2025-09-09T19:15:56,938 Created temporary directory: /tmp/pip-build-tracker-8r683uzs
2025-09-09T19:15:56,938 Initialized build tracking at /tmp/pip-build-tracker-8r683uzs
2025-09-09T19:15:56,938 Created build tracker: /tmp/pip-build-tracker-8r683uzs
2025-09-09T19:15:56,939 Entered build tracker: /tmp/pip-build-tracker-8r683uzs
2025-09-09T19:15:56,939 Created temporary directory: /tmp/pip-wheel-8ojvw3mb
2025-09-09T19:15:56,942 Created temporary directory: /tmp/pip-ephem-wheel-cache-qr59_t4e
2025-09-09T19:15:56,997 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-09-09T19:15:57,000 2 location(s) to search for versions of pyckmeans:
2025-09-09T19:15:57,000 * https://pypi.org/simple/pyckmeans/
2025-09-09T19:15:57,000 * https://www.piwheels.org/simple/pyckmeans/
2025-09-09T19:15:57,000 Fetching project page and analyzing links: https://pypi.org/simple/pyckmeans/
2025-09-09T19:15:57,000 Getting page https://pypi.org/simple/pyckmeans/
2025-09-09T19:15:57,001 Found index url https://pypi.org/simple/
2025-09-09T19:15:57,075 Fetched page https://pypi.org/simple/pyckmeans/ as application/vnd.pypi.simple.v1+json
2025-09-09T19:15:57,087   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)
2025-09-09T19:15:57,088   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)
2025-09-09T19:15:57,088   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)
2025-09-09T19:15:57,088   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)
2025-09-09T19:15:57,089   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
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2025-09-09T19:15:57,089   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)
2025-09-09T19:15:57,089   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)
2025-09-09T19:15:57,089   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)
2025-09-09T19:15:57,090   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
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2025-09-09T19:15:57,090   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)
2025-09-09T19:15:57,090   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)
2025-09-09T19:15:57,090   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)
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2025-09-09T19:15:57,091   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)
2025-09-09T19:15:57,091   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)
2025-09-09T19:15:57,091   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)
2025-09-09T19:15:57,091   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)
2025-09-09T19:15:57,091   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)
2025-09-09T19:15:57,092   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)
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2025-09-09T19:15:57,092   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)
2025-09-09T19:15:57,092   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)
2025-09-09T19:15:57,093   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)
2025-09-09T19:15:57,093   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)
2025-09-09T19:15:57,093   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)
2025-09-09T19:15:57,093   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)
2025-09-09T19:15:57,093   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)
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2025-09-09T19:15:57,094   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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2025-09-09T19:15:57,222   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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2025-09-09T19:15:57,223   Skipping link: No binaries permitted for pyckmeans: https://archive1.piwheels.org/simple/pyckmeans/pyckmeans-0.4.0-cp37-cp37m-linux_armv7l.whl#sha256=3ce14a9d9c6d38292fa0b21ae357dea7cf25fe1d2bab349e5f21cc18cd9c1aa9 (from https://www.piwheels.org/simple/pyckmeans/) (requires-python:>=3.6)
2025-09-09T19:15:57,223   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)
2025-09-09T19:15:57,223   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)
2025-09-09T19:15:57,224 Skipping link: not a file: https://www.piwheels.org/simple/pyckmeans/
2025-09-09T19:15:57,224 Skipping link: not a file: https://pypi.org/simple/pyckmeans/
2025-09-09T19:15:57,246 Given no hashes to check 1 links for project 'pyckmeans': discarding no candidates
2025-09-09T19:15:57,247 Collecting pyckmeans==0.8.0
