2025-09-09T19:06:11,351 Created temporary directory: /tmp/pip-build-tracker-lhcgeuz5
2025-09-09T19:06:11,353 Initialized build tracking at /tmp/pip-build-tracker-lhcgeuz5
2025-09-09T19:06:11,354 Created build tracker: /tmp/pip-build-tracker-lhcgeuz5
2025-09-09T19:06:11,354 Entered build tracker: /tmp/pip-build-tracker-lhcgeuz5
2025-09-09T19:06:11,355 Created temporary directory: /tmp/pip-wheel-r5vbzsik
2025-09-09T19:06:11,365 Created temporary directory: /tmp/pip-ephem-wheel-cache-61w9mvbw
2025-09-09T19:06:11,523 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-09-09T19:06:11,530 2 location(s) to search for versions of pyckmeans:
2025-09-09T19:06:11,530 * https://pypi.org/simple/pyckmeans/
2025-09-09T19:06:11,530 * https://www.piwheels.org/simple/pyckmeans/
2025-09-09T19:06:11,531 Fetching project page and analyzing links: https://pypi.org/simple/pyckmeans/
2025-09-09T19:06:11,532 Getting page https://pypi.org/simple/pyckmeans/
2025-09-09T19:06:11,536 Found index url https://pypi.org/simple/
2025-09-09T19:06:11,708 Fetched page https://pypi.org/simple/pyckmeans/ as application/vnd.pypi.simple.v1+json
2025-09-09T19:06:11,744   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/b9/de/b88d7cf79a79413b55544b2518298d141dc0ed1eb523c9ad11a36138e898/pyckmeans-0.4.0-cp36-cp36m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,745   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/57/d5/5da769497ad168ee6529d7694269c441b3ab416b92bb9f41256be2d26b43/pyckmeans-0.4.0-cp37-cp37m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,746   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/d8/05/6aa2b5a06f19176e9207ebd22ce4d4a6667a8c606fd49dc1eba29afd8e0e/pyckmeans-0.4.0-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,746   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/28/62/743350f8f49afc793a2e91ab4523a7445ff6fa24bd2048197179df2e99de/pyckmeans-0.4.0-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,748   Found link https://files.pythonhosted.org/packages/78/97/a48f8178873dcdcdab83fbcc419e3c80ebd8cc7128b24bc16c5b6294e9c0/pyckmeans-0.4.0.tar.gz (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6), version: 0.4.0
2025-09-09T19:06:11,749   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/83/f7/9bef4342f20a1bad591d43bfe81132594cb3c2a970194243dac4f4aac2c2/pyckmeans-0.5.0-cp36-cp36m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,750   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/b6/63/6d4ec459f0fe9a3701e34f8c1d0a7508691f9a11b626fb619e7f7ace2b0d/pyckmeans-0.5.0-cp37-cp37m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,750   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/29/96/022e5cd2da35200b47f4eb6be702b6c9ebe565056b2e3282caca13c46d71/pyckmeans-0.5.0-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,751   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/78/e2/0cd85235fadff92995027121701789d834648654346d146dae672a0d88a7/pyckmeans-0.5.0-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,752   Found link https://files.pythonhosted.org/packages/09/52/c44e7ae21dedb7303be86860b235681d8920546c43350be71c82557f5dba/pyckmeans-0.5.0.tar.gz (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6), version: 0.5.0
2025-09-09T19:06:11,753   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/4d/04/08d7d11b806b9864c51111a0d33619c0ae431dd73968bdf3f9a237c6d0d7/pyckmeans-0.6.0-cp36-cp36m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,754   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/31/32/553ccffbd908bb6842ff8c932756b418698042e1c94eaf38100fbdf3dd96/pyckmeans-0.6.0-cp37-cp37m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,755   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/ef/ce/5d6de11a933c49b3c2e485b28e4ae91ec65bdb30d9d809bd68b289a55e1c/pyckmeans-0.6.0-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,755   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/b5/a8/04c6c8ddc29443c8052a2578592fd54ae63aa8b7c7675bd1dcf9bab5c325/pyckmeans-0.6.0-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,756   Found link https://files.pythonhosted.org/packages/66/4a/274ddf2960f9a60d24ce2e4647ded134b72f91148b0005d412e48df4b8b1/pyckmeans-0.6.0.tar.gz (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6), version: 0.6.0
