2025-09-07T23:58:45,654 Created temporary directory: /tmp/pip-build-tracker-fanm2dd_ 2025-09-07T23:58:45,654 Initialized build tracking at /tmp/pip-build-tracker-fanm2dd_ 2025-09-07T23:58:45,655 Created build tracker: /tmp/pip-build-tracker-fanm2dd_ 2025-09-07T23:58:45,655 Entered build tracker: /tmp/pip-build-tracker-fanm2dd_ 2025-09-07T23:58:45,655 Created temporary directory: /tmp/pip-wheel-wq2ynixx 2025-09-07T23:58:45,658 Created temporary directory: /tmp/pip-ephem-wheel-cache-2t0ivoay 2025-09-07T23:58:45,717 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T23:58:45,719 2 location(s) to search for versions of scikit-bio: 2025-09-07T23:58:45,719 * https://pypi.org/simple/scikit-bio/ 2025-09-07T23:58:45,719 * https://www.piwheels.org/simple/scikit-bio/ 2025-09-07T23:58:45,719 Fetching project page and analyzing links: https://pypi.org/simple/scikit-bio/ 2025-09-07T23:58:45,720 Getting page https://pypi.org/simple/scikit-bio/ 2025-09-07T23:58:45,721 Found index url https://pypi.org/simple/ 2025-09-07T23:58:45,791 Fetched page https://pypi.org/simple/scikit-bio/ as application/vnd.pypi.simple.v1+json 2025-09-07T23:58:45,798 Found link https://files.pythonhosted.org/packages/e0/4f/9e53704ce04a5e60511449a5e16511c6e20219ed0932e4aeea84fe2189fd/scikit-bio-0.1.0.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.1.0 2025-09-07T23:58:45,798 Found link https://files.pythonhosted.org/packages/91/8b/ea20137d6b84808b3dd6a7ad162dd80dcda40934428824d1ce87b8983b81/scikit-bio-0.1.1.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.1.1 2025-09-07T23:58:45,799 Found link https://files.pythonhosted.org/packages/5f/6e/adc704fa25e9789bfc17882261010320ea9c6148d9d2e28083a5e57a3e9f/scikit-bio-0.1.2.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.1.2 2025-09-07T23:58:45,799 Found link https://files.pythonhosted.org/packages/da/03/82ad31dc38265135b432b34b2cec0680fee841e0bdc5f90b5a4596beafb3/scikit-bio-0.1.3.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.1.3 2025-09-07T23:58:45,799 Found link https://files.pythonhosted.org/packages/b0/70/92b5bb9fc66ef4d54e1bf67626bda04a41ed723b5eb25c018154728e2b26/scikit-bio-0.1.4.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.1.4 2025-09-07T23:58:45,799 Found link https://files.pythonhosted.org/packages/5f/21/c6879978a222a04f1ac1b0a535a18111c84367ee22a5c93e6c0503f57e01/scikit-bio-0.1.5.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.1.5 2025-09-07T23:58:45,800 Found link https://files.pythonhosted.org/packages/99/76/0c0bd2d6d9973a001477535c68772ff35f543324e36afe21c4f7d6721327/scikit-bio-0.2.0.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.2.0 2025-09-07T23:58:45,800 Found link 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https://files.pythonhosted.org/packages/98/ee/08995b89efccf2bf8a0307a1eb7825dceb199e64a3db24cec832c0ca0baf/scikit-bio-0.5.2.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.5.2 2025-09-07T23:58:45,802 Found link https://files.pythonhosted.org/packages/39/07/4e3bcf7a7c254154ac445684d5f646ccc4a6ce6bfc3b0cc8030136215b8a/scikit-bio-0.5.3.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.5.3 2025-09-07T23:58:45,802 Found link https://files.pythonhosted.org/packages/ed/e0/3ae790c5c260be0968a6d41108e35f327365e5460c9d8672714fd136817d/scikit-bio-0.5.4.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.5.4 2025-09-07T23:58:45,802 Found link https://files.pythonhosted.org/packages/2d/ff/3a909ae8c212305846f7e87f86f3902408b55b958eccedf5d4349e76c671/scikit-bio-0.5.5.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.5.5 2025-09-07T23:58:45,803 Found link https://files.pythonhosted.org/packages/66/b0/054ef21e024d24422882958072973cd192b492e004a3ce4e9614ef173d9b/scikit-bio-0.5.6.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.5.6 2025-09-07T23:58:45,803 Found link https://files.pythonhosted.org/packages/8c/a4/6ec875ba9a56f7705529aecc745ca3eaee6d90b87cd103281be7a032b412/scikit-bio-0.5.7.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.5.7 2025-09-07T23:58:45,803 Found link https://files.pythonhosted.org/packages/f3/5b/7ae2c3cca0cee7825a24b9c68d7ba0893ef816c41e43aeccf9ca3bc63cb7/scikit-bio-0.5.8.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.5.8 2025-09-07T23:58:45,803 Found link https://files.pythonhosted.org/packages/0b/ff/c3ed458b9c7b1cfdaadfcab2e015f3e21672bd57a8e216a319442e4c8a1b/scikit-bio-0.5.9.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.5.9 2025-09-07T23:58:45,803 Found link https://files.pythonhosted.org/packages/9d/77/531cf69c99cb398c5abf8545259b88ee256bfdb72e5972bcfdbcb9942751/scikit-bio-0.6.0.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.6.0 2025-09-07T23:58:45,804 Found link https://files.pythonhosted.org/packages/12/6b/1a01f3df88503d9a11916972f0b0c2aed13d516f159336b4bdcfcd04098a/scikit-bio-0.6.1.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.6.1 2025-09-07T23:58:45,804 Found link https://files.pythonhosted.org/packages/29/28/07326aa931c67d491d3053e2875b6c8f2904e661d9ab7c2840c3ae6b3780/scikit-bio-0.6.2.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.6.2 2025-09-07T23:58:45,804 Found link https://files.pythonhosted.org/packages/65/59/31e499edc0d045acab799b7117130e9c9de22371be57ac311f2f0b235dc4/scikit-bio-0.6.3.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.6.3 2025-09-07T23:58:45,804 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/59/8b/f90ee0325c7f59573bdf8d4a5a5717ca710f067a081fd46f3768600a200d/scikit_bio-0.7.0-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,805 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/57/c6/0864476e63935459eb4d474f210e70ca1b0aa9689bb1beccbeae582587ce/scikit_bio-0.7.0-cp310-cp310-macosx_11_0_arm64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,805 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/2c/ca/087675f3fd6608142be8c53e6875a1a730e0fa1250a85421677570445839/scikit_bio-0.7.