2025-09-09T19:15:57,248   Created temporary directory: /tmp/pip-unpack-jyw5kh6e
2025-09-09T19:15:57,387   Downloading pyckmeans-0.8.0.tar.gz (44 kB)
2025-09-09T19:15:57,440   Added pyckmeans==0.8.0 from https://files.pythonhosted.org/packages/fe/48/2b6e70758277599b2316f4fe42caacda43aa5d8e331d526d64e32adc119f/pyckmeans-0.8.0.tar.gz to build tracker '/tmp/pip-build-tracker-8r683uzs'
2025-09-09T19:15:57,441   Running setup.py (path:/tmp/pip-wheel-8ojvw3mb/pyckmeans_e46acff871e64d93991b563bfe84a931/setup.py) egg_info for package pyckmeans
2025-09-09T19:15:57,442   Created temporary directory: /tmp/pip-pip-egg-info-eehantz4
2025-09-09T19:15:57,442   Preparing metadata (setup.py): started
2025-09-09T19:15:57,443   Running command python setup.py egg_info
2025-09-09T19:15:58,594   running egg_info
2025-09-09T19:15:58,667   creating /tmp/pip-pip-egg-info-eehantz4/pyckmeans.egg-info
2025-09-09T19:15:58,668   writing /tmp/pip-pip-egg-info-eehantz4/pyckmeans.egg-info/PKG-INFO
2025-09-09T19:15:58,669   writing dependency_links to /tmp/pip-pip-egg-info-eehantz4/pyckmeans.egg-info/dependency_links.txt
2025-09-09T19:15:58,669   writing requirements to /tmp/pip-pip-egg-info-eehantz4/pyckmeans.egg-info/requires.txt
2025-09-09T19:15:58,670   writing top-level names to /tmp/pip-pip-egg-info-eehantz4/pyckmeans.egg-info/top_level.txt
2025-09-09T19:15:58,670   writing manifest file '/tmp/pip-pip-egg-info-eehantz4/pyckmeans.egg-info/SOURCES.txt'
2025-09-09T19:15:58,895   reading manifest file '/tmp/pip-pip-egg-info-eehantz4/pyckmeans.egg-info/SOURCES.txt'
2025-09-09T19:15:58,898   writing manifest file '/tmp/pip-pip-egg-info-eehantz4/pyckmeans.egg-info/SOURCES.txt'
2025-09-09T19:15:59,010   Preparing metadata (setup.py): finished with status 'done'
2025-09-09T19:15:59,015   Source in /tmp/pip-wheel-8ojvw3mb/pyckmeans_e46acff871e64d93991b563bfe84a931 has version 0.8.0, which satisfies requirement pyckmeans==0.8.0 from https://files.pythonhosted.org/packages/fe/48/2b6e70758277599b2316f4fe42caacda43aa5d8e331d526d64e32adc119f/pyckmeans-0.8.0.tar.gz
2025-09-09T19:15:59,015   Removed pyckmeans==0.8.0 from https://files.pythonhosted.org/packages/fe/48/2b6e70758277599b2316f4fe42caacda43aa5d8e331d526d64e32adc119f/pyckmeans-0.8.0.tar.gz from build tracker '/tmp/pip-build-tracker-8r683uzs'
2025-09-09T19:15:59,019 Created temporary directory: /tmp/pip-unpack-bp65ori0
2025-09-09T19:15:59,020 Created temporary directory: /tmp/pip-unpack-03izrbot
2025-09-09T19:15:59,020 Building wheels for collected packages: pyckmeans
2025-09-09T19:15:59,021   Created temporary directory: /tmp/pip-wheel-cbiv21f2
2025-09-09T19:15:59,022   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
2025-09-09T19:15:59,023   Building wheel for pyckmeans (setup.py): started
2025-09-09T19:15:59,024   Destination directory: /tmp/pip-wheel-cbiv21f2
2025-09-09T19:15:59,024   Running command python setup.py bdist_wheel
2025-09-09T19:16:00,343   running bdist_wheel
2025-09-09T19:16:00,640   running build
2025-09-09T19:16:00,640   running build_py
2025-09-09T19:16:00,718   creating build/lib.linux-armv7l-cpython-313/pyckmeans
2025-09-09T19:16:00,718   copying pyckmeans/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans
2025-09-09T19:16:00,719   creating build/lib.linux-armv7l-cpython-313/pyckmeans/utils
2025-09-09T19:16:00,719   copying pyckmeans/utils/progressbar.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/utils
2025-09-09T19:16:00,720   copying pyckmeans/utils/plotting.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/utils
2025-09-09T19:16:00,720   copying pyckmeans/utils/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/utils
2025-09-09T19:16:00,721   creating build/lib.linux-armv7l-cpython-313/pyckmeans/ordination
2025-09-09T19:16:00,721   copying pyckmeans/ordination/utils.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/ordination
2025-09-09T19:16:00,722   copying pyckmeans/ordination/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/ordination
2025-09-09T19:16:00,723   creating build/lib.linux-armv7l-cpython-313/pyckmeans/ordering
2025-09-09T19:16:00,723   copying pyckmeans/ordering/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/ordering
2025-09-09T19:16:00,724   creating build/lib.linux-armv7l-cpython-313/pyckmeans/knee
2025-09-09T19:16:00,724   copying pyckmeans/knee/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/knee
