2023-09-14T14:38:11,638 Created temporary directory: /tmp/pip-build-tracker-xx941zdv
2023-09-14T14:38:11,640 Initialized build tracking at /tmp/pip-build-tracker-xx941zdv
2023-09-14T14:38:11,640 Created build tracker: /tmp/pip-build-tracker-xx941zdv
2023-09-14T14:38:11,641 Entered build tracker: /tmp/pip-build-tracker-xx941zdv
2023-09-14T14:38:11,641 Created temporary directory: /tmp/pip-wheel-ns62k8tw
2023-09-14T14:38:11,644 Created temporary directory: /tmp/pip-ephem-wheel-cache-1gtrlz4l
2023-09-14T14:38:11,666 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-14T14:38:11,670 2 location(s) to search for versions of pyckmeans:
2023-09-14T14:38:11,670 * https://pypi.org/simple/pyckmeans/
2023-09-14T14:38:11,670 * https://www.piwheels.org/simple/pyckmeans/
2023-09-14T14:38:11,670 Fetching project page and analyzing links: https://pypi.org/simple/pyckmeans/
2023-09-14T14:38:11,671 Getting page https://pypi.org/simple/pyckmeans/
2023-09-14T14:38:11,673 Found index url https://pypi.org/simple/
2023-09-14T14:38:11,814 Fetched page https://pypi.org/simple/pyckmeans/ as application/vnd.pypi.simple.v1+json
2023-09-14T14:38:11,830   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)
2023-09-14T14:38:11,831   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)
2023-09-14T14:38:11,832   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)
2023-09-14T14:38:11,832   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)
2023-09-14T14:38:11,834   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
2023-09-14T14:38:11,834   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)
2023-09-14T14:38:11,835   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)
2023-09-14T14:38:11,836   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)
2023-09-14T14:38:11,837   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)
2023-09-14T14:38:11,837   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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2023-09-14T14:38:11,839   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)
2023-09-14T14:38:11,840   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)
2023-09-14T14:38:11,840   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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2023-09-14T14:38:11,843   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)
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2023-09-14T14:38:11,844   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)
2023-09-14T14:38:11,845   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)
2023-09-14T14:38:11,846   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)
2023-09-14T14:38:11,847   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
2023-09-14T14:38:11,847   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)
2023-09-14T14:38:11,848   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)
2023-09-14T14:38:11,849   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)
2023-09-14T14:38:11,849   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)
2023-09-14T14:38:11,850   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)
2023-09-14T14:38:11,850   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)
2023-09-14T14:38:11,851   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)
2023-09-14T14:38:11,851   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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2023-09-14T14:38:11,854   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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2023-09-14T14:38:11,855   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)
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2023-09-14T14:38:12,170   Skipping link: No binaries permitted for pyckmeans: https://www.piwheels.org/simple/pyckmeans/pyckmeans-0.6.0-cp37-cp37m-linux_armv7l.whl#sha256=cb53b9cdf6bd087dee0318d6d4dff8bcec1bfb55674d4ddbab113a3162cc4fbb (from https://www.piwheels.org/simple/pyckmeans/) (requires-python:>=3.6)
