2025-10-15T23:08:58,553 Created temporary directory: /tmp/pip-ephem-wheel-cache-jm_so3kk
2025-10-15T23:08:58,555 Created temporary directory: /tmp/pip-build-tracker-rp4paula
2025-10-15T23:08:58,556 Initialized build tracking at /tmp/pip-build-tracker-rp4paula
2025-10-15T23:08:58,556 Created build tracker: /tmp/pip-build-tracker-rp4paula
2025-10-15T23:08:58,557 Entered build tracker: /tmp/pip-build-tracker-rp4paula
2025-10-15T23:08:58,558 Created temporary directory: /tmp/pip-wheel-thxwmc5o
2025-10-15T23:08:58,561 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
2025-10-15T23:08:58,563 Created temporary directory: /tmp/pip-ephem-wheel-cache-g3uy1sgp
2025-10-15T23:08:58,584 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-15T23:08:58,588 2 location(s) to search for versions of pcangsd:
2025-10-15T23:08:58,588 * https://pypi.org/simple/pcangsd/
2025-10-15T23:08:58,588 * https://www.piwheels.org/simple/pcangsd/
2025-10-15T23:08:58,589 Fetching project page and analyzing links: https://pypi.org/simple/pcangsd/
2025-10-15T23:08:58,589 Getting page https://pypi.org/simple/pcangsd/
2025-10-15T23:08:58,591 Found index url https://pypi.org/simple
2025-10-15T23:08:58,732 Fetched page https://pypi.org/simple/pcangsd/ as application/vnd.pypi.simple.v1+json
2025-10-15T23:08:58,734   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
2025-10-15T23:08:58,735   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
2025-10-15T23:08:58,736   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
2025-10-15T23:08:58,737   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
2025-10-15T23:08:58,738   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
2025-10-15T23:08:58,739 Fetching project page and analyzing links: https://www.piwheels.org/simple/pcangsd/
2025-10-15T23:08:58,739 Getting page https://www.piwheels.org/simple/pcangsd/
2025-10-15T23:08:58,741 Found index url https://www.piwheels.org/simple
2025-10-15T23:08:58,904 Fetched page https://www.piwheels.org/simple/pcangsd/ as text/html
2025-10-15T23:08:58,907   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)
2025-10-15T23:08:58,908   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)
2025-10-15T23:08:58,909   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)
2025-10-15T23:08:58,909   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)
2025-10-15T23:08:58,910   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)
2025-10-15T23:08:58,911   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)
2025-10-15T23:08:58,911 Skipping link: not a file: https://www.piwheels.org/simple/pcangsd/
2025-10-15T23:08:58,912 Skipping link: not a file: https://pypi.org/simple/pcangsd/
2025-10-15T23:08:58,931 Given no hashes to check 1 links for project 'pcangsd': discarding no candidates
2025-10-15T23:08:59,169 Collecting pcangsd==1.36.3
2025-10-15T23:08:59,171   Created temporary directory: /tmp/pip-unpack-zsj8d_t0
2025-10-15T23:08:59,411   Downloading pcangsd-1.36.3.tar.gz (998 kB)
2025-10-15T23:08:59,870   Added pcangsd==1.36.3 from https://files.pythonhosted.org/packages/86/33/3e0e52bbe5f313f5ed3414364ddbcb590706ff56b52aca77c7219b3b0626/pcangsd-1.36.3.tar.gz to build tracker '/tmp/pip-build-tracker-rp4paula'
2025-10-15T23:08:59,876   Created temporary directory: /tmp/pip-build-env-q4_tr32f
2025-10-15T23:08:59,881   Installing build dependencies: started
2025-10-15T23:08:59,882   Running command pip subprocess to install build dependencies
2025-10-15T23:09:01,013   Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11)
2025-10-15T23:09:01,634   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
2025-10-15T23:09:01,657   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-10-15T23:09:03,523   Collecting setuptools>=0.61
2025-10-15T23:09:03,618     Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB)
2025-10-15T23:09:05,428   Collecting cython>3.0.0
2025-10-15T23:09:05,451     Using cached cython-3.1.4-py3-none-any.whl (1.2 MB)
2025-10-15T23:09:06,483     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)
2025-10-15T23:09:06,491     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)
