info/WHEEL'
2025-10-15T16:55:18,125   adding 'pcangsd-1.36.2.dist-info/entry_points.txt'
2025-10-15T16:55:18,126   adding 'pcangsd-1.36.2.dist-info/top_level.txt'
2025-10-15T16:55:18,127   adding 'pcangsd-1.36.2.dist-info/RECORD'
2025-10-15T16:55:18,134   removing build/bdist.linux-armv7l/wheel
2025-10-15T16:55:18,313   Building wheel for pcangsd (pyproject.toml): finished with status 'done'
2025-10-15T16:55:18,335   Created wheel for pcangsd: filename=pcangsd-1.36.2-cp311-cp311-linux_armv7l.whl size=619106 sha256=5f120afe8e78823a8b1c6ebdd7a6ccecc865f96e08fb904a26b672f2bd294333
2025-10-15T16:55:18,337   Stored in directory: /tmp/pip-ephem-wheel-cache-2eltui8c/wheels/20/28/19/63f1e235d5d8afb02b840935f5061ecd1367a0ae219d6b150c
2025-10-15T16:55:18,349 Successfully built pcangsd
2025-10-15T16:55:18,376 Removed build tracker: '/tmp/pip-build-tracker-cnc1hhnt'