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2023-09-14T14:38:12,173   Skipping link: No binaries permitted for pyckmeans: https://www.piwheels.org/simple/pyckmeans/pyckmeans-0.5.0-cp37-cp37m-linux_armv7l.whl#sha256=2c63a4c49c60988e501b29a42a9bc6a18226b39af3af371d790cd0222c59fc78 (from https://www.piwheels.org/simple/pyckmeans/) (requires-python:>=3.6)
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2023-09-14T14:38:12,174   Skipping link: No binaries permitted for pyckmeans: https://www.piwheels.org/simple/pyckmeans/pyckmeans-0.4.0-cp311-cp311-linux_armv7l.whl#sha256=8c9f8d52d596b22328726ae44433c3ac78b42c98885711457fc27390b49e2965 (from https://www.piwheels.org/simple/pyckmeans/) (requires-python:>=3.6)
2023-09-14T14:38:12,175   Skipping link: No binaries permitted for pyckmeans: https://www.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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2023-09-14T14:38:12,176   Skipping link: No binaries permitted for pyckmeans: https://www.piwheels.org/simple/pyckmeans/pyckmeans-0.4.0-cp39-cp39-linux_armv6l.whl#sha256=0e412147006636ef292af891010598fa650941f952b974cb293175a25a706fdb (from https://www.piwheels.org/simple/pyckmeans/) (requires-python:>=3.6)
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2023-09-14T14:38:12,177   Skipping link: No binaries permitted for pyckmeans: https://www.piwheels.org/simple/pyckmeans/pyckmeans-0.4.0-cp37-cp37m-linux_armv6l.whl#sha256=3ce14a9d9c6d38292fa0b21ae357dea7cf25fe1d2bab349e5f21cc18cd9c1aa9 (from https://www.piwheels.org/simple/pyckmeans/) (requires-python:>=3.6)
2023-09-14T14:38:12,178 Skipping link: not a file: https://www.piwheels.org/simple/pyckmeans/
2023-09-14T14:38:12,178 Skipping link: not a file: https://pypi.org/simple/pyckmeans/
2023-09-14T14:38:12,197 Given no hashes to check 1 links for project 'pyckmeans': discarding no candidates
2023-09-14T14:38:12,215 Collecting pyckmeans==0.9.2
2023-09-14T14:38:12,217   Created temporary directory: /tmp/pip-unpack-5e3ahksl
2023-09-14T14:38:12,432   Downloading pyckmeans-0.9.2.tar.gz (50 kB)
2023-09-14T14:38:12,541   Added pyckmeans==0.9.2 from https://files.pythonhosted.org/packages/18/2e/8141265817253d676fd291048750fcf7eecd63edde73ec7ea83b42d7cdf8/pyckmeans-0.9.2.tar.gz to build tracker '/tmp/pip-build-tracker-xx941zdv'
2023-09-14T14:38:12,543   Running setup.py (path:/tmp/pip-wheel-ns62k8tw/pyckmeans_b12f624b48014994850325e61b802f3c/setup.py) egg_info for package pyckmeans
2023-09-14T14:38:12,543   Created temporary directory: /tmp/pip-pip-egg-info-enwof62e
2023-09-14T14:38:12,544   Preparing metadata (setup.py): started
2023-09-14T14:38:12,545   Running command python setup.py egg_info
2023-09-14T14:38:13,572   running egg_info
2023-09-14T14:38:13,573   creating /tmp/pip-pip-egg-info-enwof62e/pyckmeans.egg-info
2023-09-14T14:38:13,598   writing /tmp/pip-pip-egg-info-enwof62e/pyckmeans.egg-info/PKG-INFO
2023-09-14T14:38:13,602   writing dependency_links to /tmp/pip-pip-egg-info-enwof62e/pyckmeans.egg-info/dependency_links.txt
2023-09-14T14:38:13,604   writing requirements to /tmp/pip-pip-egg-info-enwof62e/pyckmeans.egg-info/requires.txt
2023-09-14T14:38:13,605   writing top-level names to /tmp/pip-pip-egg-info-enwof62e/pyckmeans.egg-info/top_level.txt
2023-09-14T14:38:13,606   writing manifest file '/tmp/pip-pip-egg-info-enwof62e/pyckmeans.egg-info/SOURCES.txt'
2023-09-14T14:38:13,685   reading manifest file '/tmp/pip-pip-egg-info-enwof62e/pyckmeans.egg-info/SOURCES.txt'
2023-09-14T14:38:13,688   writing manifest file '/tmp/pip-pip-egg-info-enwof62e/pyckmeans.egg-info/SOURCES.txt'
2023-09-14T14:38:13,797   Preparing metadata (setup.py): finished with status 'done'
2023-09-14T14:38:13,802   Source in /tmp/pip-wheel-ns62k8tw/pyckmeans_b12f624b48014994850325e61b802f3c has version 0.9.2, which satisfies requirement pyckmeans==0.9.2 from https://files.pythonhosted.org/packages/18/2e/8141265817253d676fd291048750fcf7eecd63edde73ec7ea83b42d7cdf8/pyckmeans-0.9.2.tar.gz