2025-10-15T23:09:06,497     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)
2025-10-15T23:09:06,504     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)
2025-10-15T23:09:06,512     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)
2025-10-15T23:09:07,116   Collecting numpy>2.0.0
2025-10-15T23:09:08,437     Using cached https://www.piwheels.org/simple/numpy/numpy-2.3.3-cp311-cp311-linux_armv7l.whl (6.1 MB)
2025-10-15T23:09:09,147     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)
2025-10-15T23:09:09,152     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)
2025-10-15T23:09:09,157     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)
2025-10-15T23:09:09,162     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)
2025-10-15T23:09:09,168     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)
2025-10-15T23:09:09,175     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)
2025-10-15T23:09:09,181     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)
2025-10-15T23:09:09,186     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)
2025-10-15T23:09:09,192     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)
2025-10-15T23:09:09,198     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)
2025-10-15T23:09:09,203     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)
2025-10-15T23:09:09,209     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)
2025-10-15T23:09:09,766   Collecting scipy>1.14.0
2025-10-15T23:09:11,343     Using cached https://www.piwheels.org/simple/scipy/scipy-1.16.2-cp311-cp311-linux_armv7l.whl (22.9 MB)
2025-10-15T23:09:15,311   Installing collected packages: setuptools, numpy, cython, scipy
2025-10-15T23:09:27,754     Creating /tmp/pip-build-env-q4_tr32f/overlay/local/bin
2025-10-15T23:09:27,756     changing mode of /tmp/pip-build-env-q4_tr32f/overlay/local/bin/f2py to 755
2025-10-15T23:09:27,758     changing mode of /tmp/pip-build-env-q4_tr32f/overlay/local/bin/numpy-config to 755
2025-10-15T23:09:30,674     changing mode of /tmp/pip-build-env-q4_tr32f/overlay/local/bin/cygdb to 755
2025-10-15T23:09:30,676     changing mode of /tmp/pip-build-env-q4_tr32f/overlay/local/bin/cython to 755
2025-10-15T23:09:30,678     changing mode of /tmp/pip-build-env-q4_tr32f/overlay/local/bin/cythonize to 755
2025-10-15T23:09:48,394   Successfully installed cython-3.1.4 numpy-2.3.3 scipy-1.16.2 setuptools-80.9.0
2025-10-15T23:09:48,887   Installing build dependencies: finished with status 'done'
2025-10-15T23:09:48,894   Getting requirements to build wheel: started
2025-10-15T23:09:48,895   Running command Getting requirements to build wheel
2025-10-15T23:10:20,969   Compiling pcangsd/reader_cy.pyx because it changed.
2025-10-15T23:10:20,970   Compiling pcangsd/shared_cy.pyx because it changed.
2025-10-15T23:10:20,971   Compiling pcangsd/covariance_cy.pyx because it changed.
2025-10-15T23:10:20,971   Compiling pcangsd/inbreed_cy.pyx because it changed.
2025-10-15T23:10:20,972   Compiling pcangsd/admixture_cy.pyx because it changed.
2025-10-15T23:10:20,972   Compiling pcangsd/tree_cy.pyx because it changed.
2025-10-15T23:10:20,973   [1/6] Cythonizing pcangsd/admixture_cy.pyx
2025-10-15T23:10:20,973   [2/6] Cythonizing pcangsd/covariance_cy.pyx
2025-10-15T23:10:20,974   [3/6] Cythonizing pcangsd/inbreed_cy.pyx
2025-10-15T23:10:20,974   [4/6] Cythonizing pcangsd/reader_cy.pyx
2025-10-15T23:10:20,975   [5/6] Cythonizing pcangsd/shared_cy.pyx
2025-10-15T23:10:20,975   [6/6] Cythonizing pcangsd/tree_cy.pyx
2025-10-15T23:10:21,030   /tmp/pip-build-env-q4_tr32f/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T23:10:21,031   !!

2025-10-15T23:10:21,032           ********************************************************************************
2025-10-15T23:10:21,032           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T23:10:21,034           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2025-10-15T23:10:21,035           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T23:10:21,035           ********************************************************************************

2025-10-15T23:10:21,036   !!