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,805 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/c8/69/da203001d9a0d4f2dc14426617e5eed76c9ff059f6c2a94023bf48e204cb/scikit_bio-0.7.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,805 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/45/97/3b928b1f075a6033326244e125f0e3a518fe75c17278359d1835ca4ccb24/scikit_bio-0.7.0-cp310-cp310-win_amd64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,805 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/3d/66/5f238ff8fa25080d5baf82287297bfd1e6dbeab45ef3ff1b0f6e1a7c017e/scikit_bio-0.7.0-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,805 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/f9/8b/8ef6e40a818067bdaf57fa779eadbc8ef73f333dbd50fb09daeae13de1f2/scikit_bio-0.7.0-cp311-cp311-macosx_11_0_arm64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,805 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/f0/66/6cb6e9ba1e67f65a27b34fcd33b457cb0fea73f93dc184ea1bf38562f012/scikit_bio-0.7.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,806 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/ad/27/e359f131018cf988f1e4f5e7380db7db43ba4202ffc9ba9e8f6cfb1988f5/scikit_bio-0.7.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,806 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/db/99/6b0ce81f81e2cfe06c899455b149e7f8393cd3ba9a8905efe18c36894420/scikit_bio-0.7.0-cp311-cp311-win_amd64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,806 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/43/9b/bf339d439568a4fa0ab6e7e545c4487b1cf86e6245f98be0d922f4677ddc/scikit_bio-0.7.0-cp312-cp312-macosx_10_13_x86_64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,806 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/1d/e9/7a5dd2e04bbd361907f5a1942fa4b6aeecfa453801f4c047c55b51036df2/scikit_bio-0.7.0-cp312-cp312-macosx_11_0_arm64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,806 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/19/4b/b63123cf09c3375fa90cbfc02febf32cc20429a49c03d71f37febed7c52d/scikit_bio-0.7.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,806 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/f5/02/b178ca48305a230e080732dd02233e0824b1a9b41b273acf2444de116be2/scikit_bio-0.7.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,806 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/5f/a8/199cafe05bb77bf274f0a3db8f5199f4b2966db37589f9e5ec6a212c0b9c/scikit_bio-0.7.0-cp312-cp312-win_amd64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,806 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/d4/31/b943fcf7d4579b4751002ad9a48e62e9f0c7db542dd440f7e3e82f50f58b/scikit_bio-0.7.0-cp313-cp313-macosx_10_13_x86_64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,807 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/e7/af/5f3452f0dce0f0a3c7ccb9f067e410b50a8d188c4fb56426f8785317333d/scikit_bio-0.7.0-cp313-cp313-macosx_11_0_arm64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,807 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/7d/20/ef1d2a8accb946cc31b5b987a46d197f69d1e89bab76b5e9cb4235a355f9/scikit_bio-0.7.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,807 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/1c/46/3f05eedb58e13c21f5ab7496e9735da2f008aa66038b268ea46138a3e48d/scikit_bio-0.7.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,807 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/40/e9/2f7d72ef933e9328b929295ada98ad2c5fbdc5b3c6bd2f4d886f14d4f90a/scikit_bio-0.7.0-cp313-cp313-win_amd64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,807 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/b5/fa/3a7770c445111c6b957aba701887f22506faef8145965a6b9d2816cfd896/scikit_bio-0.7.0-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,807 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/4e/07/e2a29ccbb31208c98ff2c7b61b00614885f781474891ebf249d85495e238/scikit_bio-0.7.0-cp39-cp39-macosx_11_0_arm64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,807 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/89/15/829f7da8e5083f4d2e3dd1ef24faa6b32da2bf492547bd6d385e92fda127/scikit_bio-0.7.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,808 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/4a/34/687f9e4dc73e39a56277e2aa900577fccb3c99ef28a5acc5fc258028e2ac/scikit_bio-0.7.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,808 Skipping link: No binaries permitted for scikit-bio: https://files.pythonhosted.org/packages/6c/a5/75fd40c8bf70836216fffe57bdd80c78959d5cc21c23927ada892b246f3d/scikit_bio-0.7.0-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9) 2025-09-07T23:58:45,808 Found link https://files.pythonhosted.org/packages/90/fe/be2d10a390ceea3a3657e77a5ebd16aa167509b10a709125f3a8e4fd663a/scikit_bio-0.7.0.tar.gz (from https://pypi.org/simple/scikit-bio/) (requires-python:>=3.9), version: 0.7.0 2025-09-07T23:58:45,809 Fetching project page and analyzing links: https://www.piwheels.org/simple/scikit-bio/ 2025-09-07T23:58:45,809 Getting page https://www.piwheels.org/simple/scikit-bio/ 2025-09-07T23:58:45,810 Found index url https://www.piwheels.org/simple/ 2025-09-07T23:58:45,911 Fetched page https://www.piwheels.org/simple/scikit-bio/ as text/html 2025-09-07T23:58:45,917 Skipping link: No binaries permitted for scikit-bio: 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https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.7-cp39-cp39-linux_armv6l.whl#sha256=1fc89935500ef73303aef4292735583d83456271b51534e31497a2d5eb2b8d3b (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:58:45,921 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.7-cp39-cp39-linux_armv7l.whl#sha256=1fc89935500ef73303aef4292735583d83456271b51534e31497a2d5eb2b8d3b (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:58:45,921 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.7-cp37-cp37m-linux_armv6l.whl#sha256=fb1f612aaab958a170d467b2c9a6c1c6c2249bce52c095b7d7b7d8cc07c9ce31 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:58:45,921 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.7-cp37-cp37m-linux_armv7l.whl#sha256=fb1f612aaab958a170d467b2c9a6c1c6c2249bce52c095b7d7b7d8cc07c9ce31 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:58:45,922 Skipping link: not a file: https://www.piwheels.org/simple/scikit-bio/ 2025-09-07T23:58:45,922 Skipping link: not a file: https://pypi.org/simple/scikit-bio/ 2025-09-07T23:58:45,949 Given no hashes to check 1 links for project 'scikit-bio': discarding no candidates 2025-09-07T23:58:45,950 Collecting scikit-bio==0.1.3 2025-09-07T23:58:45,951 Created temporary directory: /tmp/pip-unpack-1_9qt_7v 2025-09-07T23:58:46,252 Downloading scikit-bio-0.1.3.tar.gz (1.7 MB) 2025-09-07T23:58:46,773 Added scikit-bio==0.1.3 from https://files.pythonhosted.org/packages/da/03/82ad31dc38265135b432b34b2cec0680fee841e0bdc5f90b5a4596beafb3/scikit-bio-0.1.3.tar.gz to build tracker '/tmp/pip-build-tracker-fanm2dd_' 2025-09-07T23:58:46,774 Running setup.py (path:/tmp/pip-wheel-wq2ynixx/scikit-bio_3914b064406a4be0b52bb926f44abf99/setup.py) egg_info for package scikit-bio 2025-09-07T23:58:46,774 Created temporary directory: /tmp/pip-pip-egg-info-dp4bhar_ 2025-09-07T23:58:46,775 Preparing metadata (setup.py): started 2025-09-07T23:58:46,775 Running command python setup.py egg_info 2025-09-07T23:58:47,679 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-07T23:58:47,679 warnings.warn(msg) 2025-09-07T23:58:48,094 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:58:48,094 !! 2025-09-07T23:58:48,094 ******************************************************************************** 2025-09-07T23:58:48,094 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:58:48,094 License :: OSI Approved :: BSD License 2025-09-07T23:58:48,095 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:58:48,095 ******************************************************************************** 2025-09-07T23:58:48,095 !! 2025-09-07T23:58:48,095 self._finalize_license_expression() 2025-09-07T23:58:48,168 running egg_info 2025-09-07T23:58:48,241 creating /tmp/pip-pip-egg-info-dp4bhar_/scikit_bio.egg-info 2025-09-07T23:58:48,241 writing /tmp/pip-pip-egg-info-dp4bhar_/scikit_bio.egg-info/PKG-INFO 2025-09-07T23:58:48,245 writing dependency_links to /tmp/pip-pip-egg-info-dp4bhar_/scikit_bio.egg-info/dependency_links.txt 2025-09-07T23:58:48,247 writing requirements to /tmp/pip-pip-egg-info-dp4bhar_/scikit_bio.egg-info/requires.txt 2025-09-07T23:58:48,247 writing top-level names to /tmp/pip-pip-egg-info-dp4bhar_/scikit_bio.egg-info/top_level.txt 2025-09-07T23:58:48,248 writing manifest file '/tmp/pip-pip-egg-info-dp4bhar_/scikit_bio.egg-info/SOURCES.txt' 2025-09-07T23:58:48,566 reading manifest file '/tmp/pip-pip-egg-info-dp4bhar_/scikit_bio.egg-info/SOURCES.txt' 2025-09-07T23:58:48,567 reading manifest template 'MANIFEST.in' 2025-09-07T23:58:48,570 warning: no directories found matching 'examples' 2025-09-07T23:58:48,579 no previously-included directories found matching 'doc/build' 2025-09-07T23:58:48,581 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-09-07T23:58:48,582 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2025-09-07T23:58:48,583 adding license file 'COPYING.txt' 2025-09-07T23:58:48,595 writing manifest file '/tmp/pip-pip-egg-info-dp4bhar_/scikit_bio.egg-info/SOURCES.txt' 2025-09-07T23:58:48,732 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T23:58:48,737 Source in /tmp/pip-wheel-wq2ynixx/scikit-bio_3914b064406a4be0b52bb926f44abf99 has version 0.1.3, which satisfies requirement scikit-bio==0.1.3 from https://files.pythonhosted.org/packages/da/03/82ad31dc38265135b432b34b2cec0680fee841e0bdc5f90b5a4596beafb3/scikit-bio-0.1.3.tar.gz 2025-09-07T23:58:48,738 Removed scikit-bio==0.1.3 from https://files.pythonhosted.org/packages/da/03/82ad31dc38265135b432b34b2cec0680fee841e0bdc5f90b5a4596beafb3/scikit-bio-0.1.3.tar.gz from build tracker '/tmp/pip-build-tracker-fanm2dd_' 2025-09-07T23:58:48,745 Created temporary directory: /tmp/pip-unpack-65_gbako 2025-09-07T23:58:48,745 Created temporary directory: /tmp/pip-unpack-1pux2osp 2025-09-07T23:58:48,745 Building wheels for collected packages: scikit-bio 2025-09-07T23:58:48,746 Created temporary directory: /tmp/pip-wheel-agn0oa6_ 2025-09-07T23:58:48,747 DEPRECATION: Building 'scikit-bio' 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 'scikit-bio'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-07T23:58:48,748 Building wheel for scikit-bio (setup.py): started 2025-09-07T23:58:48,749 Destination directory: /tmp/pip-wheel-agn0oa6_ 2025-09-07T23:58:48,749 Running command python setup.py bdist_wheel 2025-09-07T23:58:49,639 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-07T23:58:49,639 warnings.warn(msg) 2025-09-07T23:58:50,028 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:58:50,028 !! 2025-09-07T23:58:50,028 ******************************************************************************** 2025-09-07T23:58:50,028 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:58:50,029 License :: OSI Approved :: BSD License 2025-09-07T23:58:50,029 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:58:50,029 ******************************************************************************** 2025-09-07T23:58:50,029 !! 