2025-09-09T19:06:11,757   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/a0/a3/3382a47bc2a9a8bf779a9b55326d55f5a068043eb32b9b77aea7b7f2f260/pyckmeans-0.6.1-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,758   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/96/f9/d0c5cd3d2c23f4eda290c14c6c0e5aefd46f58a80f8cca602af70a3fd767/pyckmeans-0.6.1-cp36-cp36m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,758   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/ef/a0/3bfe70379e9897e7a19758d6b1179af010b8501050db6574e701916a1d90/pyckmeans-0.6.1-cp37-cp37m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,759   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/09/3f/5f920b3406eff6893dad0b2be11a827064f484c744e8b6c261a9fe56e086/pyckmeans-0.6.1-cp37-cp37m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,760   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/ce/56/a8bafed96f0be6e2af64501801f387a5fc26127170f99152c1ab2bc9c211/pyckmeans-0.6.1-cp38-cp38-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,760   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/57/56/6760810822af255d2cd9763177543695a88b0f9dc042bde9407c38533e07/pyckmeans-0.6.1-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,761   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/43/26/b8e716fcb2a96010fd04061ab2787efd32ec99314339344e070db0bf4ac1/pyckmeans-0.6.1-cp39-cp39-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,762   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/b5/ab/7027ee76e52a46028817e8965ca6ec671f063b1fea95764a0acfbf0d7596/pyckmeans-0.6.1-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,763   Found link https://files.pythonhosted.org/packages/6a/d6/406f57ed2c6e4b627e7d00a9204712c59ed91d60f621d4bd490ce53958f3/pyckmeans-0.6.1.tar.gz (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6), version: 0.6.1
2025-09-09T19:06:11,764   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/c7/3b/2b24acaf264211fb13af47443f05dc9f17402e9eb16458161fa03fa65c82/pyckmeans-0.8.0-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,764   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/fe/00/b14a57cec4da2fccffad89c2c9d1909c76b8ba7aaba31b9b81e0cebbfe46/pyckmeans-0.8.0-cp36-cp36m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,765   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/e2/21/0962e892ef24ef9b86872033d2d18d072bd6782b674b7d1386c7215c384a/pyckmeans-0.8.0-cp37-cp37m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,767   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/ce/e5/4c3a9ac1e68afd848f4fa9a8264b8db583a98142fe1c4acd28935b156bfc/pyckmeans-0.8.0-cp37-cp37m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,767   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/c4/b8/250a329203c4017c83e3b99dfcb8ecc6ce7c97c6100973914c7881d43ae6/pyckmeans-0.8.0-cp38-cp38-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,768   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/be/a8/65a40e13b7b860dc7df7937b365cc70259e700fe83500808df8b919d1eba/pyckmeans-0.8.0-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,769   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/81/10/86a16f70893eb1cf303fe66b36e7a957824f1124a77ffa0ffc6b7228120e/pyckmeans-0.8.0-cp39-cp39-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,770   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/ba/82/cc2fe56f2fcb73ad57ecdff17bc79974db79d1a4bbfedfe1416782346761/pyckmeans-0.8.0-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,771   Found link https://files.pythonhosted.org/packages/fe/48/2b6e70758277599b2316f4fe42caacda43aa5d8e331d526d64e32adc119f/pyckmeans-0.8.0.tar.gz (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6), version: 0.8.0