2025-10-15T23:10:21,037     self._finalize_license_expression()
2025-10-15T23:10:21,057   running egg_info
2025-10-15T23:10:21,066   writing pcangsd.egg-info/PKG-INFO
2025-10-15T23:10:21,069   writing dependency_links to pcangsd.egg-info/dependency_links.txt
2025-10-15T23:10:21,071   writing entry points to pcangsd.egg-info/entry_points.txt
2025-10-15T23:10:21,072   writing requirements to pcangsd.egg-info/requires.txt
2025-10-15T23:10:21,073   writing top-level names to pcangsd.egg-info/top_level.txt
2025-10-15T23:10:21,117   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,117   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,118   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,118   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,119   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,120   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,120   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,121   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,121   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,122   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,122   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,123   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,123   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,124   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,124   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,125   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,126   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,126   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,127   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,127   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,128   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,128   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,129   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,129   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,130   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,130   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,131   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,131   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,132   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,132   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:21,133   reading manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-15T23:10:21,133   reading manifest template 'MANIFEST.in'
2025-10-15T23:10:21,137   adding license file 'LICENSE'
2025-10-15T23:10:21,141   writing manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-15T23:10:22,039   Getting requirements to build wheel: finished with status 'done'
2025-10-15T23:10:22,042   Created temporary directory: /tmp/pip-modern-metadata-b87pvl5w
2025-10-15T23:10:22,045   Preparing metadata (pyproject.toml): started
2025-10-15T23:10:22,046   Running command Preparing metadata (pyproject.toml)
2025-10-15T23:10:23,735   /tmp/pip-build-env-q4_tr32f/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T23:10:23,735   !!

2025-10-15T23:10:23,736           ********************************************************************************
2025-10-15T23:10:23,737           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T23:10:23,738           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2025-10-15T23:10:23,739           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T23:10:23,739           ********************************************************************************

2025-10-15T23:10:23,740   !!
2025-10-15T23:10:23,741     self._finalize_license_expression()
2025-10-15T23:10:23,765   running dist_info
2025-10-15T23:10:23,780   creating /tmp/pip-modern-metadata-b87pvl5w/pcangsd.egg-info
2025-10-15T23:10:23,781   writing /tmp/pip-modern-metadata-b87pvl5w/pcangsd.egg-info/PKG-INFO
2025-10-15T23:10:23,784   writing dependency_links to /tmp/pip-modern-metadata-b87pvl5w/pcangsd.egg-info/dependency_links.txt
2025-10-15T23:10:23,786   writing entry points to /tmp/pip-modern-metadata-b87pvl5w/pcangsd.egg-info/entry_points.txt
2025-10-15T23:10:23,787   writing requirements to /tmp/pip-modern-metadata-b87pvl5w/pcangsd.egg-info/requires.txt
2025-10-15T23:10:23,788   writing top-level names to /tmp/pip-modern-metadata-b87pvl5w/pcangsd.egg-info/top_level.txt
2025-10-15T23:10:23,790   writing manifest file '/tmp/pip-modern-metadata-b87pvl5w/pcangsd.egg-info/SOURCES.txt'