2025-09-07T23:58:50,029 self._finalize_license_expression() 2025-09-07T23:58:50,030 running bdist_wheel 2025-09-07T23:58:50,396 running build 2025-09-07T23:58:50,396 running build_py 2025-09-07T23:58:50,472 creating build/lib.linux-armv7l-cpython-313/skbio 2025-09-07T23:58:50,473 copying skbio/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio 2025-09-07T23:58:50,474 creating build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:58:50,474 copying skbio/util/testing.py -> build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:58:50,475 copying skbio/util/sort.py -> build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:58:50,475 copying skbio/util/misc.py -> build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:58:50,476 copying skbio/util/io.py -> build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:58:50,476 copying skbio/util/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:58:50,477 creating build/lib.linux-armv7l-cpython-313/skbio/parse 2025-09-07T23:58:50,477 copying skbio/parse/record_finder.py -> build/lib.linux-armv7l-cpython-313/skbio/parse 2025-09-07T23:58:50,478 copying skbio/parse/record.py -> build/lib.linux-armv7l-cpython-313/skbio/parse 2025-09-07T23:58:50,478 copying skbio/parse/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/parse 2025-09-07T23:58:50,479 creating build/lib.linux-armv7l-cpython-313/skbio/math 2025-09-07T23:58:50,479 copying skbio/math/subsample.py -> build/lib.linux-armv7l-cpython-313/skbio/math 2025-09-07T23:58:50,480 copying skbio/math/gradient.py -> build/lib.linux-armv7l-cpython-313/skbio/math 2025-09-07T23:58:50,481 copying skbio/math/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math 2025-09-07T23:58:50,481 creating build/lib.linux-armv7l-cpython-313/skbio/format 2025-09-07T23:58:50,481 copying skbio/format/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/format 2025-09-07T23:58:50,482 creating build/lib.linux-armv7l-cpython-313/skbio/draw 2025-09-07T23:58:50,482 copying skbio/draw/distributions.py -> build/lib.linux-armv7l-cpython-313/skbio/draw 2025-09-07T23:58:50,483 copying skbio/draw/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/draw 2025-09-07T23:58:50,484 creating build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:58:50,484 copying skbio/core/workflow.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:58:50,485 copying skbio/core/warning.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:58:50,485 copying skbio/core/sequence.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:58:50,486 copying skbio/core/genetic_code.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:58:50,487 copying skbio/core/exception.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:58:50,487 copying skbio/core/distance.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:58:50,488 copying skbio/core/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:58:50,489 creating build/lib.linux-armv7l-cpython-313/skbio/app 2025-09-07T23:58:50,489 copying skbio/app/util.py -> build/lib.linux-armv7l-cpython-313/skbio/app 2025-09-07T23:58:50,489 copying skbio/app/parameters.py -> build/lib.linux-armv7l-cpython-313/skbio/app 2025-09-07T23:58:50,490 copying skbio/app/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/app 2025-09-07T23:58:50,491 creating build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:58:50,491 copying skbio/util/tests/test_testing.py -> build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:58:50,492 copying skbio/util/tests/test_sort.py -> build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:58:50,492 copying skbio/util/tests/test_misc.py -> build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:58:50,493 copying skbio/util/tests/test_io.py -> build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:58:50,493 copying skbio/util/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:58:50,494 creating build/lib.linux-armv7l-cpython-313/skbio/parse/tests 2025-09-07T23:58:50,494 copying skbio/parse/tests/test_record_finder.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/tests 2025-09-07T23:58:50,495 copying skbio/parse/tests/test_record.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/tests 2025-09-07T23:58:50,495 copying skbio/parse/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/tests 2025-09-07T23:58:50,496 creating build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:58:50,496 copying skbio/parse/sequences/iterator.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:58:50,497 copying skbio/parse/sequences/fastq.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:58:50,497 copying skbio/parse/sequences/fasta.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:58:50,498 copying skbio/parse/sequences/factory.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:58:50,498 copying skbio/parse/sequences/clustal.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:58:50,499 copying skbio/parse/sequences/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:58:50,500 creating build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:58:50,500 copying skbio/parse/sequences/tests/test_iterator.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:58:50,501 copying skbio/parse/sequences/tests/test_fastq.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:58:50,501 copying skbio/parse/sequences/tests/test_fasta.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:58:50,502 copying skbio/parse/sequences/tests/test_factory.