2025-09-09T19:06:11,772   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/eb/42/91be076e635ad4b4021f22e65ecab8debfa766f55acda8dd0ce15081fab1/pyckmeans-0.8.1-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,773   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/5b/55/085d7b4872458e47063137126d0235d2fa6764f9b871fdafbdb21e232f3d/pyckmeans-0.8.1-cp36-cp36m-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,775   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/4a/cc/07ad2b5b03c4e69418cd4301aaa4a65a5483b52d167edaf76e5e9f904746/pyckmeans-0.8.1-cp37-cp37m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
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2025-09-09T19:06:11,777   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/4c/a2/09f4fd2a0365aea5e1a983ddbe270e75a178063e747057766005cf1e073b/pyckmeans-0.8.1-cp38-cp38-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:11,778   Skipping link: No binaries permitted for pyckmeans: https://files.pythonhosted.org/packages/9a/ea/05e022686680d17c217a950ae8e92202fd165f7ec64235a5659bb7cf96b1/pyckmeans-0.8.1-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/pyckmeans/) (requires-python:>=3.6)
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2025-09-09T19:06:12,052   Skipping link: No binaries permitted for pyckmeans: https://archive1.piwheels.org/simple/pyckmeans/pyckmeans-0.4.0-cp311-cp311-linux_armv6l.whl#sha256=8c9f8d52d596b22328726ae44433c3ac78b42c98885711457fc27390b49e2965 (from https://www.piwheels.org/simple/pyckmeans/) (requires-python:>=3.6)
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2025-09-09T19:06:12,056   Skipping link: No binaries permitted for pyckmeans: https://www.piwheels.org/simple/pyckmeans/pyckmeans-0.4.0-cp313-cp313-linux_armv6l.whl#sha256=cc15bbd2e79e8d5b79d55cb7e36cc78421bb2cf914e95523938ae8f334a8bed5 (from https://www.piwheels.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:12,056   Skipping link: No binaries permitted for pyckmeans: https://www.piwheels.org/simple/pyckmeans/pyckmeans-0.4.0-cp313-cp313-linux_armv7l.whl#sha256=cc15bbd2e79e8d5b79d55cb7e36cc78421bb2cf914e95523938ae8f334a8bed5 (from https://www.piwheels.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:06:12,057 Skipping link: not a file: https://www.piwheels.org/simple/pyckmeans/
2025-09-09T19:06:12,058 Skipping link: not a file: https://pypi.org/simple/pyckmeans/
2025-09-09T19:06:12,120 Given no hashes to check 1 links for project 'pyckmeans': discarding no candidates
2025-09-09T19:06:12,124 Collecting pyckmeans==0.5.0
2025-09-09T19:06:12,127   Created temporary directory: /tmp/pip-unpack-vhujhggf
2025-09-09T19:06:12,363   Downloading pyckmeans-0.5.0.tar.gz (52 kB)
2025-09-09T19:06:12,559   Added pyckmeans==0.5.0 from https://files.pythonhosted.org/packages/09/52/c44e7ae21dedb7303be86860b235681d8920546c43350be71c82557f5dba/pyckmeans-0.5.0.tar.gz to build tracker '/tmp/pip-build-tracker-lhcgeuz5'
2025-09-09T19:06:12,564   Running setup.py (path:/tmp/pip-wheel-r5vbzsik/pyckmeans_aba7705a7b1444c38584990422f007c4/setup.py) egg_info for package pyckmeans
2025-09-09T19:06:12,565   Created temporary directory: /tmp/pip-pip-egg-info-x4fpjoag
2025-09-09T19:06:12,565   Preparing metadata (setup.py): started
2025-09-09T19:06:12,568   Running command python setup.py egg_info
2025-09-09T19:06:15,700   running egg_info
2025-09-09T19:06:15,981   creating /tmp/pip-pip-egg-info-x4fpjoag/pyckmeans.egg-info
2025-09-09T19:06:15,982   writing /tmp/pip-pip-egg-info-x4fpjoag/pyckmeans.egg-info/PKG-INFO
2025-09-09T19:06:15,985   writing dependency_links to /tmp/pip-pip-egg-info-x4fpjoag/pyckmeans.egg-info/dependency_links.txt
2025-09-09T19:06:15,987   writing requirements to /tmp/pip-pip-egg-info-x4fpjoag/pyckmeans.egg-info/requires.txt
2025-09-09T19:06:15,988   writing top-level names to /tmp/pip-pip-egg-info-x4fpjoag/pyckmeans.egg-info/top_level.txt
2025-09-09T19:06:15,989   writing manifest file '/tmp/pip-pip-egg-info-x4fpjoag/pyckmeans.egg-info/SOURCES.txt'
2025-09-09T19:06:16,857   reading manifest file '/tmp/pip-pip-egg-info-x4fpjoag/pyckmeans.egg-info/SOURCES.txt'
2025-09-09T19:06:16,859   adding license file 'LICENSE'