2025-09-09T19:16:00,725   creating build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:16:00,725   copying pyckmeans/io/phylip.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:16:00,726   copying pyckmeans/io/nucleotide_alignment.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:16:00,726   copying pyckmeans/io/fasta.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:16:00,727   copying pyckmeans/io/csv.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:16:00,727   copying pyckmeans/io/c_interop.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:16:00,728   copying pyckmeans/io/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/io
2025-09-09T19:16:00,728   creating build/lib.linux-armv7l-cpython-313/pyckmeans/distance
2025-09-09T19:16:00,729   copying pyckmeans/distance/c_interop.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/distance
2025-09-09T19:16:00,729   copying pyckmeans/distance/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/distance
2025-09-09T19:16:00,730   creating build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:16:00,730   copying pyckmeans/core/wecr.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:16:00,731   copying pyckmeans/core/utils.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:16:00,731   copying pyckmeans/core/multickmeans.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:16:00,732   copying pyckmeans/core/ckmeans.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:16:00,733   copying pyckmeans/core/__init__.py -> build/lib.linux-armv7l-cpython-313/pyckmeans/core
2025-09-09T19:16:00,737   running build_ext
2025-09-09T19:16:00,743   building 'pyckmeans.distance.lib.distance' extension
2025-09-09T19:16:00,744   creating build/temp.linux-armv7l-cpython-313/pyckmeans/distance/src
2025-09-09T19:16:00,744   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
2025-09-09T19:16:02,258   pyckmeans/distance/src/distance.cpp: In function ‘std::vector<bool> completeDeletionSites(uint8_t*, int, int)’:
2025-09-09T19:16:02,258   pyckmeans/distance/src/distance.cpp:107:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,258     107 |     for (size_t i = 0; i < m; ++i) {
2025-09-09T19:16:02,258         |                        ~~^~~
2025-09-09T19:16:02,259   pyckmeans/distance/src/distance.cpp:109:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,259     109 |         for (size_t j = 0; j < n; ++j) {
2025-09-09T19:16:02,259         |                            ~~^~~
2025-09-09T19:16:02,261   pyckmeans/distance/src/distance.cpp: In function ‘void pDistance(uint8_t*, int, int, bool, double*)’:
2025-09-09T19:16:02,261   pyckmeans/distance/src/distance.cpp:133:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,261     133 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2025-09-09T19:16:02,262         |                              ~~~~^~~~~~~~~
2025-09-09T19:16:02,262   pyckmeans/distance/src/distance.cpp:134:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,262     134 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2025-09-09T19:16:02,262         |                                          ~~~~^~~
2025-09-09T19:16:02,263   pyckmeans/distance/src/distance.cpp:138:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,263     138 |                 for (size_t j = 0; j < m; ++j) {
2025-09-09T19:16:02,263         |                                    ~~^~~
2025-09-09T19:16:02,264   pyckmeans/distance/src/distance.cpp:163:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,264     163 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2025-09-09T19:16:02,264         |                              ~~~~^~~~~~~~~
2025-09-09T19:16:02,265   pyckmeans/distance/src/distance.cpp:164:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,265     164 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2025-09-09T19:16:02,265         |                                          ~~~~^~~
2025-09-09T19:16:02,265   pyckmeans/distance/src/distance.cpp:168:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,266     168 |                 for (size_t j = 0; j < m; ++j) {
2025-09-09T19:16:02,266         |                                    ~~^~~
2025-09-09T19:16:02,267   pyckmeans/distance/src/distance.cpp: In function ‘void jcDistance(uint8_t*, int, int, bool, double*)’:
2025-09-09T19:16:02,268   pyckmeans/distance/src/distance.cpp:202:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,268     202 |     for (size_t i = 0; i < n; ++i) {
2025-09-09T19:16:02,268         |                        ~~^~~