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:58:50,502 copying skbio/parse/sequences/tests/test_clustal.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:58:50,503 copying skbio/parse/sequences/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:58:50,503 creating build/lib.linux-armv7l-cpython-313/skbio/math/tests 2025-09-07T23:58:50,504 copying skbio/math/tests/test_subsample.py -> build/lib.linux-armv7l-cpython-313/skbio/math/tests 2025-09-07T23:58:50,504 copying skbio/math/tests/test_gradient.py -> build/lib.linux-armv7l-cpython-313/skbio/math/tests 2025-09-07T23:58:50,505 copying skbio/math/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/tests 2025-09-07T23:58:50,506 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats 2025-09-07T23:58:50,506 copying skbio/math/stats/spatial.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats 2025-09-07T23:58:50,507 copying skbio/math/stats/misc.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats 2025-09-07T23:58:50,507 copying skbio/math/stats/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats 2025-09-07T23:58:50,508 creating build/lib.linux-armv7l-cpython-313/skbio/math/diversity 2025-09-07T23:58:50,508 copying skbio/math/diversity/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity 2025-09-07T23:58:50,509 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/tests 2025-09-07T23:58:50,509 copying skbio/math/stats/tests/test_spatial.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/tests 2025-09-07T23:58:50,509 copying skbio/math/stats/tests/test_misc.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/tests 2025-09-07T23:58:50,510 copying skbio/math/stats/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/tests 2025-09-07T23:58:50,511 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:58:50,511 copying skbio/math/stats/ordination/utils.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:58:50,512 copying skbio/math/stats/ordination/redundancy_analysis.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:58:50,512 copying skbio/math/stats/ordination/principal_coordinate_analysis.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:58:50,513 copying skbio/math/stats/ordination/correspondence_analysis.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:58:50,513 copying skbio/math/stats/ordination/canonical_correspondence_analysis.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:58:50,514 copying skbio/math/stats/ordination/base.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:58:50,514 copying skbio/math/stats/ordination/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:58:50,515 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:58:50,516 copying skbio/math/stats/distance/permanova.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:58:50,516 copying skbio/math/stats/distance/base.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:58:50,517 copying skbio/math/stats/distance/anosim.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:58:50,517 copying skbio/math/stats/distance/_mantel.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:58:50,518 copying skbio/math/stats/distance/_bioenv.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:58:50,518 copying skbio/math/stats/distance/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:58:50,519 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests 2025-09-07T23:58:50,519 copying skbio/math/stats/ordination/tests/test_ordination.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests 2025-09-07T23:58:50,520 copying skbio/math/stats/ordination/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests 2025-09-07T23:58:50,521 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:58:50,521 copying skbio/math/stats/distance/tests/test_permanova.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:58:50,521 copying skbio/math/stats/distance/tests/test_mantel.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:58:50,522 copying skbio/math/stats/distance/tests/test_bioenv.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:58:50,523 copying skbio/math/stats/distance/tests/test_base.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:58:50,523 copying skbio/math/stats/distance/tests/test_anosim.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:58:50,524 copying skbio/math/stats/distance/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:58:50,525 creating build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:58:50,525 copying skbio/math/diversity/alpha/lladser.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:58:50,525 copying skbio/math/diversity/alpha/gini.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:58:50,526 copying skbio/math/diversity/alpha/chao1.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:58:50,526 copying skbio/math/diversity/alpha/base.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:58:50,527 copying skbio/math/diversity/alpha/ace.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:58:50,528 copying skbio/math/diversity/alpha/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:58:50,528 creating build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:58:50,529 copying skbio/math/diversity/alpha/tests/test_lladser.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:58:50,529 copying skbio/math/diversity/alpha/tests/test_gini.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:58:50,530 copying skbio/math/diversity/alpha/tests/test_chao1.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:58:50,530 copying skbio/math/diversity/alpha/tests/test_base.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:58:50,531 copying skbio/math/diversity/alpha/tests/test_ace.