2025-09-08T06:46:44,129 Created temporary directory: /tmp/pip-build-tracker-28w_illp 2025-09-08T06:46:44,130 Initialized build tracking at /tmp/pip-build-tracker-28w_illp 2025-09-08T06:46:44,130 Created build tracker: /tmp/pip-build-tracker-28w_illp 2025-09-08T06:46:44,130 Entered build tracker: /tmp/pip-build-tracker-28w_illp 2025-09-08T06:46:44,130 Created temporary directory: /tmp/pip-wheel-7dh5ohhe 2025-09-08T06:46:44,133 Created temporary directory: /tmp/pip-ephem-wheel-cache-ad8332kk 2025-09-08T06:46:44,190 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T06:46:44,192 2 location(s) to search for versions of limix-inference: 2025-09-08T06:46:44,192 * https://pypi.org/simple/limix-inference/ 2025-09-08T06:46:44,192 * https://www.piwheels.org/simple/limix-inference/ 2025-09-08T06:46:44,192 Fetching project page and analyzing links: https://pypi.org/simple/limix-inference/ 2025-09-08T06:46:44,193 Getting page https://pypi.org/simple/limix-inference/ 2025-09-08T06:46:44,194 Found index url https://pypi.org/simple/ 2025-09-08T06:46:44,265 Fetched page https://pypi.org/simple/limix-inference/ as application/vnd.pypi.simple.v1+json 2025-09-08T06:46:44,269 Found link https://files.pythonhosted.org/packages/2f/8b/58de27bc3ca08177dc6dd881665924c7a84460676a3c51cb8babe7c566e9/limix-inference-1.0.2.dev1.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.2.dev1 2025-09-08T06:46:44,270 Found link https://files.pythonhosted.org/packages/26/fb/ef0d4f233d2924bcd50c0130cbde768c92f9ff985b19fa7b5a9b60f79404/limix-inference-1.0.2.dev2.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.2.dev2 2025-09-08T06:46:44,270 Found link https://files.pythonhosted.org/packages/53/e7/bbd64f5d5a69d001309eab399227436898368064bf4414f38f44d9a35d38/limix-inference-1.0.2.dev3.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.2.dev3 2025-09-08T06:46:44,270 Found link https://files.pythonhosted.org/packages/24/86/6d5b17f7d90242e26a1b17e2b5b79ce801567feda2ca45757578ebdc48d1/limix-inference-1.0.2.dev4.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.2.dev4 2025-09-08T06:46:44,270 Found link https://files.pythonhosted.org/packages/c2/e1/b042df0253b31583b3a6658c89050e66c7e7b6f1fb038fd6f9d52f51285b/limix-inference-1.0.2.dev5.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.2.dev5 2025-09-08T06:46:44,271 Found link https://files.pythonhosted.org/packages/73/24/13172b0c6b09c5eaa607e8157d48b24fa4c6635d3c39e6eccf574a596077/limix-inference-1.0.2rc0.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.2rc0 2025-09-08T06:46:44,271 Found link https://files.pythonhosted.org/packages/cf/b5/4e4decf10b7eb305450ceb4cc9b9be40a4783e2abbaeee0e49a216542db6/limix-inference-1.0.2rc1.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.2rc1 2025-09-08T06:46:44,271 Found link https://files.pythonhosted.org/packages/05/36/dc8947547cb84436e86e1c7845eb0c232e3da227055f2d6d614b8d8a6f28/limix-inference-1.0.2rc2.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.2rc2 2025-09-08T06:46:44,271 Found link https://files.pythonhosted.org/packages/1f/a9/6401795d463c6cc4ae061fa7dfcf9656cf58e42e3b8f90917498406439f0/limix-inference-1.0.2rc3.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.2rc3 2025-09-08T06:46:44,272 Found link https://files.pythonhosted.org/packages/0b/8a/750cfdae71af53c974ae61078f584520fb3d2a042ed57017278480cdd787/limix-inference-1.0.2.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.2 2025-09-08T06:46:44,272 Found link https://files.pythonhosted.org/packages/74/39/b0f4e1d92fa676c3f8c517e0e660ecd3f37f71d0d6afb90341d70221ab4a/limix-inference-1.0.3.dev0.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.3.dev0 2025-09-08T06:46:44,272 Found link https://files.pythonhosted.org/packages/61/e8/46d507060eaa4fa30615f0df8495283f90218f0555a1b3d8edd6ca6ab68c/limix-inference-1.0.3.dev1.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.3.dev1 2025-09-08T06:46:44,272 Found link https://files.pythonhosted.org/packages/1d/04/ae91040538e401464b76b12f1540605d90d6686ef61d76062608a99f1967/limix-inference-1.0.3.dev2.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.3.dev2 2025-09-08T06:46:44,272 Found link https://files.pythonhosted.org/packages/7a/ed/f57224335a6c15c05414e95a3342e3a0332e0888ff736959f868d9487ee6/limix-inference-1.0.3.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.3 2025-09-08T06:46:44,273 Found link https://files.pythonhosted.org/packages/1f/24/71bd9dc38e67eaa2d52c7600d34cb287bd82bd154109dda9a3c344e5d697/limix-inference-1.0.4.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.4 2025-09-08T06:46:44,273 Found link https://files.pythonhosted.org/packages/15/13/4d41ac421df2679bce96b28e1d82ee70c3cebed001364a876aa866dbc02e/limix-inference-1.0.5.dev0.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.5.dev0 2025-09-08T06:46:44,273 Found link https://files.pythonhosted.org/packages/e7/93/319869046632d2f7281357239b0d2a552f15b963b532a20827b2f516bcc7/limix-inference-1.0.5rc2.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.5rc2 2025-09-08T06:46:44,273 Found link https://files.pythonhosted.org/packages/ef/22/931c0b5f96e5bf76fd1c18f8409f3bba62aa26192a18d110085f883e8941/limix-inference-1.0.5.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.5 2025-09-08T06:46:44,273 Found link https://files.pythonhosted.org/packages/da/2e/229c9e464e22ba501eb487bc87306499717cb04150209d8f2db3711c124c/limix-inference-1.0.6.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.6 2025-09-08T06:46:44,274 Found link https://files.pythonhosted.org/packages/7e/a7/d7abc015f9b6d5733a721f3736bbb60ed6e18e583645e9f207e50fec8c41/limix-inference-1.0.7.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.7 2025-09-08T06:46:44,274 Found link https://files.pythonhosted.org/packages/97/0a/f00eb1d98dfdd39ba64fa03e93c3488a328df3f8311957689cecf9572a3e/limix-inference-1.0.8.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.8 2025-09-08T06:46:44,274 Found link https://files.pythonhosted.org/packages/8a/9c/ef7e7616c368a36455739118b978b73914bec42c6a01c7f1cd47b4cb044b/limix-inference-1.0.9rc1.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.9rc1 2025-09-08T06:46:44,274 Found link https://files.pythonhosted.org/packages/97/f7/4d0d3ff7f95db4b9aefd4bab221f7e0d318351fac276473e69d82a62d90a/limix-inference-1.0.9rc2.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.9rc2 2025-09-08T06:46:44,274 Found link https://files.pythonhosted.org/packages/34/b0/f351f591df6657a59dfbc1fff339a21984fc6ec4890b77a7da32bfc94c7b/limix-inference-1.0.9.