2025-09-09T19:06:16,865   writing manifest file '/tmp/pip-pip-egg-info-x4fpjoag/pyckmeans.egg-info/SOURCES.txt'
2025-09-09T19:06:17,103   Preparing metadata (setup.py): finished with status 'done'
2025-09-09T19:06:17,116   Source in /tmp/pip-wheel-r5vbzsik/pyckmeans_aba7705a7b1444c38584990422f007c4 has version 0.5.0, which satisfies requirement pyckmeans==0.5.0 from https://files.pythonhosted.org/packages/09/52/c44e7ae21dedb7303be86860b235681d8920546c43350be71c82557f5dba/pyckmeans-0.5.0.tar.gz
2025-09-09T19:06:17,117   Removed pyckmeans==0.5.0 from https://files.pythonhosted.org/packages/09/52/c44e7ae21dedb7303be86860b235681d8920546c43350be71c82557f5dba/pyckmeans-0.5.0.tar.gz from build tracker '/tmp/pip-build-tracker-lhcgeuz5'
2025-09-09T19:06:17,134 Created temporary directory: /tmp/pip-unpack-hhg_u9xu
2025-09-09T19:06:17,135 Created temporary directory: /tmp/pip-unpack-qjqa1vee
2025-09-09T19:06:17,136 Building wheels for collected packages: pyckmeans
2025-09-09T19:06:17,140   Created temporary directory: /tmp/pip-wheel-0ft7m_d5
2025-09-09T19:06:17,142   DEPRECATION: Building 'pyckmeans' 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 'pyckmeans'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-09-09T19:06:17,145   Building wheel for pyckmeans (setup.py): started
2025-09-09T19:06:17,148   Destination directory: /tmp/pip-wheel-0ft7m_d5
2025-09-09T19:06:17,148   Running command python setup.py bdist_wheel
2025-09-09T19:06:19,889   running bdist_wheel
2025-09-09T19:06:21,014   running build
2025-09-09T19:06:21,015   running build_py
2025-09-09T19:06:21,304   creating build/lib.linux-armv7l-cpython-313/pyckmeans
2025-09-09T19:06:21,305   copying pyckmeans/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans
2025-09-09T19:06:21,307   creating build/lib.linux-armv7l-cpython-313/pyckmeans/utils
2025-09-09T19:06:21,308   copying pyckmeans/utils/progressbar.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/utils
2025-09-09T19:06:21,310   copying pyckmeans/utils/plotting.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/utils
2025-09-09T19:06:21,312   copying pyckmeans/utils/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/utils
2025-09-09T19:06:21,314   creating build/lib.linux-armv7l-cpython-313/pyckmeans/ordination
2025-09-09T19:06:21,315   copying pyckmeans/ordination/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/ordination
2025-09-09T19:06:21,318   creating build/lib.linux-armv7l-cpython-313/pyckmeans/ordering
2025-09-09T19:06:21,319   copying pyckmeans/ordering/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/ordering
2025-09-09T19:06:21,321   creating build/lib.linux-armv7l-cpython-313/pyckmeans/knee
2025-09-09T19:06:21,323   copying pyckmeans/knee/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/knee
2025-09-09T19:06:21,324   creating build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:06:21,325   copying pyckmeans/io/phylip.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:06:21,327   copying pyckmeans/io/nucleotide_alignment.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:06:21,329   copying pyckmeans/io/fasta.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:06:21,330   copying pyckmeans/io/csv.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:06:21,332   copying pyckmeans/io/c_interop.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:06:21,334   copying pyckmeans/io/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:06:21,336   creating build/lib.linux-armv7l-cpython-313/pyckmeans/distance
2025-09-09T19:06:21,337   copying pyckmeans/distance/c_interop.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/distance
2025-09-09T19:06:21,339   copying pyckmeans/distance/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/distance
2025-09-09T19:06:21,341   creating build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:06:21,343   copying pyckmeans/core/wecr.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:06:21,344   copying pyckmeans/core/multickmeans.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:06:21,346   copying pyckmeans/core/ckmeans.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:06:21,348   copying pyckmeans/core/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:06:21,362   running build_ext