2025-10-15T23:10:23,826   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,827   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,828   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,828   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,829   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,829   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,829   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,830   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,830   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,831   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,831   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,832   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,832   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,833   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,833   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,834   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,834   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,835   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,835   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,836   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,836   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,837   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,837   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,838   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,839   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,839   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,839   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,840   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,841   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,841   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:10:23,842   reading manifest file '/tmp/pip-modern-metadata-b87pvl5w/pcangsd.egg-info/SOURCES.txt'
2025-10-15T23:10:23,845   reading manifest template 'MANIFEST.in'
2025-10-15T23:10:23,849   adding license file 'LICENSE'
2025-10-15T23:10:23,852   writing manifest file '/tmp/pip-modern-metadata-b87pvl5w/pcangsd.egg-info/SOURCES.txt'
2025-10-15T23:10:23,853   creating '/tmp/pip-modern-metadata-b87pvl5w/pcangsd-1.36.3.dist-info'
2025-10-15T23:10:24,061   Preparing metadata (pyproject.toml): finished with status 'done'
2025-10-15T23:10:24,066   Source in /tmp/pip-wheel-thxwmc5o/pcangsd_c24fbe8d382f40b0bc41de643fe475a3 has version 1.36.3, which satisfies requirement pcangsd==1.36.3 from https://files.pythonhosted.org/packages/86/33/3e0e52bbe5f313f5ed3414364ddbcb590706ff56b52aca77c7219b3b0626/pcangsd-1.36.3.tar.gz
2025-10-15T23:10:24,067   Removed pcangsd==1.36.3 from https://files.pythonhosted.org/packages/86/33/3e0e52bbe5f313f5ed3414364ddbcb590706ff56b52aca77c7219b3b0626/pcangsd-1.36.3.tar.gz from build tracker '/tmp/pip-build-tracker-rp4paula'
2025-10-15T23:10:24,073 Created temporary directory: /tmp/pip-unpack-42hn2g9n
2025-10-15T23:10:24,073 Building wheels for collected packages: pcangsd
2025-10-15T23:10:24,078   Created temporary directory: /tmp/pip-wheel-_xr6_q55
2025-10-15T23:10:24,079   Destination directory: /tmp/pip-wheel-_xr6_q55
2025-10-15T23:10:24,081   Building wheel for pcangsd (pyproject.toml): started
2025-10-15T23:10:24,082   Running command Building wheel for pcangsd (pyproject.toml)
2025-10-15T23:10:25,695   /tmp/pip-build-env-q4_tr32f/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-10-15T23:10:25,695   !!

2025-10-15T23:10:25,696           ********************************************************************************
2025-10-15T23:10:25,696           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-10-15T23:10:25,697           License :: OSI Approved :: GNU General Public License v3 (GPLv3)

2025-10-15T23:10:25,698           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-10-15T23:10:25,698           ********************************************************************************

2025-10-15T23:10:25,699   !!
2025-10-15T23:10:25,700     self._finalize_license_expression()
2025-10-15T23:10:25,723   running bdist_wheel
2025-10-15T23:10:25,762   running build
2025-10-15T23:10:25,763   running build_py
2025-10-15T23:10:25,773   creating build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T23:10:25,775   copying pcangsd/tree.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T23:10:25,777   copying pcangsd/admixture.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T23:10:25,780   copying pcangsd/shared.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T23:10:25,781   copying pcangsd/inbreed.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T23:10:25,783   copying pcangsd/__init__.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T23:10:25,785   copying pcangsd/selection.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T23:10:25,787   copying pcangsd/covariance.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T23:10:25,789   copying pcangsd/main.py -> build/lib.linux-armv7l-cpython-311/pcangsd
2025-10-15T23:10:25,792   running build_ext
2025-10-15T23:10:25,800   building 'pcangsd.reader_cy' extension
2025-10-15T23:10:25,801   creating build/temp.linux-armv7l-cpython-311/pcangsd
2025-10-15T23:10:25,802   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-q4_tr32f/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
2025-10-15T23:10:49,205   In function ‘PyArrayObject* __pyx_f_7pcangsd_9reader_cy_readBeagle(PyObject*, int)’,
2025-10-15T23:10:49,206       inlined from ‘PyObject* __pyx_pf_7pcangsd_9reader_cy_readBeagle(PyObject*, PyObject*)’ at pcangsd/reader_cy.cpp:20328:66,
2025-10-15T23:10:49,206       inlined from ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_1readBeagle(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at pcangsd/reader_cy.cpp:20300:52:
2025-10-15T23:10:49,207   pcangsd/reader_cy.cpp:20039:52: warning: ‘__pyx_v_N’ may be used uninitialized [-Wmaybe-uninitialized]