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.9 2025-09-08T06:46:44,275 Found link https://files.pythonhosted.org/packages/0a/3e/0eb0ec71af8e9d9b0ec775a55e7f09a5d934e2065f0dd9b0163c45928a2f/limix-inference-1.0.10.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.10 2025-09-08T06:46:44,275 Found link https://files.pythonhosted.org/packages/f3/0b/fe943247409fe618597b48b966c8f6e363bf968128a894ccfcea56bced37/limix-inference-1.0.11.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.11 2025-09-08T06:46:44,275 Found link https://files.pythonhosted.org/packages/9e/da/8081cb1b13bdfde2be017d96696993d257841e63f362fa7437f70ee46d02/limix-inference-1.0.12.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.12 2025-09-08T06:46:44,275 Found link https://files.pythonhosted.org/packages/98/39/971375136c6018d27ced04b9e344cf85f4e3c1a669e33b3356e80dc45989/limix-inference-1.0.13.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.13 2025-09-08T06:46:44,275 Found link https://files.pythonhosted.org/packages/cc/56/9f10fa9e2965fda10b78df287a5576ed6efe8b8d8c375165bfaf56e5213d/limix-inference-1.0.14.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.14 2025-09-08T06:46:44,276 Found link https://files.pythonhosted.org/packages/84/89/05477413b3509de33ce70839d07f640c8b6e2284a8949dc4940ebee4bd95/limix-inference-1.0.15.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.15 2025-09-08T06:46:44,276 Found link https://files.pythonhosted.org/packages/12/83/9edd063f755274ac4523205409a457c8686d1aea35924dee9d88b14938bb/limix-inference-1.0.16.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.16 2025-09-08T06:46:44,276 Found link https://files.pythonhosted.org/packages/8f/10/66e9cdcb2ef933c923699226f89b29fcefb3bb49c3a0b52acc6ad40ba52a/limix-inference-1.0.17.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.17 2025-09-08T06:46:44,276 Found link https://files.pythonhosted.org/packages/d3/0b/06b762dbbd232c3bea3507e778595f5b35dfbd6e20f0a507d0e18e82b3d2/limix-inference-1.0.18.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.0.18 2025-09-08T06:46:44,276 Found link https://files.pythonhosted.org/packages/1b/2a/d82ab7ad141afb87ff931739b716d90173d2d62b9a335bf799143eb8d3cb/limix-inference-1.1.0.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.1.0 2025-09-08T06:46:44,277 Found link https://files.pythonhosted.org/packages/f4/91/cbeb78ff426af4125fe1b9a9786cec411f751369d2a985ab62dd5e2460da/limix-inference-1.1.1.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.1.1 2025-09-08T06:46:44,277 Found link https://files.pythonhosted.org/packages/b8/e8/c54d52bdcd945b9a4c71fbbcf03797d190000ce37126c9f9ae3d46619dcf/limix-inference-1.1.2.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.1.2 2025-09-08T06:46:44,277 Found link https://files.pythonhosted.org/packages/7e/09/2c88d1b16d0cde089f51eb54790c7ce0cdf5afc57592b7b55e8222203ce0/limix-inference-1.1.3.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.1.3 2025-09-08T06:46:44,277 Found link https://files.pythonhosted.org/packages/cf/21/4f4f8caaf4ebef6d5948528c8a0dcf5863ab819faf97123797c57fe2c675/limix-inference-1.1.4.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.1.4 2025-09-08T06:46:44,277 Found link https://files.pythonhosted.org/packages/e8/cd/0dddf22fb999f514e9d2f6a4a95a5ebe4fbf677fae4c3136d14d258ce1c8/limix-inference-1.1.5.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.1.5 2025-09-08T06:46:44,278 Found link https://files.pythonhosted.org/packages/37/90/968ce27b1e6d3350b72dbebe7cec3652856460991565a814850b63c91bc9/limix-inference-1.1.6.tar.gz (from https://pypi.org/simple/limix-inference/), version: 1.1.6 2025-09-08T06:46:44,278 Fetching project page and analyzing links: https://www.piwheels.org/simple/limix-inference/ 2025-09-08T06:46:44,278 Getting page https://www.piwheels.org/simple/limix-inference/ 2025-09-08T06:46:44,279 Found index url https://www.piwheels.org/simple/ 2025-09-08T06:46:44,374 Fetched page https://www.piwheels.org/simple/limix-inference/ as text/html 2025-09-08T06:46:44,377 Skipping link: No binaries permitted for limix-inference: https://archive1.piwheels.org/simple/limix-inference/limix_inference-1.1.6-py3-none-any.whl#sha256=651f7582bd2a442b4225a69469bcda5fbf76a162526fbc7a729f3c500e3a1213 (from https://www.piwheels.org/simple/limix-inference/) 2025-09-08T06:46:44,378 Skipping link: No binaries permitted for limix-inference: https://archive1.piwheels.org/simple/limix-inference/limix_inference-1.1.5-py3-none-any.whl#sha256=5bda56053fd5f49df45a3fa0355aa2e8eb7188b2034a5f8f3ef53a34d59f3c4c (from https://www.piwheels.org/simple/limix-inference/) 2025-09-08T06:46:44,378 Skipping link: No binaries permitted for limix-inference: https://archive1.piwheels.org/simple/limix-inference/limix_inference-1.1.4-py3-none-any.whl#sha256=8ac3fc4a2bb47fe430b536bd2ab999c9f1adf98649c81b84e3c3375bae68a7f5 (from https://www.piwheels.org/simple/limix-inference/) 2025-09-08T06:46:44,378 Skipping link: No binaries permitted for limix-inference: https://archive1.piwheels.org/simple/limix-inference/limix_inference-1.1.3-py3-none-any.whl#sha256=ea94a7bf8b3e34500a9a155260fba2b2080259767f9520885d86caa0db8f82be (from https://www.piwheels.org/simple/limix-inference/) 2025-09-08T06:46:44,378 Skipping link: No binaries permitted for limix-inference: https://archive1.piwheels.org/simple/limix-inference/limix_inference-1.1.2-py3-none-any.whl#sha256=dd03018c1fab1132bb8de87bb4acad84ea64bc1ef102b6468e39cc3402fb53ff (from https://www.piwheels.org/simple/limix-inference/) 2025-09-08T06:46:44,378 Skipping link: No binaries permitted for limix-inference: https://archive1.piwheels.org/simple/limix-inference/limix_inference-1.1.1-py3-none-any.whl#sha256=e2cf1f0dceb70a5e3e8c599f7b837ff2e5f720a0b8eeadc3a753f67d5ced9884 (from https://www.piwheels.org/simple/limix-inference/) 2025-09-08T06:46:44,379 Skipping link: No binaries permitted for limix-inference: https://archive1.piwheels.org/simple/limix-inference/limix_inference-1.1.0-py3-none-any.whl#sha256=91b43e3e511c0d914e6a452b861a3ac5f01283a03917ed6fe513e7e1d56a9f60 (from https://www.piwheels.org/simple/limix-inference/) 2025-09-08T06:46:44,379 Skipping link: No binaries permitted for limix-inference: https://archive1.piwheels.org/simple/limix-inference/limix_inference-1.0.2.dev2-py3-none-any.whl#sha256=bef50a5f6deb5259a976b1356a18e19f2d77ab81d9e24ea0289eff832e394a68 (from https://www.piwheels.org/simple/limix-inference/) 2025-09-08T06:46:44,379 Skipping link: No binaries permitted for limix-inference: https://archive1.piwheels.org/simple/limix-inference/limix_inference-1.0.2.dev1-py3-none-any.whl#sha256=94b2feb2718da440d09feb6bb06ec54ff2d5b2dec96f825271b8c3834da7e1cd (from https://www.piwheels.org/simple/limix-inference/) 2025-09-08T06:46:44,379 Skipping link: not a file: https://www.piwheels.org/simple/limix-inference/ 2025-09-08T06:46:44,379 Skipping link: not a file: https://pypi.org/simple/limix-inference/ 2025-09-08T06:46:44,407 Given no hashes to check 1 links for project 'limix-inference': discarding no candidates 2025-09-08T06:46:44,408 Collecting limix-inference==1.0.4 2025-09-08T06:46:44,409 Created temporary directory: /tmp/pip-unpack-ulhypyog 2025-09-08T06:46:44,548 Downloading limix-inference-1.0.4.tar.gz (25 kB) 2025-09-08T06:46:44,609 Added limix-inference==1.0.4 from https://files.pythonhosted.org/packages/1f/24/71bd9dc38e67eaa2d52c7600d34cb287bd82bd154109dda9a3c344e5d697/limix-inference-1.0.4.tar.gz to build tracker '/tmp/pip-build-tracker-28w_illp' 2025-09-08T06:46:44,610 Running setup.py (path:/tmp/pip-wheel-7dh5ohhe/limix-inference_5b6de6d09e9e4c0da53d49572765410b/setup.py) egg_info for package limix-inference 2025-09-08T06:46:44,610 Created temporary directory: /tmp/pip-pip-egg-info-2tlc1xpb 2025-09-08T06:46:44,611 Preparing metadata (setup.py): started 2025-09-08T06:46:44,611 Running command python setup.py egg_info 2025-09-08T06:46:45,606 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T06:46:45,607 !! 2025-09-08T06:46:45,607 ******************************************************************************** 2025-09-08T06:46:45,607 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T06:46:45,607 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T06:46:45,607 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T06:46:45,607 or your builds will no longer be supported. 2025-09-08T06:46:45,607 ******************************************************************************** 2025-09-08T06:46:45,608 !! 2025-09-08T06:46:45,608 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T06:46:45,707 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-08T06:46:45,707 warnings.warn(msg) 2025-09-08T06:46:46,179 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T06:46:46,179 !! 2025-09-08T06:46:46,179 ******************************************************************************** 2025-09-08T06:46:46,179 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T06:46:46,180 License :: OSI Approved :: MIT License 2025-09-08T06:46:46,180 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T06:46:46,180 ******************************************************************************** 2025-09-08T06:46:46,180 !! 2025-09-08T06:46:46,180 self._finalize_license_expression() 2025-09-08T06:46:46,255 running egg_info 2025-09-08T06:46:46,330 creating /tmp/pip-pip-egg-info-2tlc1xpb/limix_inference.egg-info 2025-09-08T06:46:46,330 writing /tmp/pip-pip-egg-info-2tlc1xpb/limix_inference.egg-info/PKG-INFO 2025-09-08T06:46:46,332 writing dependency_links to /tmp/pip-pip-egg-info-2tlc1xpb/limix_inference.egg-info/dependency_links.txt 2025-09-08T06:46:46,333 writing requirements to /tmp/pip-pip-egg-info-2tlc1xpb/limix_inference.egg-info/requires.txt 2025-09-08T06:46:46,333 writing top-level names to /tmp/pip-pip-egg-info-2tlc1xpb/limix_inference.egg-info/top_level.txt 2025-09-08T06:46:46,333 writing manifest file '/tmp/pip-pip-egg-info-2tlc1xpb/limix_inference.egg-info/SOURCES.txt' 2025-09-08T06:46:46,566 reading manifest file '/tmp/pip-pip-egg-info-2tlc1xpb/limix_inference.egg-info/SOURCES.txt' 2025-09-08T06:46:46,566 reading manifest template 'MANIFEST.in' 2025-09-08T06:46:46,571 adding license file 'LICENSE' 2025-09-08T06:46:46,575 writing manifest file '/tmp/pip-pip-egg-info-2tlc1xpb/limix_inference.egg-info/SOURCES.txt' 2025-09-08T06:46:46,701 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T06:46:46,706 Source in /tmp/pip-wheel-7dh5ohhe/limix-inference_5b6de6d09e9e4c0da53d49572765410b has version 1.0.4, which satisfies requirement limix-inference==1.0.4 from https://files.pythonhosted.org/packages/1f/24/71bd9dc38e67eaa2d52c7600d34cb287bd82bd154109dda9a3c344e5d697/limix-inference-1.0.4.tar.gz 2025-09-08T06:46:46,706 Removed limix-inference==1.0.4 from https://files.pythonhosted.org/packages/1f/24/71bd9dc38e67eaa2d52c7600d34cb287bd82bd154109dda9a3c344e5d697/limix-inference-1.0.4.tar.gz from build tracker '/tmp/pip-build-tracker-28w_illp' 2025-09-08T06:46:46,711 Created temporary directory: /tmp/pip-unpack-spvih7mb 2025-09-08T06:46:46,711 Created temporary directory: /tmp/pip-unpack-gitmqp0g 2025-09-08T06:46:46,711 Building wheels for collected packages: limix-inference 2025-09-08T06:46:46,712 Created temporary directory: /tmp/pip-wheel-5btm_97i 2025-09-08T06:46:46,713 DEPRECATION: Building 'limix-inference' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'limix-inference'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T06:46:46,714 Building wheel for limix-inference (setup.py): started 2025-09-08T06:46:46,715 Destination directory: /tmp/pip-wheel-5btm_97i 2025-09-08T06:46:46,715 Running command python setup.py bdist_wheel 2025-09-08T06:46:47,735 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T06:46:47,735 !! 2025-09-08T06:46:47,735 ******************************************************************************** 2025-09-08T06:46:47,735 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T06:46:47,735 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T06:46:47,736 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T06:46:47,736 or your builds will no longer be supported. 2025-09-08T06:46:47,736 ******************************************************************************** 2025-09-08T06:46:47,736 !! 2025-09-08T06:46:47,736 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T06:46:47,834 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-08T06:46:47,834 warnings.warn(msg) 2025-09-08T06:46:48,300 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T06:46:48,300 !! 2025-09-08T06:46:48,300 ******************************************************************************** 2025-09-08T06:46:48,300 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T06:46:48,301 License :: OSI Approved :: MIT License 2025-09-08T06:46:48,301 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T06:46:48,301 ******************************************************************************** 2025-09-08T06:46:48,301 !! 