2025-09-09T19:06:21,377   building 'pyckmeans.distance.lib.distance' extension
2025-09-09T19:06:21,379   creating build/temp.linux-armv7l-cpython-313/pyckmeans/distance/src
2025-09-09T19:06:21,380   arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/python3.13 -c pyckmeans/distance/src/distance.cpp -o build/temp.linux-armv7l-cpython-313/pyckmeans/distance/src/distance.o
2025-09-09T19:06:25,446   pyckmeans/distance/src/distance.cpp: In function ‘std::vector<bool> completeDeletionSites(uint8_t*, int, int)’:
2025-09-09T19:06:25,447   pyckmeans/distance/src/distance.cpp:107:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,447     107 |     for (size_t i = 0; i < m; ++i) {
2025-09-09T19:06:25,448         |                        ~~^~~
2025-09-09T19:06:25,448   pyckmeans/distance/src/distance.cpp:109:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,449     109 |         for (size_t j = 0; j < n; ++j) {
2025-09-09T19:06:25,449         |                            ~~^~~
2025-09-09T19:06:25,453   pyckmeans/distance/src/distance.cpp: In function ‘void pDistance(uint8_t*, int, int, bool, double*)’:
2025-09-09T19:06:25,453   pyckmeans/distance/src/distance.cpp:133:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,454     133 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2025-09-09T19:06:25,455         |                              ~~~~^~~~~~~~~
2025-09-09T19:06:25,455   pyckmeans/distance/src/distance.cpp:134:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,456     134 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2025-09-09T19:06:25,456         |                                          ~~~~^~~
2025-09-09T19:06:25,457   pyckmeans/distance/src/distance.cpp:138:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,458     138 |                 for (size_t j = 0; j < m; ++j) {
2025-09-09T19:06:25,458         |                                    ~~^~~
2025-09-09T19:06:25,459   pyckmeans/distance/src/distance.cpp:163:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,459     163 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2025-09-09T19:06:25,460         |                              ~~~~^~~~~~~~~
2025-09-09T19:06:25,461   pyckmeans/distance/src/distance.cpp:164:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,461     164 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2025-09-09T19:06:25,462         |                                          ~~~~^~~
2025-09-09T19:06:25,462   pyckmeans/distance/src/distance.cpp:168:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,463     168 |                 for (size_t j = 0; j < m; ++j) {
2025-09-09T19:06:25,464         |                                    ~~^~~
2025-09-09T19:06:25,464   pyckmeans/distance/src/distance.cpp: In function ‘void jcDistance(uint8_t*, int, int, bool, double*)’:
2025-09-09T19:06:25,465   pyckmeans/distance/src/distance.cpp:202:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,465     202 |     for (size_t i = 0; i < n; ++i) {
2025-09-09T19:06:25,466         |                        ~~^~~
2025-09-09T19:06:25,467   pyckmeans/distance/src/distance.cpp:203:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,467     203 |         for (size_t j = 0; j < n; ++j) {
2025-09-09T19:06:25,468         |                            ~~^~~
2025-09-09T19:06:25,468   pyckmeans/distance/src/distance.cpp: In function ‘void k2pDistance(uint8_t*, int, int, bool, double*)’:
2025-09-09T19:06:25,469   pyckmeans/distance/src/distance.cpp:221:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,469     221 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2025-09-09T19:06:25,470         |                              ~~~~^~~~~~~~~
2025-09-09T19:06:25,471   pyckmeans/distance/src/distance.cpp:222:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,471     222 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2025-09-09T19:06:25,472         |                                          ~~~~^~~