2023-09-14T14:38:13,803   Removed pyckmeans==0.9.2 from https://files.pythonhosted.org/packages/18/2e/8141265817253d676fd291048750fcf7eecd63edde73ec7ea83b42d7cdf8/pyckmeans-0.9.2.tar.gz from build tracker '/tmp/pip-build-tracker-xx941zdv'
2023-09-14T14:38:13,810 Created temporary directory: /tmp/pip-unpack-66zwa54j
2023-09-14T14:38:13,811 Created temporary directory: /tmp/pip-unpack-y5r_bkr7
2023-09-14T14:38:13,820 Building wheels for collected packages: pyckmeans
2023-09-14T14:38:13,824   Created temporary directory: /tmp/pip-wheel-q1oi2_6d
2023-09-14T14:38:13,825   Building wheel for pyckmeans (setup.py): started
2023-09-14T14:38:13,826   Destination directory: /tmp/pip-wheel-q1oi2_6d
2023-09-14T14:38:13,827   Running command python setup.py bdist_wheel
2023-09-14T14:38:14,800   running bdist_wheel
2023-09-14T14:38:14,869   running build
2023-09-14T14:38:14,870   running build_py
2023-09-14T14:38:14,896   creating build
2023-09-14T14:38:14,896   creating build/lib.linux-armv7l-cpython-311
2023-09-14T14:38:14,897   creating build/lib.linux-armv7l-cpython-311/pyckmeans
2023-09-14T14:38:14,899   copying pyckmeans/__init__.py -> build/lib.linux-armv7l-cpython-311/pyckmeans
2023-09-14T14:38:14,901   creating build/lib.linux-armv7l-cpython-311/pyckmeans/ordering
2023-09-14T14:38:14,902   copying pyckmeans/ordering/__init__.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/ordering
2023-09-14T14:38:14,904   creating build/lib.linux-armv7l-cpython-311/pyckmeans/knee
2023-09-14T14:38:14,905   copying pyckmeans/knee/__init__.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/knee
2023-09-14T14:38:14,908   creating build/lib.linux-armv7l-cpython-311/pyckmeans/distance
2023-09-14T14:38:14,909   copying pyckmeans/distance/__init__.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/distance
2023-09-14T14:38:14,911   copying pyckmeans/distance/c_interop.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/distance
2023-09-14T14:38:14,914   creating build/lib.linux-armv7l-cpython-311/pyckmeans/core
2023-09-14T14:38:14,914   copying pyckmeans/core/multickmeans.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/core
2023-09-14T14:38:14,917   copying pyckmeans/core/utils.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/core
2023-09-14T14:38:14,918   copying pyckmeans/core/wecr.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/core
2023-09-14T14:38:14,921   copying pyckmeans/core/ckmeans.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/core
2023-09-14T14:38:14,924   copying pyckmeans/core/__init__.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/core
2023-09-14T14:38:14,926   creating build/lib.linux-armv7l-cpython-311/pyckmeans/io
2023-09-14T14:38:14,927   copying pyckmeans/io/phylip.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/io
2023-09-14T14:38:14,929   copying pyckmeans/io/fasta.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/io
2023-09-14T14:38:14,930   copying pyckmeans/io/nucleotide_alignment.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/io
2023-09-14T14:38:14,933   copying pyckmeans/io/__init__.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/io
2023-09-14T14:38:14,935   copying pyckmeans/io/csv.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/io
2023-09-14T14:38:14,936   copying pyckmeans/io/c_interop.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/io
2023-09-14T14:38:14,939   creating build/lib.linux-armv7l-cpython-311/pyckmeans/utils
2023-09-14T14:38:14,939   copying pyckmeans/utils/plotting.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/utils
2023-09-14T14:38:14,942   copying pyckmeans/utils/__init__.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/utils
2023-09-14T14:38:14,943   copying pyckmeans/utils/progressbar.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/utils