2025-09-08T06:46:48,301 self._finalize_license_expression() 2025-09-08T06:46:48,302 running bdist_wheel 2025-09-08T06:46:48,587 running build 2025-09-08T06:46:48,587 running build_py 2025-09-08T06:46:48,663 creating build/lib.linux-armv7l-cpython-313/limix_inference 2025-09-08T06:46:48,664 copying limix_inference/fruits.py -> build/lib.linux-armv7l-cpython-313/limix_inference 2025-09-08T06:46:48,665 copying limix_inference/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference 2025-09-08T06:46:48,665 creating build/lib.linux-armv7l-cpython-313/limix_inference/mean 2025-09-08T06:46:48,666 copying limix_inference/mean/_offset.py -> build/lib.linux-armv7l-cpython-313/limix_inference/mean 2025-09-08T06:46:48,666 copying limix_inference/mean/_linear.py -> build/lib.linux-armv7l-cpython-313/limix_inference/mean 2025-09-08T06:46:48,667 copying limix_inference/mean/_sum.py -> build/lib.linux-armv7l-cpython-313/limix_inference/mean 2025-09-08T06:46:48,667 copying limix_inference/mean/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/mean 2025-09-08T06:46:48,668 creating build/lib.linux-armv7l-cpython-313/limix_inference/lik 2025-09-08T06:46:48,668 copying limix_inference/lik/_expfam.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lik 2025-09-08T06:46:48,669 copying limix_inference/lik/_prod.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lik 2025-09-08T06:46:48,669 copying limix_inference/lik/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lik 2025-09-08T06:46:48,670 creating build/lib.linux-armv7l-cpython-313/limix_inference/lmm 2025-09-08T06:46:48,670 copying limix_inference/lmm/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lmm 2025-09-08T06:46:48,671 creating build/lib.linux-armv7l-cpython-313/limix_inference/liknorm 2025-09-08T06:46:48,671 copying limix_inference/liknorm/_machine.py -> build/lib.linux-armv7l-cpython-313/limix_inference/liknorm 2025-09-08T06:46:48,672 copying limix_inference/liknorm/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/liknorm 2025-09-08T06:46:48,672 copying limix_inference/liknorm/_build.py -> build/lib.linux-armv7l-cpython-313/limix_inference/liknorm 2025-09-08T06:46:48,673 creating build/lib.linux-armv7l-cpython-313/limix_inference/random 2025-09-08T06:46:48,673 copying limix_inference/random/_glmm.py -> build/lib.linux-armv7l-cpython-313/limix_inference/random 2025-09-08T06:46:48,674 copying limix_inference/random/_canonical.py -> build/lib.linux-armv7l-cpython-313/limix_inference/random 2025-09-08T06:46:48,674 copying limix_inference/random/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/random 2025-09-08T06:46:48,675 creating build/lib.linux-armv7l-cpython-313/limix_inference/glmm 2025-09-08T06:46:48,675 copying limix_inference/glmm/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/glmm 2025-09-08T06:46:48,676 creating build/lib.linux-armv7l-cpython-313/limix_inference/link 2025-09-08T06:46:48,676 copying limix_inference/link/_link.py -> build/lib.linux-armv7l-cpython-313/limix_inference/link 2025-09-08T06:46:48,677 copying limix_inference/link/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/link 2025-09-08T06:46:48,677 creating build/lib.linux-armv7l-cpython-313/limix_inference/cov 2025-09-08T06:46:48,678 copying limix_inference/cov/_linear.py -> build/lib.linux-armv7l-cpython-313/limix_inference/cov 2025-09-08T06:46:48,678 copying limix_inference/cov/_sum.py -> build/lib.linux-armv7l-cpython-313/limix_inference/cov 2025-09-08T06:46:48,679 copying limix_inference/cov/_eye.py -> build/lib.linux-armv7l-cpython-313/limix_inference/cov 2025-09-08T06:46:48,679 copying limix_inference/cov/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/cov 2025-09-08T06:46:48,680 creating build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_fastlmm 2025-09-08T06:46:48,680 copying limix_inference/lmm/_fastlmm/_fastlmm.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_fastlmm 2025-09-08T06:46:48,681 copying limix_inference/lmm/_fastlmm/_core.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_fastlmm 2025-09-08T06:46:48,681 copying limix_inference/lmm/_fastlmm/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_fastlmm 2025-09-08T06:46:48,682 creating build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_slowlmm 2025-09-08T06:46:48,682 copying limix_inference/lmm/_slowlmm/_slowlmm.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_slowlmm 2025-09-08T06:46:48,683 copying limix_inference/lmm/_slowlmm/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_slowlmm 2025-09-08T06:46:48,684 creating build/lib.linux-armv7l-cpython-313/limix_inference/glmm/_ep 2025-09-08T06:46:48,684 copying limix_inference/glmm/_ep/_fixed.py -> build/lib.linux-armv7l-cpython-313/limix_inference/glmm/_ep 2025-09-08T06:46:48,684 copying limix_inference/glmm/_ep/_expfam.py -> build/lib.linux-armv7l-cpython-313/limix_inference/glmm/_ep 2025-09-08T06:46:48,685 copying limix_inference/glmm/_ep/_ep.py -> build/lib.linux-armv7l-cpython-313/limix_inference/glmm/_ep 2025-09-08T06:46:48,685 copying limix_inference/glmm/_ep/_conditioning.py -> build/lib.linux-armv7l-cpython-313/limix_inference/glmm/_ep 2025-09-08T06:46:48,686 copying limix_inference/glmm/_ep/__init__.py -> build/lib.linux-armv7l-cpython-313/limix_inference/glmm/_ep 2025-09-08T06:46:48,686 running egg_info 2025-09-08T06:46:48,765 writing limix_inference.egg-info/PKG-INFO 2025-09-08T06:46:48,766 writing dependency_links to limix_inference.egg-info/dependency_links.txt 2025-09-08T06:46:48,767 writing requirements to limix_inference.egg-info/requires.txt 2025-09-08T06:46:48,767 writing top-level names to limix_inference.egg-info/top_level.txt 2025-09-08T06:46:48,845 reading manifest file 'limix_inference.egg-info/SOURCES.txt' 2025-09-08T06:46:48,848 reading manifest template 'MANIFEST.in' 2025-09-08T06:46:48,853 adding license file 'LICENSE' 2025-09-08T06:46:48,858 writing manifest file 'limix_inference.egg-info/SOURCES.txt' 2025-09-08T06:46:48,859 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'limix_inference.cov.test' is absent from the `packages` configuration. 2025-09-08T06:46:48,859 !! 2025-09-08T06:46:48,859 ******************************************************************************** 2025-09-08T06:46:48,860 ############################ 2025-09-08T06:46:48,860 # Package would be ignored # 2025-09-08T06:46:48,860 ############################ 2025-09-08T06:46:48,860 Python recognizes 'limix_inference.cov.test' as an importable package[^1], 2025-09-08T06:46:48,860 but it is absent from setuptools' `packages` configuration. 2025-09-08T06:46:48,860 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T06:46:48,860 package, please make sure that 'limix_inference.cov.test' is explicitly added 2025-09-08T06:46:48,860 to the `packages` configuration field. 