2025-09-09T19:06:25,472   pyckmeans/distance/src/distance.cpp:227:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,473     227 |                 for (size_t j = 0; j < m; ++j) {
2025-09-09T19:06:25,474         |                                    ~~^~~
2025-09-09T19:06:25,474   pyckmeans/distance/src/distance.cpp:263:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,475     263 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2025-09-09T19:06:25,475         |                              ~~~~^~~~~~~~~
2025-09-09T19:06:25,476   pyckmeans/distance/src/distance.cpp:264:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,477     264 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2025-09-09T19:06:25,477         |                                          ~~~~^~~
2025-09-09T19:06:25,478   pyckmeans/distance/src/distance.cpp:269:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:25,479     269 |                 for (size_t j = 0; j < m; ++j) {
2025-09-09T19:06:25,479         |                                    ~~^~~
2025-09-09T19:06:27,619   creating build/lib.linux-armv7l-cpython-313/pyckmeans/distance/lib
2025-09-09T19:06:27,620   arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/pyckmeans/distance/src/distance.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/pyckmeans/distance/lib/distance.so
2025-09-09T19:06:28,176   building 'pyckmeans.io.lib.nucencode' extension
2025-09-09T19:06:28,178   creating build/temp.linux-armv7l-cpython-313/pyckmeans/io/src
2025-09-09T19:06:28,179   arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/include/python3.13 -c pyckmeans/io/src/nucencode.cpp -o build/temp.linux-armv7l-cpython-313/pyckmeans/io/src/nucencode.o
2025-09-09T19:06:28,325   pyckmeans/io/src/nucencode.cpp: In function ‘void encodeNucleotides(uint8_t*, int, int)’:
2025-09-09T19:06:28,326   pyckmeans/io/src/nucencode.cpp:73:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:28,326      73 |     for (size_t i = 0; i < n; i++) {
2025-09-09T19:06:28,327         |                        ~~^~~
2025-09-09T19:06:28,328   pyckmeans/io/src/nucencode.cpp:74:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:28,328      74 |         for (size_t j = 0; j < m; j++) {
2025-09-09T19:06:28,329         |                            ~~^~~
2025-09-09T19:06:28,329   pyckmeans/io/src/nucencode.cpp: In function ‘void encodeNucleotides_uint32(uint32_t*, int, int, uint8_t*)’:
2025-09-09T19:06:28,330   pyckmeans/io/src/nucencode.cpp:86:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:28,330      86 |     for (size_t i = 0; i < n; i++) {
2025-09-09T19:06:28,331         |                        ~~^~~
2025-09-09T19:06:28,331   pyckmeans/io/src/nucencode.cpp:87:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:06:28,332      87 |         for (size_t j = 0; j < m; j++) {
2025-09-09T19:06:28,333         |                            ~~^~~
2025-09-09T19:06:28,525   creating build/lib.linux-armv7l-cpython-313/pyckmeans/io/lib
2025-09-09T19:06:28,526   arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/pyckmeans/io/src/nucencode.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/pyckmeans/io/lib/nucencode.so
2025-09-09T19:06:29,068   /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-09-09T19:06:29,068   !!

2025-09-09T19:06:29,069           ********************************************************************************
2025-09-09T19:06:29,070           Please avoid running ``setup.py`` directly.
2025-09-09T19:06:29,070           Instead, use pypa/build, pypa/installer or other
2025-09-09T19:06:29,070           standards-based tools.

2025-09-09T19:06:29,071           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-09-09T19:06:29,071           or your builds will no longer be supported.

2025-09-09T19:06:29,072           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-09-09T19:06:29,073           ********************************************************************************

2025-09-09T19:06:29,074   !!