2025-09-09T19:16:02,268   pyckmeans/distance/src/distance.cpp:203:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,268     203 |         for (size_t j = 0; j < n; ++j) {
2025-09-09T19:16:02,269         |                            ~~^~~
2025-09-09T19:16:02,270   pyckmeans/distance/src/distance.cpp: In function ‘void k2pDistance(uint8_t*, int, int, bool, double*)’:
2025-09-09T19:16:02,270   pyckmeans/distance/src/distance.cpp:221:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,270     221 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2025-09-09T19:16:02,270         |                              ~~~~^~~~~~~~~
2025-09-09T19:16:02,270   pyckmeans/distance/src/distance.cpp:222:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,271     222 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2025-09-09T19:16:02,271         |                                          ~~~~^~~
2025-09-09T19:16:02,271   pyckmeans/distance/src/distance.cpp:227:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,271     227 |                 for (size_t j = 0; j < m; ++j) {
2025-09-09T19:16:02,271         |                                    ~~^~~
2025-09-09T19:16:02,273   pyckmeans/distance/src/distance.cpp:263:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,273     263 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2025-09-09T19:16:02,273         |                              ~~~~^~~~~~~~~
2025-09-09T19:16:02,274   pyckmeans/distance/src/distance.cpp:264:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,274     264 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2025-09-09T19:16:02,274         |                                          ~~~~^~~
2025-09-09T19:16:02,274   pyckmeans/distance/src/distance.cpp:269:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:02,275     269 |                 for (size_t j = 0; j < m; ++j) {
2025-09-09T19:16:02,275         |                                    ~~^~~
2025-09-09T19:16:03,185   creating build/lib.linux-armv7l-cpython-313/pyckmeans/distance/lib
2025-09-09T19:16:03,185   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
2025-09-09T19:16:03,461   building 'pyckmeans.io.lib.nucencode' extension
2025-09-09T19:16:03,461   creating build/temp.linux-armv7l-cpython-313/pyckmeans/io/src
2025-09-09T19:16:03,462   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
2025-09-09T19:16:03,536   pyckmeans/io/src/nucencode.cpp: In function ‘void encodeNucleotides(uint8_t*, int, int)’:
2025-09-09T19:16:03,537   pyckmeans/io/src/nucencode.cpp:73:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:03,537      73 |     for (size_t i = 0; i < n; i++) {
2025-09-09T19:16:03,537         |                        ~~^~~
2025-09-09T19:16:03,537   pyckmeans/io/src/nucencode.cpp:74:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:03,537      74 |         for (size_t j = 0; j < m; j++) {
2025-09-09T19:16:03,537         |                            ~~^~~
2025-09-09T19:16:03,537   pyckmeans/io/src/nucencode.cpp: In function ‘void encodeNucleotides_uint32(uint32_t*, int, int, uint8_t*)’:
2025-09-09T19:16:03,538   pyckmeans/io/src/nucencode.cpp:86:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:03,538      86 |     for (size_t i = 0; i < n; i++) {
2025-09-09T19:16:03,538         |                        ~~^~~
2025-09-09T19:16:03,538   pyckmeans/io/src/nucencode.cpp:87:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2025-09-09T19:16:03,538      87 |         for (size_t j = 0; j < m; j++) {
2025-09-09T19:16:03,538         |                            ~~^~~
2025-09-09T19:16:03,621   creating build/lib.linux-armv7l-cpython-313/pyckmeans/io/lib
2025-09-09T19:16:03,621   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
2025-09-09T19:16:03,817   /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-09-09T19:16:03,817   !!

2025-09-09T19:16:03,817           ********************************************************************************
2025-09-09T19:16:03,818           Please avoid running ``setup.py`` directly.
2025-09-09T19:16:03,818           Instead, use pypa/build, pypa/installer or other
2025-09-09T19:16:03,818           standards-based tools.

2025-09-09T19:16:03,818           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-09-09T19:16:03,818           or your builds will no longer be supported.

2025-09-09T19:16:03,818           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-09-09T19:16:03,818           ********************************************************************************

2025-09-09T19:16:03,819   !!