2025-09-08T06:46:48,861 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T06:46:48,861 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T06:46:48,861 instead of `find_packages(...)`/`find:`). 2025-09-08T06:46:48,861 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T06:46:48,861 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T06:46:48,861 If you don't want 'limix_inference.cov.test' to be distributed and are 2025-09-08T06:46:48,861 already explicitly excluding 'limix_inference.cov.test' via 2025-09-08T06:46:48,861 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T06:46:48,862 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T06:46:48,862 combination with a more fine grained `package-data` configuration. 2025-09-08T06:46:48,862 You can read more about "package data files" on setuptools documentation page: 2025-09-08T06:46:48,862 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T06:46:48,862 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T06:46:48,862 even if it does not contain any `.py` files. 2025-09-08T06:46:48,862 On the other hand, currently there is no concept of package data 2025-09-08T06:46:48,862 directory, all directories are treated like packages. 2025-09-08T06:46:48,863 ******************************************************************************** 2025-09-08T06:46:48,863 !! 2025-09-08T06:46:48,863 check.warn(importable) 2025-09-08T06:46:48,863 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'limix_inference.glmm._ep.test' is absent from the `packages` configuration. 2025-09-08T06:46:48,863 !! 2025-09-08T06:46:48,863 ******************************************************************************** 2025-09-08T06:46:48,863 ############################ 2025-09-08T06:46:48,863 # Package would be ignored # 2025-09-08T06:46:48,864 ############################ 2025-09-08T06:46:48,864 Python recognizes 'limix_inference.glmm._ep.test' as an importable package[^1], 2025-09-08T06:46:48,864 but it is absent from setuptools' `packages` configuration. 2025-09-08T06:46:48,864 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T06:46:48,864 package, please make sure that 'limix_inference.glmm._ep.test' is explicitly added 2025-09-08T06:46:48,864 to the `packages` configuration field. 2025-09-08T06:46:48,864 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T06:46:48,864 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T06:46:48,864 instead of `find_packages(...)`/`find:`). 2025-09-08T06:46:48,865 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T06:46:48,865 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T06:46:48,865 If you don't want 'limix_inference.glmm._ep.test' to be distributed and are 2025-09-08T06:46:48,865 already explicitly excluding 'limix_inference.glmm._ep.test' via 2025-09-08T06:46:48,865 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T06:46:48,865 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T06:46:48,865 combination with a more fine grained `package-data` configuration. 2025-09-08T06:46:48,865 You can read more about "package data files" on setuptools documentation page: 2025-09-08T06:46:48,866 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T06:46:48,866 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T06:46:48,866 even if it does not contain any `.py` files. 2025-09-08T06:46:48,866 On the other hand, currently there is no concept of package data 2025-09-08T06:46:48,866 directory, all directories are treated like packages. 2025-09-08T06:46:48,866 ******************************************************************************** 2025-09-08T06:46:48,866 !! 2025-09-08T06:46:48,866 check.warn(importable) 2025-09-08T06:46:48,867 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'limix_inference.link.test' is absent from the `packages` configuration. 2025-09-08T06:46:48,867 !! 2025-09-08T06:46:48,867 ******************************************************************************** 2025-09-08T06:46:48,867 ############################ 2025-09-08T06:46:48,867 # Package would be ignored # 2025-09-08T06:46:48,867 ############################ 2025-09-08T06:46:48,867 Python recognizes 'limix_inference.link.test' as an importable package[^1], 2025-09-08T06:46:48,867 but it is absent from setuptools' `packages` configuration. 2025-09-08T06:46:48,867 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T06:46:48,868 package, please make sure that 'limix_inference.link.test' is explicitly added 2025-09-08T06:46:48,868 to the `packages` configuration field. 2025-09-08T06:46:48,868 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T06:46:48,868 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T06:46:48,868 instead of `find_packages(...)`/`find:`). 2025-09-08T06:46:48,868 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T06:46:48,868 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T06:46:48,869 If you don't want 'limix_inference.link.test' to be distributed and are 2025-09-08T06:46:48,869 already explicitly excluding 'limix_inference.link.test' via 2025-09-08T06:46:48,869 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T06:46:48,869 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T06:46:48,869 combination with a more fine grained `package-data` configuration. 2025-09-08T06:46:48,869 You can read more about "package data files" on setuptools documentation page: 2025-09-08T06:46:48,869 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T06:46:48,869 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T06:46:48,870 even if it does not contain any `.py` files. 2025-09-08T06:46:48,870 On the other hand, currently there is no concept of package data 2025-09-08T06:46:48,870 directory, all directories are treated like packages. 2025-09-08T06:46:48,870 ******************************************************************************** 2025-09-08T06:46:48,870 !! 2025-09-08T06:46:48,870 check.warn(importable) 2025-09-08T06:46:48,870 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'limix_inference.lmm._fastlmm.test' is absent from the `packages` configuration. 2025-09-08T06:46:48,870 !! 2025-09-08T06:46:48,871 ******************************************************************************** 2025-09-08T06:46:48,871 ############################ 2025-09-08T06:46:48,871 # Package would be ignored # 2025-09-08T06:46:48,871 ############################ 2025-09-08T06:46:48,871 Python recognizes 'limix_inference.lmm._fastlmm.test' as an importable package[^1], 2025-09-08T06:46:48,871 but it is absent from setuptools' `packages` configuration. 