2023-09-14T14:38:14,946   creating build/lib.linux-armv7l-cpython-311/pyckmeans/ordination
2023-09-14T14:38:14,947   copying pyckmeans/ordination/utils.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/ordination
2023-09-14T14:38:14,948   copying pyckmeans/ordination/__init__.py -> build/lib.linux-armv7l-cpython-311/pyckmeans/ordination
2023-09-14T14:38:14,954   running build_ext
2023-09-14T14:38:14,960   building 'pyckmeans.distance.lib.distance' extension
2023-09-14T14:38:14,960   creating build/temp.linux-armv7l-cpython-311
2023-09-14T14:38:14,961   creating build/temp.linux-armv7l-cpython-311/pyckmeans
2023-09-14T14:38:14,961   creating build/temp.linux-armv7l-cpython-311/pyckmeans/distance
2023-09-14T14:38:14,962   creating build/temp.linux-armv7l-cpython-311/pyckmeans/distance/src
2023-09-14T14:38:14,963   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.11 -c pyckmeans/distance/src/distance.cpp -o build/temp.linux-armv7l-cpython-311/pyckmeans/distance/src/distance.o
2023-09-14T14:38:16,489   pyckmeans/distance/src/distance.cpp: In function ‘std::vector<bool> completeDeletionSites(uint8_t*, int, int)’:
2023-09-14T14:38:16,490   pyckmeans/distance/src/distance.cpp:107:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,491     107 |     for (size_t i = 0; i < m; ++i) {
2023-09-14T14:38:16,492         |                        ~~^~~
2023-09-14T14:38:16,492   pyckmeans/distance/src/distance.cpp:109:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,493     109 |         for (size_t j = 0; j < n; ++j) {
2023-09-14T14:38:16,493         |                            ~~^~~
2023-09-14T14:38:16,494   pyckmeans/distance/src/distance.cpp: In function ‘void pDistance(uint8_t*, int, int, bool, double*)’:
2023-09-14T14:38:16,494   pyckmeans/distance/src/distance.cpp:133:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,495     133 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2023-09-14T14:38:16,496         |                              ~~~~^~~~~~~~~
2023-09-14T14:38:16,496   pyckmeans/distance/src/distance.cpp:134:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,497     134 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2023-09-14T14:38:16,497         |                                          ~~~~^~~
2023-09-14T14:38:16,498   pyckmeans/distance/src/distance.cpp:138:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,498     138 |                 for (size_t j = 0; j < m; ++j) {
2023-09-14T14:38:16,499         |                                    ~~^~~
2023-09-14T14:38:16,500   pyckmeans/distance/src/distance.cpp:163:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,501     163 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2023-09-14T14:38:16,501         |                              ~~~~^~~~~~~~~
2023-09-14T14:38:16,502   pyckmeans/distance/src/distance.cpp:164:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,503     164 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2023-09-14T14:38:16,504         |                                          ~~~~^~~
2023-09-14T14:38:16,504   pyckmeans/distance/src/distance.cpp:168:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,505     168 |                 for (size_t j = 0; j < m; ++j) {
2023-09-14T14:38:16,506         |                                    ~~^~~
2023-09-14T14:38:16,507   pyckmeans/distance/src/distance.cpp: In function ‘void jcDistance(uint8_t*, int, int, bool, double*)’:
2023-09-14T14:38:16,507   pyckmeans/distance/src/distance.cpp:202:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,508     202 |     for (size_t i = 0; i < n; ++i) {
2023-09-14T14:38:16,509         |                        ~~^~~
2023-09-14T14:38:16,509   pyckmeans/distance/src/distance.cpp:203:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,510     203 |         for (size_t j = 0; j < n; ++j) {
2023-09-14T14:38:16,511         |                            ~~^~~
2023-09-14T14:38:16,511   pyckmeans/distance/src/distance.cpp: In function ‘void k2pDistance(uint8_t*, int, int, bool, double*)’:
2023-09-14T14:38:16,512   pyckmeans/distance/src/distance.cpp:221:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,513     221 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2023-09-14T14:38:16,514         |                              ~~~~^~~~~~~~~
2023-09-14T14:38:16,515   pyckmeans/distance/src/distance.cpp:222:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,515     222 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2023-09-14T14:38:16,516         |                                          ~~~~^~~
2023-09-14T14:38:16,516   pyckmeans/distance/src/distance.cpp:227:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,517     227 |                 for (size_t j = 0; j < m; ++j) {
2023-09-14T14:38:16,517         |                                    ~~^~~
2023-09-14T14:38:16,518   pyckmeans/distance/src/distance.cpp:263:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,518     263 |         for (size_t i_a = 0; i_a < (n - 1); ++i_a) {
2023-09-14T14:38:16,519         |                              ~~~~^~~~~~~~~
2023-09-14T14:38:16,520   pyckmeans/distance/src/distance.cpp:264:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,520     264 |             for (size_t i_b = (i_a + 1); i_b < n; ++i_b) {
2023-09-14T14:38:16,521         |                                          ~~~~^~~
2023-09-14T14:38:16,521   pyckmeans/distance/src/distance.cpp:269:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:16,522     269 |                 for (size_t j = 0; j < m; ++j) {
2023-09-14T14:38:16,523         |                                    ~~^~~
2023-09-14T14:38:17,433   creating build/lib.linux-armv7l-cpython-311/pyckmeans/distance/lib
2023-09-14T14:38:17,433   arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pyckmeans/distance/src/distance.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pyckmeans/distance/lib/distance.so
2023-09-14T14:38:17,669   building 'pyckmeans.io.lib.nucencode' extension
2023-09-14T14:38:17,670   creating build/temp.linux-armv7l-cpython-311/pyckmeans/io
2023-09-14T14:38:17,672   creating build/temp.linux-armv7l-cpython-311/pyckmeans/io/src
2023-09-14T14:38:17,675   arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.11 -c pyckmeans/io/src/nucencode.cpp -o build/temp.linux-armv7l-cpython-311/pyckmeans/io/src/nucencode.o
2023-09-14T14:38:17,752   pyckmeans/io/src/nucencode.cpp: In function ‘void encodeNucleotides(uint8_t*, int, int)’:
2023-09-14T14:38:17,753   pyckmeans/io/src/nucencode.cpp:73:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:17,754      73 |     for (size_t i = 0; i < n; i++) {
2023-09-14T14:38:17,754         |                        ~~^~~
2023-09-14T14:38:17,755   pyckmeans/io/src/nucencode.cpp:74:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:17,756      74 |         for (size_t j = 0; j < m; j++) {
2023-09-14T14:38:17,756         |                            ~~^~~
2023-09-14T14:38:17,757   pyckmeans/io/src/nucencode.cpp: In function ‘void encodeNucleotides_uint32(uint32_t*, int, int, uint8_t*)’:
2023-09-14T14:38:17,758   pyckmeans/io/src/nucencode.cpp:86:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:17,758      86 |     for (size_t i = 0; i < n; i++) {
2023-09-14T14:38:17,759         |                        ~~^~~
2023-09-14T14:38:17,760   pyckmeans/io/src/nucencode.cpp:87:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-14T14:38:17,760      87 |         for (size_t j = 0; j < m; j++) {
2023-09-14T14:38:17,761         |                            ~~^~~
2023-09-14T14:38:17,836   creating build/lib.linux-armv7l-cpython-311/pyckmeans/io/lib
2023-09-14T14:38:17,837   arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pyckmeans/io/src/nucencode.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pyckmeans/io/lib/nucencode.so
2023-09-14T14:38:17,978   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2023-09-14T14:38:17,978   !!