2025-09-09T19:16:03,819     self.initialize_options()
2025-09-09T19:16:03,890   installing to build/bdist.linux-armv7l/wheel
2025-09-09T19:16:03,890   running install
2025-09-09T19:16:03,913   running install_lib
2025-09-09T19:16:03,987   creating build/bdist.linux-armv7l/wheel
2025-09-09T19:16:03,987   creating build/bdist.linux-armv7l/wheel/pyckmeans
2025-09-09T19:16:03,987   creating build/bdist.linux-armv7l/wheel/pyckmeans/core
2025-09-09T19:16:03,988   copying build/lib.linux-armv7l-cpython-313/pyckmeans/core/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/core
2025-09-09T19:16:03,988   copying build/lib.linux-armv7l-cpython-313/pyckmeans/core/ckmeans.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/core
2025-09-09T19:16:03,989   copying build/lib.linux-armv7l-cpython-313/pyckmeans/core/multickmeans.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/core
2025-09-09T19:16:03,989   copying build/lib.linux-armv7l-cpython-313/pyckmeans/core/utils.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/core
2025-09-09T19:16:03,990   copying build/lib.linux-armv7l-cpython-313/pyckmeans/core/wecr.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/core
2025-09-09T19:16:03,990   creating build/bdist.linux-armv7l/wheel/pyckmeans/distance
2025-09-09T19:16:03,991   creating build/bdist.linux-armv7l/wheel/pyckmeans/distance/lib
2025-09-09T19:16:03,991   copying build/lib.linux-armv7l-cpython-313/pyckmeans/distance/lib/distance.so -> build/bdist.linux-armv7l/wheel/./pyckmeans/distance/lib
2025-09-09T19:16:03,992   copying build/lib.linux-armv7l-cpython-313/pyckmeans/distance/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/distance
2025-09-09T19:16:03,992   copying build/lib.linux-armv7l-cpython-313/pyckmeans/distance/c_interop.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/distance
2025-09-09T19:16:03,993   creating build/bdist.linux-armv7l/wheel/pyckmeans/io
2025-09-09T19:16:03,993   creating build/bdist.linux-armv7l/wheel/pyckmeans/io/lib
2025-09-09T19:16:03,994   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/lib/nucencode.so -> build/bdist.linux-armv7l/wheel/./pyckmeans/io/lib
2025-09-09T19:16:03,994   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:16:03,995   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/c_interop.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:16:03,995   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/csv.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:16:03,995   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/fasta.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:16:03,996   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/nucleotide_alignment.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:16:03,996   copying build/lib.linux-armv7l-cpython-313/pyckmeans/io/phylip.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/io
2025-09-09T19:16:03,997   creating build/bdist.linux-armv7l/wheel/pyckmeans/knee
2025-09-09T19:16:03,997   copying build/lib.linux-armv7l-cpython-313/pyckmeans/knee/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/knee
2025-09-09T19:16:03,998   creating build/bdist.linux-armv7l/wheel/pyckmeans/ordering
2025-09-09T19:16:03,998   copying build/lib.linux-armv7l-cpython-313/pyckmeans/ordering/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/ordering
2025-09-09T19:16:03,999   creating build/bdist.linux-armv7l/wheel/pyckmeans/ordination
2025-09-09T19:16:03,999   copying build/lib.linux-armv7l-cpython-313/pyckmeans/ordination/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/ordination
2025-09-09T19:16:03,999   copying build/lib.linux-armv7l-cpython-313/pyckmeans/ordination/utils.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/ordination
2025-09-09T19:16:04,000   creating build/bdist.linux-armv7l/wheel/pyckmeans/utils