2025-09-08T06:46:48,871 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T06:46:48,871 package, please make sure that 'limix_inference.lmm._fastlmm.test' is explicitly added 2025-09-08T06:46:48,871 to the `packages` configuration field. 2025-09-08T06:46:48,872 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T06:46:48,872 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T06:46:48,872 instead of `find_packages(...)`/`find:`). 2025-09-08T06:46:48,872 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T06:46:48,872 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T06:46:48,872 If you don't want 'limix_inference.lmm._fastlmm.test' to be distributed and are 2025-09-08T06:46:48,872 already explicitly excluding 'limix_inference.lmm._fastlmm.test' via 2025-09-08T06:46:48,872 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T06:46:48,872 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T06:46:48,873 combination with a more fine grained `package-data` configuration. 2025-09-08T06:46:48,873 You can read more about "package data files" on setuptools documentation page: 2025-09-08T06:46:48,873 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T06:46:48,873 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T06:46:48,873 even if it does not contain any `.py` files. 2025-09-08T06:46:48,873 On the other hand, currently there is no concept of package data 2025-09-08T06:46:48,873 directory, all directories are treated like packages. 2025-09-08T06:46:48,874 ******************************************************************************** 2025-09-08T06:46:48,874 !! 2025-09-08T06:46:48,874 check.warn(importable) 2025-09-08T06:46:48,874 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'limix_inference.lmm._slowlmm.test' is absent from the `packages` configuration. 2025-09-08T06:46:48,874 !! 2025-09-08T06:46:48,874 ******************************************************************************** 2025-09-08T06:46:48,874 ############################ 2025-09-08T06:46:48,874 # Package would be ignored # 2025-09-08T06:46:48,874 ############################ 2025-09-08T06:46:48,874 Python recognizes 'limix_inference.lmm._slowlmm.test' as an importable package[^1], 2025-09-08T06:46:48,875 but it is absent from setuptools' `packages` configuration. 2025-09-08T06:46:48,875 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T06:46:48,875 package, please make sure that 'limix_inference.lmm._slowlmm.test' is explicitly added 2025-09-08T06:46:48,875 to the `packages` configuration field. 2025-09-08T06:46:48,875 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T06:46:48,875 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T06:46:48,875 instead of `find_packages(...)`/`find:`). 2025-09-08T06:46:48,875 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T06:46:48,876 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T06:46:48,876 If you don't want 'limix_inference.lmm._slowlmm.test' to be distributed and are 2025-09-08T06:46:48,876 already explicitly excluding 'limix_inference.lmm._slowlmm.test' via 2025-09-08T06:46:48,876 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T06:46:48,876 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T06:46:48,876 combination with a more fine grained `package-data` configuration. 2025-09-08T06:46:48,876 You can read more about "package data files" on setuptools documentation page: 2025-09-08T06:46:48,876 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T06:46:48,877 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T06:46:48,877 even if it does not contain any `.py` files. 2025-09-08T06:46:48,877 On the other hand, currently there is no concept of package data 2025-09-08T06:46:48,877 directory, all directories are treated like packages. 2025-09-08T06:46:48,877 ******************************************************************************** 2025-09-08T06:46:48,877 !! 2025-09-08T06:46:48,877 check.warn(importable) 2025-09-08T06:46:48,877 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'limix_inference.mean.test' is absent from the `packages` configuration. 2025-09-08T06:46:48,878 !! 2025-09-08T06:46:48,878 ******************************************************************************** 2025-09-08T06:46:48,878 ############################ 2025-09-08T06:46:48,878 # Package would be ignored # 2025-09-08T06:46:48,878 ############################ 2025-09-08T06:46:48,878 Python recognizes 'limix_inference.mean.test' as an importable package[^1], 2025-09-08T06:46:48,878 but it is absent from setuptools' `packages` configuration. 2025-09-08T06:46:48,878 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T06:46:48,878 package, please make sure that 'limix_inference.mean.test' is explicitly added 2025-09-08T06:46:48,878 to the `packages` configuration field. 2025-09-08T06:46:48,879 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T06:46:48,879 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T06:46:48,879 instead of `find_packages(...)`/`find:`). 2025-09-08T06:46:48,879 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T06:46:48,879 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T06:46:48,879 If you don't want 'limix_inference.mean.test' to be distributed and are 2025-09-08T06:46:48,879 already explicitly excluding 'limix_inference.mean.test' via 2025-09-08T06:46:48,880 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T06:46:48,880 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T06:46:48,880 combination with a more fine grained `package-data` configuration. 2025-09-08T06:46:48,880 You can read more about "package data files" on setuptools documentation page: 2025-09-08T06:46:48,880 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T06:46:48,880 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T06:46:48,881 even if it does not contain any `.py` files. 2025-09-08T06:46:48,881 On the other hand, currently there is no concept of package data 2025-09-08T06:46:48,881 directory, all directories are treated like packages. 2025-09-08T06:46:48,881 ******************************************************************************** 2025-09-08T06:46:48,881 !! 2025-09-08T06:46:48,881 check.warn(importable) 2025-09-08T06:46:48,881 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'limix_inference.random.test' is absent from the `packages` configuration. 2025-09-08T06:46:48,881 !! 