2023-09-14T14:38:17,979           ********************************************************************************
2023-09-14T14:38:17,980           Please avoid running ``setup.py`` directly.
2023-09-14T14:38:17,980           Instead, use pypa/build, pypa/installer or other
2023-09-14T14:38:17,981           standards-based tools.

2023-09-14T14:38:17,982           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2023-09-14T14:38:17,982           ********************************************************************************

2023-09-14T14:38:17,983   !!
2023-09-14T14:38:17,983     self.initialize_options()
2023-09-14T14:38:18,001   installing to build/bdist.linux-armv7l/wheel
2023-09-14T14:38:18,002   running install
2023-09-14T14:38:18,025   running install_lib
2023-09-14T14:38:18,049   creating build/bdist.linux-armv7l
2023-09-14T14:38:18,050   creating build/bdist.linux-armv7l/wheel
2023-09-14T14:38:18,051   creating build/bdist.linux-armv7l/wheel/pyckmeans
2023-09-14T14:38:18,053   creating build/bdist.linux-armv7l/wheel/pyckmeans/ordering
2023-09-14T14:38:18,054   copying build/lib.linux-armv7l-cpython-311/pyckmeans/ordering/__init__.py -> build/bdist.linux-armv7l/wheel/pyckmeans/ordering
2023-09-14T14:38:18,057   creating build/bdist.linux-armv7l/wheel/pyckmeans/knee
2023-09-14T14:38:18,058   copying build/lib.linux-armv7l-cpython-311/pyckmeans/knee/__init__.py -> build/bdist.linux-armv7l/wheel/pyckmeans/knee
2023-09-14T14:38:18,061   creating build/bdist.linux-armv7l/wheel/pyckmeans/distance
2023-09-14T14:38:18,062   creating build/bdist.linux-armv7l/wheel/pyckmeans/distance/lib
2023-09-14T14:38:18,063   copying build/lib.linux-armv7l-cpython-311/pyckmeans/distance/lib/distance.so -> build/bdist.linux-armv7l/wheel/pyckmeans/distance/lib
2023-09-14T14:38:18,067   copying build/lib.linux-armv7l-cpython-311/pyckmeans/distance/__init__.py -> build/bdist.linux-armv7l/wheel/pyckmeans/distance
2023-09-14T14:38:18,069   copying build/lib.linux-armv7l-cpython-311/pyckmeans/distance/c_interop.py -> build/bdist.linux-armv7l/wheel/pyckmeans/distance
2023-09-14T14:38:18,071   creating build/bdist.linux-armv7l/wheel/pyckmeans/core
2023-09-14T14:38:18,072   copying build/lib.linux-armv7l-cpython-311/pyckmeans/core/multickmeans.py -> build/bdist.linux-armv7l/wheel/pyckmeans/core
2023-09-14T14:38:18,075   copying build/lib.linux-armv7l-cpython-311/pyckmeans/core/utils.py -> build/bdist.linux-armv7l/wheel/pyckmeans/core
2023-09-14T14:38:18,077   copying build/lib.linux-armv7l-cpython-311/pyckmeans/core/wecr.py -> build/bdist.linux-armv7l/wheel/pyckmeans/core
2023-09-14T14:38:18,080   copying build/lib.linux-armv7l-cpython-311/pyckmeans/core/ckmeans.py -> build/bdist.linux-armv7l/wheel/pyckmeans/core