2025-09-09T19:16:04,000   copying build/lib.linux-armv7l-cpython-313/pyckmeans/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/utils
2025-09-09T19:16:04,000   copying build/lib.linux-armv7l-cpython-313/pyckmeans/utils/plotting.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/utils
2025-09-09T19:16:04,001   copying build/lib.linux-armv7l-cpython-313/pyckmeans/utils/progressbar.py -> build/bdist.linux-armv7l/wheel/./pyckmeans/utils
2025-09-09T19:16:04,001   copying build/lib.linux-armv7l-cpython-313/pyckmeans/__init__.py -> build/bdist.linux-armv7l/wheel/./pyckmeans
2025-09-09T19:16:04,002   running install_egg_info
2025-09-09T19:16:04,079   running egg_info
2025-09-09T19:16:04,155   writing pyckmeans.egg-info/PKG-INFO
2025-09-09T19:16:04,156   writing dependency_links to pyckmeans.egg-info/dependency_links.txt
2025-09-09T19:16:04,157   writing requirements to pyckmeans.egg-info/requires.txt
2025-09-09T19:16:04,157   writing top-level names to pyckmeans.egg-info/top_level.txt
2025-09-09T19:16:04,236   reading manifest file 'pyckmeans.egg-info/SOURCES.txt'
2025-09-09T19:16:04,241   writing manifest file 'pyckmeans.egg-info/SOURCES.txt'
2025-09-09T19:16:04,241   Copying pyckmeans.egg-info to build/bdist.linux-armv7l/wheel/./pyckmeans-0.8.0-py3.13.egg-info
2025-09-09T19:16:04,243   running install_scripts
2025-09-09T19:16:04,291   creating build/bdist.linux-armv7l/wheel/pyckmeans-0.8.0.dist-info/WHEEL
2025-09-09T19:16:04,292   creating '/tmp/pip-wheel-cbiv21f2/pyckmeans-0.8.0-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-09-09T19:16:04,294   adding 'pyckmeans/__init__.py'
2025-09-09T19:16:04,294   adding 'pyckmeans/core/__init__.py'
2025-09-09T19:16:04,298   adding 'pyckmeans/core/ckmeans.py'
2025-09-09T19:16:04,299   adding 'pyckmeans/core/multickmeans.py'
2025-09-09T19:16:04,300   adding 'pyckmeans/core/utils.py'
2025-09-09T19:16:04,304   adding 'pyckmeans/core/wecr.py'
2025-09-09T19:16:04,305   adding 'pyckmeans/distance/__init__.py'
2025-09-09T19:16:04,306   adding 'pyckmeans/distance/c_interop.py'
2025-09-09T19:16:04,321   adding 'pyckmeans/distance/lib/distance.so'
2025-09-09T19:16:04,322   adding 'pyckmeans/io/__init__.py'
2025-09-09T19:16:04,323   adding 'pyckmeans/io/c_interop.py'
2025-09-09T19:16:04,324   adding 'pyckmeans/io/csv.py'
2025-09-09T19:16:04,325   adding 'pyckmeans/io/fasta.py'
2025-09-09T19:16:04,326   adding 'pyckmeans/io/nucleotide_alignment.py'
2025-09-09T19:16:04,327   adding 'pyckmeans/io/phylip.py'
2025-09-09T19:16:04,330   adding 'pyckmeans/io/lib/nucencode.so'
2025-09-09T19:16:04,332   adding 'pyckmeans/knee/__init__.py'
2025-09-09T19:16:04,334   adding 'pyckmeans/ordering/__init__.py'
2025-09-09T19:16:04,336   adding 'pyckmeans/ordination/__init__.py'
2025-09-09T19:16:04,337   adding 'pyckmeans/ordination/utils.py'
2025-09-09T19:16:04,337   adding 'pyckmeans/utils/__init__.py'
2025-09-09T19:16:04,338   adding 'pyckmeans/utils/plotting.py'
2025-09-09T19:16:04,339   adding 'pyckmeans/utils/progressbar.py'
2025-09-09T19:16:04,340   adding 'pyckmeans-0.8.0.dist-info/METADATA'
2025-09-09T19:16:04,340   adding 'pyckmeans-0.8.0.dist-info/WHEEL'
2025-09-09T19:16:04,341   adding 'pyckmeans-0.8.0.dist-info/top_level.txt'
2025-09-09T19:16:04,341   adding 'pyckmeans-0.8.0.dist-info/RECORD'
2025-09-09T19:16:04,342   removing build/bdist.linux-armv7l/wheel
2025-09-09T19:16:04,458   Building wheel for pyckmeans (setup.py): finished with status 'done'
2025-09-09T19:16:04,460   Created wheel for pyckmeans: filename=pyckmeans-0.8.0-cp313-cp313-linux_armv7l.whl size=87440 sha256=30010085633534317c018dbde38e88f7ba67645c2e820afcab0760557fdb3306
2025-09-09T19:16:04,461   Stored in directory: /tmp/pip-ephem-wheel-cache-qr59_t4e/wheels/15/77/9c/7bc8d3b9ad10fbb815f1d3eaaaf056089b62184412c87b144f
2025-09-09T19:16:04,469 Successfully built pyckmeans
2025-09-09T19:16:04,470 Removed build tracker: '/tmp/pip-build-tracker-8r683uzs'