2025-09-08T06:46:48,881 ******************************************************************************** 2025-09-08T06:46:48,882 ############################ 2025-09-08T06:46:48,882 # Package would be ignored # 2025-09-08T06:46:48,882 ############################ 2025-09-08T06:46:48,882 Python recognizes 'limix_inference.random.test' as an importable package[^1], 2025-09-08T06:46:48,882 but it is absent from setuptools' `packages` configuration. 2025-09-08T06:46:48,882 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T06:46:48,882 package, please make sure that 'limix_inference.random.test' is explicitly added 2025-09-08T06:46:48,882 to the `packages` configuration field. 2025-09-08T06:46:48,882 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T06:46:48,882 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T06:46:48,883 instead of `find_packages(...)`/`find:`). 2025-09-08T06:46:48,883 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T06:46:48,883 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T06:46:48,883 If you don't want 'limix_inference.random.test' to be distributed and are 2025-09-08T06:46:48,883 already explicitly excluding 'limix_inference.random.test' via 2025-09-08T06:46:48,883 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T06:46:48,883 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T06:46:48,883 combination with a more fine grained `package-data` configuration. 2025-09-08T06:46:48,884 You can read more about "package data files" on setuptools documentation page: 2025-09-08T06:46:48,884 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T06:46:48,884 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T06:46:48,884 even if it does not contain any `.py` files. 2025-09-08T06:46:48,884 On the other hand, currently there is no concept of package data 2025-09-08T06:46:48,884 directory, all directories are treated like packages. 2025-09-08T06:46:48,885 ******************************************************************************** 2025-09-08T06:46:48,885 !! 2025-09-08T06:46:48,885 check.warn(importable) 2025-09-08T06:46:48,885 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'limix_inference.test' is absent from the `packages` configuration. 2025-09-08T06:46:48,885 !! 2025-09-08T06:46:48,885 ******************************************************************************** 2025-09-08T06:46:48,885 ############################ 2025-09-08T06:46:48,885 # Package would be ignored # 2025-09-08T06:46:48,885 ############################ 2025-09-08T06:46:48,886 Python recognizes 'limix_inference.test' as an importable package[^1], 2025-09-08T06:46:48,886 but it is absent from setuptools' `packages` configuration. 2025-09-08T06:46:48,886 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T06:46:48,886 package, please make sure that 'limix_inference.test' is explicitly added 2025-09-08T06:46:48,886 to the `packages` configuration field. 2025-09-08T06:46:48,886 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T06:46:48,886 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T06:46:48,886 instead of `find_packages(...)`/`find:`). 2025-09-08T06:46:48,887 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T06:46:48,887 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T06:46:48,887 If you don't want 'limix_inference.test' to be distributed and are 2025-09-08T06:46:48,887 already explicitly excluding 'limix_inference.test' via 2025-09-08T06:46:48,887 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T06:46:48,887 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T06:46:48,887 combination with a more fine grained `package-data` configuration. 2025-09-08T06:46:48,887 You can read more about "package data files" on setuptools documentation page: 2025-09-08T06:46:48,888 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T06:46:48,888 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T06:46:48,888 even if it does not contain any `.py` files. 2025-09-08T06:46:48,888 On the other hand, currently there is no concept of package data 2025-09-08T06:46:48,888 directory, all directories are treated like packages. 2025-09-08T06:46:48,888 ******************************************************************************** 2025-09-08T06:46:48,888 !! 2025-09-08T06:46:48,888 check.warn(importable) 2025-09-08T06:46:48,889 creating build/lib.linux-armv7l-cpython-313/limix_inference/test 2025-09-08T06:46:48,889 copying limix_inference/test/test_liknorm.py -> build/lib.linux-armv7l-cpython-313/limix_inference/test 2025-09-08T06:46:48,889 creating build/lib.linux-armv7l-cpython-313/limix_inference/mean/test 2025-09-08T06:46:48,889 copying limix_inference/mean/test/test_linear_mean.py -> build/lib.linux-armv7l-cpython-313/limix_inference/mean/test 2025-09-08T06:46:48,889 copying limix_inference/mean/test/test_offset.py -> build/lib.linux-armv7l-cpython-313/limix_inference/mean/test 2025-09-08T06:46:48,889 creating build/lib.linux-armv7l-cpython-313/limix_inference/random/test 2025-09-08T06:46:48,889 copying limix_inference/random/test/test_sampling.py -> build/lib.linux-armv7l-cpython-313/limix_inference/random/test 2025-09-08T06:46:48,889 creating build/lib.linux-armv7l-cpython-313/limix_inference/link/test 2025-09-08T06:46:48,889 copying limix_inference/link/test/test_link.py -> build/lib.linux-armv7l-cpython-313/limix_inference/link/test 2025-09-08T06:46:48,890 creating build/lib.linux-armv7l-cpython-313/limix_inference/cov/test 2025-09-08T06:46:48,890 copying limix_inference/cov/test/test_eye_cov.py -> build/lib.linux-armv7l-cpython-313/limix_inference/cov/test 2025-09-08T06:46:48,890 copying limix_inference/cov/test/test_linear_cov.py -> build/lib.linux-armv7l-cpython-313/limix_inference/cov/test 2025-09-08T06:46:48,890 copying limix_inference/cov/test/test_sum_cov.py -> build/lib.linux-armv7l-cpython-313/limix_inference/cov/test 2025-09-08T06:46:48,890 creating build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_fastlmm/test 2025-09-08T06:46:48,890 copying limix_inference/lmm/_fastlmm/test/test_fastlmm.