2023-09-14T14:38:18,082   copying build/lib.linux-armv7l-cpython-311/pyckmeans/core/__init__.py -> build/bdist.linux-armv7l/wheel/pyckmeans/core
2023-09-14T14:38:18,085   creating build/bdist.linux-armv7l/wheel/pyckmeans/io
2023-09-14T14:38:18,086   copying build/lib.linux-armv7l-cpython-311/pyckmeans/io/phylip.py -> build/bdist.linux-armv7l/wheel/pyckmeans/io
2023-09-14T14:38:18,088   creating build/bdist.linux-armv7l/wheel/pyckmeans/io/lib
2023-09-14T14:38:18,089   copying build/lib.linux-armv7l-cpython-311/pyckmeans/io/lib/nucencode.so -> build/bdist.linux-armv7l/wheel/pyckmeans/io/lib
2023-09-14T14:38:18,091   copying build/lib.linux-armv7l-cpython-311/pyckmeans/io/fasta.py -> build/bdist.linux-armv7l/wheel/pyckmeans/io
2023-09-14T14:38:18,093   copying build/lib.linux-armv7l-cpython-311/pyckmeans/io/nucleotide_alignment.py -> build/bdist.linux-armv7l/wheel/pyckmeans/io
2023-09-14T14:38:18,096   copying build/lib.linux-armv7l-cpython-311/pyckmeans/io/__init__.py -> build/bdist.linux-armv7l/wheel/pyckmeans/io
2023-09-14T14:38:18,097   copying build/lib.linux-armv7l-cpython-311/pyckmeans/io/csv.py -> build/bdist.linux-armv7l/wheel/pyckmeans/io
2023-09-14T14:38:18,099   copying build/lib.linux-armv7l-cpython-311/pyckmeans/io/c_interop.py -> build/bdist.linux-armv7l/wheel/pyckmeans/io
2023-09-14T14:38:18,101   creating build/bdist.linux-armv7l/wheel/pyckmeans/utils
2023-09-14T14:38:18,102   copying build/lib.linux-armv7l-cpython-311/pyckmeans/utils/plotting.py -> build/bdist.linux-armv7l/wheel/pyckmeans/utils
2023-09-14T14:38:18,105   copying build/lib.linux-armv7l-cpython-311/pyckmeans/utils/__init__.py -> build/bdist.linux-armv7l/wheel/pyckmeans/utils
2023-09-14T14:38:18,106   copying build/lib.linux-armv7l-cpython-311/pyckmeans/utils/progressbar.py -> build/bdist.linux-armv7l/wheel/pyckmeans/utils
2023-09-14T14:38:18,108   copying build/lib.linux-armv7l-cpython-311/pyckmeans/__init__.py -> build/bdist.linux-armv7l/wheel/pyckmeans
2023-09-14T14:38:18,110   creating build/bdist.linux-armv7l/wheel/pyckmeans/ordination
2023-09-14T14:38:18,111   copying build/lib.linux-armv7l-cpython-311/pyckmeans/ordination/utils.py -> build/bdist.linux-armv7l/wheel/pyckmeans/ordination
2023-09-14T14:38:18,113   copying build/lib.linux-armv7l-cpython-311/pyckmeans/ordination/__init__.py -> build/bdist.linux-armv7l/wheel/pyckmeans/ordination
2023-09-14T14:38:18,115   running install_egg_info
2023-09-14T14:38:18,174   running egg_info
2023-09-14T14:38:18,198   writing pyckmeans.egg-info/PKG-INFO
2023-09-14T14:38:18,201   writing dependency_links to pyckmeans.egg-info/dependency_links.txt
2023-09-14T14:38:18,202   writing requirements to pyckmeans.egg-info/requires.txt
2023-09-14T14:38:18,204   writing top-level names to pyckmeans.egg-info/top_level.txt
2023-09-14T14:38:18,234   reading manifest file 'pyckmeans.egg-info/SOURCES.txt'