2025-09-09T19:06:29,074     self.initialize_options()
2025-09-09T19:06:29,350   installing to build/bdist.linux-armv7l/wheel
2025-09-09T19:06:29,350   running install
2025-09-09T19:06:29,381   running install_lib
2025-09-09T19:06:29,663   creating build/bdist.linux-armv7l/wheel
2025-09-09T19:06:29,665   creating build/bdist.linux-armv7l/wheel/pyckmeans
2025-09-09T19:06:29,667   creating build/bdist.linux-armv7l/wheel/pyckmeans/core
2025-09-09T19:06:29,667   copying build/lib.linux-armv7l-cpython-313/pyckmeans/core/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/core
2025-09-09T19:06:29,669   copying build/lib.linux-armv7l-cpython-313/pyckmeans/core/ckmeans.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/core
2025-09-09T19:06:29,670   copying build/lib.linux-armv7l-cpython-313/pyckmeans/core/multickmeans.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/core
2025-09-09T19:06:29,671   copying build/lib.linux-armv7l-cpython-313/pyckmeans/core/wecr.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/core
2025-09-09T19:06:29,673   creating build/bdist.linux-armv7l/wheel/pyckmeans/distance
2025-09-09T19:06:29,675   creating build/bdist.linux-armv7l/wheel/pyckmeans/distance/lib
2025-09-09T19:06:29,676   copying build/lib.linux-armv7l-cpython-313/pyckmeans/distance/lib/distance.so -> build/bdist.linux-armv7l/wheel/./pyckmeans/distance/lib
2025-09-09T19:06:29,678   copying build/lib.linux-armv7l-cpython-313/pyckmeans/distance/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/distance
2025-09-09T19:06:29,679   copying build/lib.linux-armv7l-cpython-313/pyckmeans/distance/c_interop.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/distance
2025-09-09T19:06:29,681   creating build/bdist.linux-armv7l/wheel/pyckmeans/io
2025-09-09T19:06:29,682   creating build/bdist.linux-armv7l/wheel/pyckmeans/io/lib
2025-09-09T19:06:29,683   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/lib/nucencode.so -> build/bdist.linux-armv7l/wheel/./pyckmeans/io/lib
2025-09-09T19:06:29,685   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:06:29,686   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/c_interop.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:06:29,688   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/csv.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:06:29,689   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/fasta.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:06:29,690   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/nucleotide_alignment.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:06:29,691   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/phylip.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:06:29,693   creating build/bdist.linux-armv7l/wheel/pyckmeans/knee
2025-09-09T19:06:29,694   copying build/lib.linux-armv7l-cpython-313/pyckmeans/knee/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/knee
2025-09-09T19:06:29,696   creating build/bdist.linux-armv7l/wheel/pyckmeans/ordering
2025-09-09T19:06:29,697   copying build/lib.linux-armv7l-cpython-313/pyckmeans/ordering/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/ordering
2025-09-09T19:06:29,699   creating build/bdist.linux-armv7l/wheel/pyckmeans/ordination
2025-09-09T19:06:29,700   copying build/lib.linux-armv7l-cpython-313/pyckmeans/ordination/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/ordination
2025-09-09T19:06:29,702   creating build/bdist.linux-armv7l/wheel/pyckmeans/utils
2025-09-09T19:06:29,703   copying build/lib.linux-armv7l-cpython-313/pyckmeans/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/utils
2025-09-09T19:06:29,704   copying build/lib.linux-armv7l-cpython-313/pyckmeans/utils/plotting.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/utils