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:58:50,531 copying skbio/math/diversity/alpha/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:58:50,532 creating build/lib.linux-armv7l-cpython-313/skbio/format/tests 2025-09-07T23:58:50,532 copying skbio/format/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/format/tests 2025-09-07T23:58:50,533 creating build/lib.linux-armv7l-cpython-313/skbio/format/sequences 2025-09-07T23:58:50,533 copying skbio/format/sequences/fastq.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences 2025-09-07T23:58:50,534 copying skbio/format/sequences/fasta.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences 2025-09-07T23:58:50,534 copying skbio/format/sequences/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences 2025-09-07T23:58:50,535 creating build/lib.linux-armv7l-cpython-313/skbio/format/sequences/tests 2025-09-07T23:58:50,535 copying skbio/format/sequences/tests/test_fastq.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences/tests 2025-09-07T23:58:50,536 copying skbio/format/sequences/tests/test_fasta.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences/tests 2025-09-07T23:58:50,536 copying skbio/format/sequences/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences/tests 2025-09-07T23:58:50,537 creating build/lib.linux-armv7l-cpython-313/skbio/draw/tests 2025-09-07T23:58:50,537 copying skbio/draw/tests/test_distributions.py -> build/lib.linux-armv7l-cpython-313/skbio/draw/tests 2025-09-07T23:58:50,538 copying skbio/draw/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/draw/tests 2025-09-07T23:58:50,539 creating build/lib.linux-armv7l-cpython-313/skbio/core/tree 2025-09-07T23:58:50,539 copying skbio/core/tree/trie.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree 2025-09-07T23:58:50,539 copying skbio/core/tree/tree.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree 2025-09-07T23:58:50,540 copying skbio/core/tree/_nj.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree 2025-09-07T23:58:50,541 copying skbio/core/tree/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree 2025-09-07T23:58:50,542 creating build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:58:50,542 copying skbio/core/tests/test_workflow.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:58:50,542 copying skbio/core/tests/test_sequence.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:58:50,543 copying skbio/core/tests/test_genetic_code.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:58:50,544 copying skbio/core/tests/test_distance.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:58:50,544 copying skbio/core/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:58:50,545 creating build/lib.linux-armv7l-cpython-313/skbio/core/alignment 2025-09-07T23:58:50,545 copying skbio/core/alignment/alignment.py -> build/lib.linux-armv7l-cpython-313/skbio/core/alignment 2025-09-07T23:58:50,546 copying skbio/core/alignment/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core/alignment 2025-09-07T23:58:50,547 creating build/lib.linux-armv7l-cpython-313/skbio/core/tree/tests 2025-09-07T23:58:50,547 copying skbio/core/tree/tests/test_trie.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree/tests 2025-09-07T23:58:50,548 copying skbio/core/tree/tests/test_tree.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree/tests 2025-09-07T23:58:50,548 copying skbio/core/tree/tests/test_nj.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree/tests 2025-09-07T23:58:50,549 copying skbio/core/tree/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree/tests 2025-09-07T23:58:50,550 creating build/lib.linux-armv7l-cpython-313/skbio/core/alignment/tests 2025-09-07T23:58:50,550 copying skbio/core/alignment/tests/test_alignment.py -> build/lib.linux-armv7l-cpython-313/skbio/core/alignment/tests 2025-09-07T23:58:50,551 copying skbio/core/alignment/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core/alignment/tests 2025-09-07T23:58:50,551 creating build/lib.linux-armv7l-cpython-313/skbio/core/alignment/ssw 2025-09-07T23:58:50,552 copying skbio/core/alignment/ssw/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core/alignment/ssw 2025-09-07T23:58:50,552 creating build/lib.linux-armv7l-cpython-313/skbio/core/alignment/ssw/tests 2025-09-07T23:58:50,553 copying skbio/core/alignment/ssw/tests/test_ssw.py -> build/lib.linux-armv7l-cpython-313/skbio/core/alignment/ssw/tests 2025-09-07T23:58:50,553 copying skbio/core/alignment/ssw/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core/alignment/ssw/tests 2025-09-07T23:58:50,554 creating build/lib.linux-armv7l-cpython-313/skbio/app/tests 2025-09-07T23:58:50,554 copying skbio/app/tests/test_util.py -> build/lib.linux-armv7l-cpython-313/skbio/app/tests 2025-09-07T23:58:50,555 copying skbio/app/tests/test_parameters.py -> build/lib.linux-armv7l-cpython-313/skbio/app/tests 2025-09-07T23:58:50,556 copying skbio/app/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/app/tests 2025-09-07T23:58:50,570 creating build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests/data 2025-09-07T23:58:50,570 copying skbio/parse/sequences/tests/data/noextensionfasta -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests/data 2025-09-07T23:58:50,571 copying skbio/parse/sequences/tests/data/fq1.fq -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests/data 2025-09-07T23:58:50,571 copying skbio/parse/sequences/tests/data/fq1.fastq.gz -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests/data 2025-09-07T23:58:50,572 copying skbio/parse/sequences/tests/data/fna1.qual -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests/data 2025-09-07T23:58:50,572 copying