2025-10-15T23:10:49,208   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)
2025-10-15T23:10:49,208         |                                         ~~~~~~~~~~~^~~~
2025-10-15T23:10:49,209   pcangsd/reader_cy.cpp: In function ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_1readBeagle(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’:
2025-10-15T23:10:49,210   pcangsd/reader_cy.cpp:19495:10: note: ‘__pyx_v_N’ was declared here
2025-10-15T23:10:49,210   19495 |   size_t __pyx_v_N;
2025-10-15T23:10:49,211         |          ^~~~~~~~~
2025-10-15T23:10:51,905   In function ‘PyArrayObject* __pyx_f_7pcangsd_9reader_cy_readBeagleFilterSites(PyObject*, __Pyx_memviewslice, int)’,
2025-10-15T23:10:51,906       inlined from ‘PyObject* __pyx_pf_7pcangsd_9reader_cy_2readBeagleFilterSites(PyObject*, PyObject*, __Pyx_memviewslice)’ at pcangsd/reader_cy.cpp:21246:77,
2025-10-15T23:10:51,906       inlined from ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_3readBeagleFilterSites(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’ at pcangsd/reader_cy.cpp:21217:64:
2025-10-15T23:10:51,907   pcangsd/reader_cy.cpp:20947:52: warning: ‘__pyx_v_N’ may be used uninitialized [-Wmaybe-uninitialized]
2025-10-15T23:10:51,907   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)
2025-10-15T23:10:51,908         |                                         ~~~~~~~~~~~^~~~
2025-10-15T23:10:51,908   pcangsd/reader_cy.cpp: In function ‘PyObject* __pyx_pw_7pcangsd_9reader_cy_3readBeagleFilterSites(PyObject*, PyObject* const*, Py_ssize_t, PyObject*)’:
2025-10-15T23:10:51,909   pcangsd/reader_cy.cpp:20365:10: note: ‘__pyx_v_N’ was declared here
2025-10-15T23:10:51,909   20365 |   size_t __pyx_v_N;
2025-10-15T23:10:51,910         |          ^~~~~~~~~
2025-10-15T23:10:52,888   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
2025-10-15T23:10:53,160   building 'pcangsd.shared_cy' extension
2025-10-15T23:10:53,161   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-q4_tr32f/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
2025-10-15T23:11:14,189   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
2025-10-15T23:11:14,306   building 'pcangsd.covariance_cy' extension
2025-10-15T23:11:14,307   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-q4_tr32f/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
2025-10-15T23:11:33,402   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
2025-10-15T23:11:33,516   building 'pcangsd.inbreed_cy' extension
2025-10-15T23:11:33,517   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-q4_tr32f/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
2025-10-15T23:11:52,597   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
2025-10-15T23:11:52,711   building 'pcangsd.admixture_cy' extension
2025-10-15T23:11:52,712   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-q4_tr32f/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
2025-10-15T23:12:10,466   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
2025-10-15T23:12:10,583   building 'pcangsd.tree_cy' extension
2025-10-15T23:12:10,583   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-q4_tr32f/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
2025-10-15T23:12:28,492   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
2025-10-15T23:12:28,629   installing to build/bdist.linux-armv7l/wheel
2025-10-15T23:12:28,630   running install
2025-10-15T23:12:28,654   running install_lib
2025-10-15T23:12:28,666   creating build/bdist.linux-armv7l/wheel
2025-10-15T23:12:28,668   creating build/bdist.linux-armv7l/wheel/pcangsd
2025-10-15T23:12:28,670   copying build/lib.linux-armv7l-cpython-311/pcangsd/reader_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,684   copying build/lib.linux-armv7l-cpython-311/pcangsd/tree.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,686   copying build/lib.linux-armv7l-cpython-311/pcangsd/admixture.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,688   copying build/lib.linux-armv7l-cpython-311/pcangsd/shared.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,690   copying build/lib.linux-armv7l-cpython-311/pcangsd/inbreed.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,693   copying build/lib.linux-armv7l-cpython-311/pcangsd/shared_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,700   copying build/lib.linux-armv7l-cpython-311/pcangsd/__init__.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,702   copying build/lib.linux-armv7l-cpython-311/pcangsd/tree_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,709   copying build/lib.linux-armv7l-cpython-311/pcangsd/covariance_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,717   copying build/lib.linux-armv7l-cpython-311/pcangsd/admixture_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,724   copying build/lib.linux-armv7l-cpython-311/pcangsd/selection.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,726   copying build/lib.linux-armv7l-cpython-311/pcangsd/covariance.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,728   copying build/lib.linux-armv7l-cpython-311/pcangsd/main.py -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,731   copying build/lib.linux-armv7l-cpython-311/pcangsd/inbreed_cy.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pcangsd