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_fastlmm/test 2025-09-08T06:46:48,890 creating build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_slowlmm/test 2025-09-08T06:46:48,890 copying limix_inference/lmm/_slowlmm/test/test_slowlmm.py -> build/lib.linux-armv7l-cpython-313/limix_inference/lmm/_slowlmm/test 2025-09-08T06:46:48,890 creating build/lib.linux-armv7l-cpython-313/limix_inference/glmm/_ep/test 2025-09-08T06:46:48,890 copying limix_inference/glmm/_ep/test/test_bernoulli.py -> build/lib.linux-armv7l-cpython-313/limix_inference/glmm/_ep/test 2025-09-08T06:46:48,891 copying limix_inference/glmm/_ep/test/test_binomial.py -> build/lib.linux-armv7l-cpython-313/limix_inference/glmm/_ep/test 2025-09-08T06:46:48,891 copying limix_inference/glmm/_ep/test/test_poisson.py -> build/lib.linux-armv7l-cpython-313/limix_inference/glmm/_ep/test 2025-09-08T06:46:48,891 running build_ext 2025-09-08T06:46:48,891 generating cffi module 'build/temp.linux-armv7l-cpython-313/limix_inference.liknorm._ffi.c' 2025-09-08T06:46:48,891 creating build/temp.linux-armv7l-cpython-313 2025-09-08T06:46:49,202 building 'limix_inference.liknorm._ffi' extension 2025-09-08T06:46:49,203 creating build/temp.linux-armv7l-cpython-313/build/temp.linux-armv7l-cpython-313 2025-09-08T06:46:49,203 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include -I/usr/include/python3.13 -c build/temp.linux-armv7l-cpython-313/limix_inference.liknorm._ffi.c -o build/temp.linux-armv7l-cpython-313/build/temp.linux-armv7l-cpython-313/limix_inference.liknorm._ffi.o 2025-09-08T06:46:49,474 build/temp.linux-armv7l-cpython-313/limix_inference.liknorm._ffi.c:574:14: fatal error: liknorm/liknorm.h: No such file or directory 2025-09-08T06:46:49,474 574 | #include "liknorm/liknorm.h" 2025-09-08T06:46:49,474 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T06:46:49,474 compilation terminated. 2025-09-08T06:46:49,477 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T06:46:49,637 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T06:46:49,648 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T06:46:49,648 exec(compile('"'"''"'"''"'"' 2025-09-08T06:46:49,648 # This is -- a caller that pip uses to run setup.py 2025-09-08T06:46:49,648 # 2025-09-08T06:46:49,648 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T06:46:49,648 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T06:46:49,648 # - It provides a clear error message when setuptools is not installed. 2025-09-08T06:46:49,648 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T06:46:49,648 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T06:46:49,648 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T06:46:49,648 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T06:46:49,648 import os, sys, tokenize, traceback 2025-09-08T06:46:49,648 2025-09-08T06:46:49,648 try: 2025-09-08T06:46:49,648 import setuptools 2025-09-08T06:46:49,648 except ImportError: 2025-09-08T06:46:49,648 print( 2025-09-08T06:46:49,648 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T06:46:49,648 "the build environment with exception:", 2025-09-08T06:46:49,648 file=sys.stderr, 2025-09-08T06:46:49,648 ) 2025-09-08T06:46:49,648 traceback.print_exc() 2025-09-08T06:46:49,648 sys.exit(1) 2025-09-08T06:46:49,648 2025-09-08T06:46:49,648 __file__ = %r 2025-09-08T06:46:49,648 sys.argv[0] = __file__ 2025-09-08T06:46:49,648 2025-09-08T06:46:49,648 if os.path.exists(__file__): 2025-09-08T06:46:49,648 filename = __file__ 2025-09-08T06:46:49,648 with tokenize.open(__file__) as f: 2025-09-08T06:46:49,648 setup_py_code = f.read() 2025-09-08T06:46:49,648 else: 2025-09-08T06:46:49,648 filename = "" 2025-09-08T06:46:49,648 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T06:46:49,648 2025-09-08T06:46:49,648 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T06:46:49,648 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-7dh5ohhe/limix-inference_5b6de6d09e9e4c0da53d49572765410b/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-5btm_97i[/] 2025-09-08T06:46:49,649 [bold magenta]cwd[/]: /tmp/pip-wheel-7dh5ohhe/limix-inference_5b6de6d09e9e4c0da53d49572765410b/ 2025-09-08T06:46:49,649 Building wheel for limix-inference (setup.py): finished with status 'error' 2025-09-08T06:46:49,649 ERROR: Failed building wheel for limix-inference 2025-09-08T06:46:49,650 Running setup.py clean for limix-inference 2025-09-08T06:46:49,651 Running command python setup.py clean 2025-09-08T06:46:50,650 /usr/local/lib/python3.13/dist-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2025-09-08T06:46:50,650 !! 2025-09-08T06:46:50,650 ******************************************************************************** 2025-09-08T06:46:50,650 Requirements should be satisfied by a PEP 517 installer. 2025-09-08T06:46:50,650 If you are using pip, you can try `pip install --use-pep517`. 2025-09-08T06:46:50,651 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-08T06:46:50,651 or your builds will no longer be supported. 2025-09-08T06:46:50,651 ******************************************************************************** 2025-09-08T06:46:50,651 !! 2025-09-08T06:46:50,651 dist.fetch_build_eggs(dist.setup_requires) 2025-09-08T06:46:50,750 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2025-09-08T06:46:50,750 warnings.warn(msg) 2025-09-08T06:46:51,220 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T06:46:51,220 !! 2025-09-08T06:46:51,221 ******************************************************************************** 2025-09-08T06:46:51,221 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T06:46:51,221 License :: OSI Approved :: MIT License 2025-09-08T06:46:51,221 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T06:46:51,221 ******************************************************************************** 2025-09-08T06:46:51,221 !! 2025-09-08T06:46:51,221 self._finalize_license_expression() 2025-09-08T06:46:51,295 running clean 2025-09-08T06:46:51,438 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T06:46:51,438 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T06:46:51,441 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T06:46:51,441 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T06:46:51,441 removing 'build' 2025-09-08T06:46:51,566 Failed to build limix-inference 2025-09-08T06:46:51,566 ERROR: Failed to build one or more wheels 2025-09-08T06:46:51,567 Exception information: 2025-09-08T06:46:51,567 Traceback (most recent call last): 2025-09-08T06:46:51,567 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T06:46:51,567 status = _inner_run() 2025-09-08T06:46:51,567 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T06:46:51,567 return self.run(options, args) 2025-09-08T06:46:51,567 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T06:46:51,567 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T06:46:51,567 return func(self, options, args) 2025-09-08T06:46:51,567 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T06:46:51,567 raise CommandError("Failed to build one or more wheels") 2025-09-08T06:46:51,567 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T06:46:51,572 Removed build tracker: '/tmp/pip-build-tracker-28w_illp'