2023-09-14T14:38:18,239   writing manifest file 'pyckmeans.egg-info/SOURCES.txt'
2023-09-14T14:38:18,240   Copying pyckmeans.egg-info to build/bdist.linux-armv7l/wheel/pyckmeans-0.9.2-py3.11.egg-info
2023-09-14T14:38:18,249   running install_scripts
2023-09-14T14:38:18,305   creating build/bdist.linux-armv7l/wheel/pyckmeans-0.9.2.dist-info/WHEEL
2023-09-14T14:38:18,307   creating '/tmp/pip-wheel-q1oi2_6d/pyckmeans-0.9.2-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-09-14T14:38:18,310   adding 'pyckmeans/__init__.py'
2023-09-14T14:38:18,312   adding 'pyckmeans/core/__init__.py'
2023-09-14T14:38:18,315   adding 'pyckmeans/core/ckmeans.py'
2023-09-14T14:38:18,318   adding 'pyckmeans/core/multickmeans.py'
2023-09-14T14:38:18,319   adding 'pyckmeans/core/utils.py'
2023-09-14T14:38:18,324   adding 'pyckmeans/core/wecr.py'
2023-09-14T14:38:18,327   adding 'pyckmeans/distance/__init__.py'
2023-09-14T14:38:18,328   adding 'pyckmeans/distance/c_interop.py'
2023-09-14T14:38:18,344   adding 'pyckmeans/distance/lib/distance.so'
2023-09-14T14:38:18,346   adding 'pyckmeans/io/__init__.py'
2023-09-14T14:38:18,347   adding 'pyckmeans/io/c_interop.py'
2023-09-14T14:38:18,349   adding 'pyckmeans/io/csv.py'
2023-09-14T14:38:18,350   adding 'pyckmeans/io/fasta.py'
2023-09-14T14:38:18,352   adding 'pyckmeans/io/nucleotide_alignment.py'
2023-09-14T14:38:18,354   adding 'pyckmeans/io/phylip.py'
2023-09-14T14:38:18,357   adding 'pyckmeans/io/lib/nucencode.so'
2023-09-14T14:38:18,359   adding 'pyckmeans/knee/__init__.py'
2023-09-14T14:38:18,362   adding 'pyckmeans/ordering/__init__.py'
2023-09-14T14:38:18,365   adding 'pyckmeans/ordination/__init__.py'
2023-09-14T14:38:18,366   adding 'pyckmeans/ordination/utils.py'
2023-09-14T14:38:18,368   adding 'pyckmeans/utils/__init__.py'
2023-09-14T14:38:18,369   adding 'pyckmeans/utils/plotting.py'
2023-09-14T14:38:18,371   adding 'pyckmeans/utils/progressbar.py'
2023-09-14T14:38:18,373   adding 'pyckmeans-0.9.2.dist-info/METADATA'
2023-09-14T14:38:18,374   adding 'pyckmeans-0.9.2.dist-info/WHEEL'
2023-09-14T14:38:18,375   adding 'pyckmeans-0.9.2.dist-info/top_level.txt'
2023-09-14T14:38:18,376   adding 'pyckmeans-0.9.2.dist-info/RECORD'
2023-09-14T14:38:18,378   removing build/bdist.linux-armv7l/wheel
2023-09-14T14:38:18,500   Building wheel for pyckmeans (setup.py): finished with status 'done'
2023-09-14T14:38:18,503   Created wheel for pyckmeans: filename=pyckmeans-0.9.2-cp311-cp311-linux_armv7l.whl size=91013 sha256=ea63d23c77f4b9af1d29af37f5e1c9bac23278e3a0a07ab8d8d0d409a71c1b63
2023-09-14T14:38:18,504   Stored in directory: /tmp/pip-ephem-wheel-cache-1gtrlz4l/wheels/75/54/91/8eeb21329967c2bcc857eb361d886f339e356d16cba6635de1
2023-09-14T14:38:18,516 Successfully built pyckmeans
2023-09-14T14:38:18,521 Removed build tracker: '/tmp/pip-build-tracker-xx941zdv'