2025-09-09T19:06:29,705   copying build/lib.linux-armv7l-cpython-313/pyckmeans/utils/progressbar.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/utils
2025-09-09T19:06:29,706   copying build/lib.linux-armv7l-cpython-313/pyckmeans/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans
2025-09-09T19:06:29,708   running install_egg_info
2025-09-09T19:06:30,000   running egg_info
2025-09-09T19:06:30,282   writing pyckmeans.egg-info/PKG-INFO
2025-09-09T19:06:30,286   writing dependency_links to pyckmeans.egg-info/dependency_links.txt
2025-09-09T19:06:30,288   writing requirements to pyckmeans.egg-info/requires.txt
2025-09-09T19:06:30,288   writing top-level names to pyckmeans.egg-info/top_level.txt
2025-09-09T19:06:30,586   reading manifest file 'pyckmeans.egg-info/SOURCES.txt'
2025-09-09T19:06:30,594   adding license file 'LICENSE'
2025-09-09T19:06:30,601   writing manifest file 'pyckmeans.egg-info/SOURCES.txt'
2025-09-09T19:06:30,602   Copying pyckmeans.egg-info to build/bdist.linux-armv7l/wheel/./pyckmeans-0.5.0-py3.13.egg-info
2025-09-09T19:06:30,608   running install_scripts
2025-09-09T19:06:30,726   creating build/bdist.linux-armv7l/wheel/pyckmeans-0.5.0.dist-info/WHEEL
2025-09-09T19:06:30,728   creating '/tmp/pip-wheel-0ft7m_d5/pyckmeans-0.5.0-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-09-09T19:06:30,731   adding 'pyckmeans/__init__.py'
2025-09-09T19:06:30,734   adding 'pyckmeans/core/__init__.py'
2025-09-09T19:06:30,738   adding 'pyckmeans/core/ckmeans.py'
2025-09-09T19:06:30,741   adding 'pyckmeans/core/multickmeans.py'
2025-09-09T19:06:30,745   adding 'pyckmeans/core/wecr.py'
2025-09-09T19:06:30,748   adding 'pyckmeans/distance/__init__.py'
2025-09-09T19:06:30,750   adding 'pyckmeans/distance/c_interop.py'
2025-09-09T19:06:30,771   adding 'pyckmeans/distance/lib/distance.so'
2025-09-09T19:06:30,774   adding 'pyckmeans/io/__init__.py'
2025-09-09T19:06:30,776   adding 'pyckmeans/io/c_interop.py'
2025-09-09T19:06:30,778   adding 'pyckmeans/io/csv.py'
2025-09-09T19:06:30,780   adding 'pyckmeans/io/fasta.py'
2025-09-09T19:06:30,783   adding 'pyckmeans/io/nucleotide_alignment.py'
2025-09-09T19:06:30,785   adding 'pyckmeans/io/phylip.py'
2025-09-09T19:06:30,790   adding 'pyckmeans/io/lib/nucencode.so'
2025-09-09T19:06:30,793   adding 'pyckmeans/knee/__init__.py'
2025-09-09T19:06:30,796   adding 'pyckmeans/ordering/__init__.py'
2025-09-09T19:06:30,799   adding 'pyckmeans/ordination/__init__.py'
2025-09-09T19:06:30,801   adding 'pyckmeans/utils/__init__.py'
2025-09-09T19:06:30,804   adding 'pyckmeans/utils/plotting.py'
2025-09-09T19:06:30,806   adding 'pyckmeans/utils/progressbar.py'
2025-09-09T19:06:30,808   adding 'pyckmeans-0.5.0.dist-info/licenses/LICENSE'
2025-09-09T19:06:30,810   adding 'pyckmeans-0.5.0.dist-info/METADATA'
2025-09-09T19:06:30,812   adding 'pyckmeans-0.5.0.dist-info/WHEEL'
2025-09-09T19:06:30,813   adding 'pyckmeans-0.5.0.dist-info/top_level.txt'
2025-09-09T19:06:30,815   adding 'pyckmeans-0.5.0.dist-info/RECORD'
2025-09-09T19:06:30,816   removing build/bdist.linux-armv7l/wheel
2025-09-09T19:06:31,062   Building wheel for pyckmeans (setup.py): finished with status 'done'
2025-09-09T19:06:31,066   Created wheel for pyckmeans: filename=pyckmeans-0.5.0-cp313-cp313-linux_armv7l.whl size=81090 sha256=597d9e0576cd9d478c603e017e5cc4c05fedd525b8b679a7ea0cfbaa43e9eed0
2025-09-09T19:06:31,068   Stored in directory: /tmp/pip-ephem-wheel-cache-61w9mvbw/wheels/18/29/29/05f37dd47fedf887595d55a30361028a727cdd7669e36ecda2
2025-09-09T19:06:31,091 Successfully built pyckmeans
2025-09-09T19:06:31,096 Removed build tracker: '/tmp/pip-build-tracker-lhcgeuz5'