2025-10-15T23:12:28,738   running install_egg_info
2025-10-15T23:12:28,763   running egg_info
2025-10-15T23:12:28,774   writing pcangsd.egg-info/PKG-INFO
2025-10-15T23:12:28,779   writing dependency_links to pcangsd.egg-info/dependency_links.txt
2025-10-15T23:12:28,781   writing entry points to pcangsd.egg-info/entry_points.txt
2025-10-15T23:12:28,783   writing requirements to pcangsd.egg-info/requires.txt
2025-10-15T23:12:28,785   writing top-level names to pcangsd.egg-info/top_level.txt
2025-10-15T23:12:28,793   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,794   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,794   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,795   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,796   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,797   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,797   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,798   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,799   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,800   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,801   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,801   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,802   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,803   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,804   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,805   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,805   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,806   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,807   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,808   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,809   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,809   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,810   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,811   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,812   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,812   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,813   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,814   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,814   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,815   dependency /tmp/pip-build-env-q4_tr32f/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
2025-10-15T23:12:28,823   reading manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-15T23:12:28,829   reading manifest template 'MANIFEST.in'
2025-10-15T23:12:28,842   adding license file 'LICENSE'
2025-10-15T23:12:28,847   writing manifest file 'pcangsd.egg-info/SOURCES.txt'
2025-10-15T23:12:28,849   Copying pcangsd.egg-info to build/bdist.linux-armv7l/wheel/./pcangsd-1.36.3-py3.11.egg-info
2025-10-15T23:12:28,862   running install_scripts
2025-10-15T23:12:28,909   creating build/bdist.linux-armv7l/wheel/pcangsd-1.36.3.dist-info/WHEEL
2025-10-15T23:12:28,913   creating '/tmp/pip-wheel-_xr6_q55/.tmp-vvlvqd32/pcangsd-1.36.3-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-10-15T23:12:28,915   adding 'pcangsd/__init__.py'
2025-10-15T23:12:28,916   adding 'pcangsd/admixture.py'
2025-10-15T23:12:28,962   adding 'pcangsd/admixture_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T23:12:28,964   adding 'pcangsd/covariance.py'
2025-10-15T23:12:29,013   adding 'pcangsd/covariance_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T23:12:29,015   adding 'pcangsd/inbreed.py'
2025-10-15T23:12:29,063   adding 'pcangsd/inbreed_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T23:12:29,068   adding 'pcangsd/main.py'
2025-10-15T23:12:29,130   adding 'pcangsd/reader_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T23:12:29,133   adding 'pcangsd/selection.py'
2025-10-15T23:12:29,135   adding 'pcangsd/shared.py'
2025-10-15T23:12:29,186   adding 'pcangsd/shared_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T23:12:29,189   adding 'pcangsd/tree.py'
2025-10-15T23:12:29,236   adding 'pcangsd/tree_cy.cpython-311-arm-linux-gnueabihf.so'
2025-10-15T23:12:29,245   adding 'pcangsd-1.36.3.dist-info/licenses/LICENSE'
2025-10-15T23:12:29,247   adding 'pcangsd-1.36.3.dist-info/METADATA'
2025-10-15T23:12:29,248   adding 'pcangsd-1.36.3.dist-info/WHEEL'
2025-10-15T23:12:29,249   adding 'pcangsd-1.36.3.dist-info/entry_points.txt'
2025-10-15T23:12:29,249   adding 'pcangsd-1.36.3.dist-info/top_level.txt'
2025-10-15T23:12:29,250   adding 'pcangsd-1.36.3.dist-info/RECORD'
2025-10-15T23:12:29,261   removing build/bdist.linux-armv7l/wheel
2025-10-15T23:12:29,444   Building wheel for pcangsd (pyproject.toml): finished with status 'done'
2025-10-15T23:12:29,461   Created wheel for pcangsd: filename=pcangsd-1.36.3-cp311-cp311-linux_armv7l.whl size=619124 sha256=9bf1d663c72beafa0ee85dca06a4a94e19b238eed20e5dc12c6df03a69e7c60d
2025-10-15T23:12:29,462   Stored in directory: /tmp/pip-ephem-wheel-cache-g3uy1sgp/wheels/f7/7c/bd/f0bfb202fcb0015a8f8885aa4048105d932ed8edd3beff73f8
2025-10-15T23:12:29,475 Successfully built pcangsd
2025-10-15T23:12:29,494 Removed build tracker: '/tmp/pip-build-tracker-rp4paula'