skbio/parse/sequences/tests/data/fna1.fna.gz -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests/data 2025-09-07T23:58:50,573 copying skbio/parse/sequences/tests/data/fna1.fasta -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests/data 2025-09-07T23:58:50,573 creating build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,573 copying skbio/math/tests/data/vr_real_raw -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,574 copying skbio/math/tests/data/vr_real_out -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,575 copying skbio/math/tests/data/vr_raw -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,575 copying skbio/math/tests/data/vr_out -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,576 copying skbio/math/tests/data/gr_wo_msg_raw -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,576 copying skbio/math/tests/data/gr_wo_msg_out -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,577 copying skbio/math/tests/data/gr_w_msg_raw -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,577 copying skbio/math/tests/data/gr_w_msg_out -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,578 copying skbio/math/tests/data/cr_no_data_raw -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,578 copying skbio/math/tests/data/cr_no_data_out -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,579 copying skbio/math/tests/data/cr_data_raw -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,579 copying skbio/math/tests/data/cr_data_out -> build/lib.linux-armv7l-cpython-313/skbio/math/tests/data 2025-09-07T23:58:50,580 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,580 copying skbio/math/stats/ordination/tests/data/v_error9 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,580 copying skbio/math/stats/ordination/tests/data/v_error8 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,581 copying skbio/math/stats/ordination/tests/data/v_error7 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,581 copying skbio/math/stats/ordination/tests/data/v_error6 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,582 copying skbio/math/stats/ordination/tests/data/v_error5 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,582 copying skbio/math/stats/ordination/tests/data/v_error4 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,583 copying skbio/math/stats/ordination/tests/data/v_error3 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,583 copying skbio/math/stats/ordination/tests/data/v_error2 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,584 copying skbio/math/stats/ordination/tests/data/v_error10 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,585 copying skbio/math/stats/ordination/tests/data/v_error1 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,585 copying skbio/math/stats/ordination/tests/data/PCoA_sample_data_3_scores -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,586 copying skbio/math/stats/ordination/tests/data/PCoA_sample_data_3 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,586 copying skbio/math/stats/ordination/tests/data/PCoA_sample_data_2 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,587 copying skbio/math/stats/ordination/tests/data/PCoA_sample_data -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,587 copying skbio/math/stats/ordination/tests/data/L&L_CA_data_scores -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,588 copying skbio/math/stats/ordination/tests/data/L&L_CA_data -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,588 copying skbio/math/stats/ordination/tests/data/exp_PCoAzeros_site -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,589 copying skbio/math/stats/ordination/tests/data/exp_PCoAEigenResults_site -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,589 copying skbio/math/stats/ordination/tests/data/exp_OrdRes_RDA_species -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,590 copying skbio/math/stats/ordination/tests/data/exp_OrdRes_RDA_site_constraints -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,590 copying skbio/math/stats/ordination/tests/data/exp_OrdRes_RDA_site -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,591 copying skbio/math/stats/ordination/tests/data/exp_OrdRes_PCoA_site -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,591 copying skbio/math/stats/ordination/tests/data/exp_OrdRes_CCA_species -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,592 copying skbio/math/stats/ordination/tests/data/exp_OrdRes_CCA_site_constraints -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,593 copying skbio/math/stats/ordination/tests/data/exp_OrdRes_CCA_site -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,593 copying skbio/math/stats/ordination/tests/data/example3_Y -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,594 copying skbio/math/stats/ordination/tests/data/example3_X -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,594 copying skbio/math/stats/ordination/tests/data/example3_species_scaling2_from_vegan -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,595 copying skbio/math/stats/ordination/tests/data/example3_species_scaling1_from_vegan -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,595 copying skbio/math/stats/ordination/tests/data/example3_site_scaling2_from_vegan -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,596 copying skbio/math/stats/ordination/tests/data/example3_site_scaling1_from_vegan -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,596 copying skbio/math/stats/ordination/tests/data/example3_scores -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,597 copying skbio/math/stats/ordination/tests/data/example2_Y -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,597 copying skbio/math/stats/ordination/tests/data/example2_X -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,598 copying skbio/math/stats/ordination/tests/data/example2_species_scaling2_from_vegan -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,598 copying skbio/math/stats/ordination/tests/data/example2_species_scaling1_from_vegan -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,599 copying skbio/math/stats/ordination/tests/data/example2_site_scaling2_from_vegan -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,599 copying skbio/math/stats/ordination/tests/data/example2_site_scaling1_from_vegan -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,600 copying skbio/math/stats/ordination/tests/data/example2_scores -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,600 copying skbio/math/stats/ordination/tests/data/error6 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,601 copying skbio/math/stats/ordination/tests/data/error5 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,601 copying skbio/math/stats/ordination/tests/data/error4 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,602 copying skbio/math/stats/ordination/tests/data/error3 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,602 copying skbio/math/stats/ordination/tests/data/error2 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,603 copying skbio/math/stats/ordination/tests/data/error1 -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests/data 2025-09-07T23:58:50,603 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,604 copying skbio/math/stats/distance/tests/data/pwmantel_exp_results_too_few_permutations.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,604 copying skbio/math/stats/distance/tests/data/pwmantel_exp_results_reordered_distance_matrices.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,605 copying skbio/math/stats/distance/tests/data/pwmantel_exp_results_na_p_value.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,606 copying skbio/math/stats/distance/tests/data/pwmantel_exp_results_minimal_with_labels.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,606 copying skbio/math/stats/distance/tests/data/pwmantel_exp_results_minimal.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,607 copying skbio/math/stats/distance/tests/data/pwmantel_exp_results_duplicate_dms.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,607 copying skbio/math/stats/distance/tests/data/mantel_veg_dm_vegan.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,608 copying skbio/math/stats/distance/tests/data/mantel_env_dm_vegan.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,608 copying skbio/math/stats/distance/tests/data/exp_results_single_column.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,609 copying skbio/math/stats/distance/tests/data/exp_results_different_column_order.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,609 copying skbio/math/stats/distance/tests/data/exp_results.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,610 copying skbio/math/stats/distance/tests/data/dm_reordered.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,610 copying skbio/math/stats/distance/tests/data/dm.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,611 copying skbio/math/stats/distance/tests/data/df_extra_column.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,611 copying skbio/math/stats/distance/tests/data/df.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,612 copying skbio/math/stats/distance/tests/data/bioenv_exp_results_vegan.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,612 copying skbio/math/stats/distance/tests/data/bioenv_dm_vegan.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,613 copying skbio/math/stats/distance/tests/data/bioenv_df_vegan.txt -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests/data 2025-09-07T23:58:50,613 creating build/lib.linux-armv7l-cpython-313/skbio/core/tests/data 2025-09-07T23:58:50,614 copying skbio/core/tests/data/dm_3x3.txt -> build/lib.linux-armv7l-cpython-313/skbio/core/tests/data 2025-09-07T23:58:50,614 copying skbio/core/tests/data/dm_2x2_asym.txt -> build/lib.linux-armv7l-cpython-313/skbio/core/tests/data 2025-09-07T23:58:50,615 copying skbio/core/tests/data/bad_dm.txt -> build/lib.linux-armv7l-cpython-313/skbio/core/tests/data 2025-09-07T23:58:50,623 running build_ext 2025-09-07T23:58:50,951 building 'skbio.math._subsample' extension 2025-09-07T23:58:50,952 creating build/temp.linux-armv7l-cpython-313/skbio/math 2025-09-07T23:58:50,952 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c skbio/math/_subsample.c -o build/temp.linux-armv7l-cpython-313/skbio/math/_subsample.o 2025-09-07T23:58:51,400 skbio/math/_subsample.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-07T23:58:51,401 skbio/math/_subsample.c:1869:52: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-07T23:58:51,401 1869 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); 2025-09-07T23:58:51,402 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,402 | PyBUF_C_CONTIGUOUS 2025-09-07T23:58:51,402 skbio/math/_subsample.c:1869:52: note: each undeclared identifier is reported only once for each function it appears in 2025-09-07T23:58:51,425 skbio/math/_subsample.c:1907:52: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-07T23:58:51,425 1907 | __pyx_t_1 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); 2025-09-07T23:58:51,425 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,425 | PyBUF_F_CONTIGUOUS 2025-09-07T23:58:51,432 skbio/math/_subsample.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-07T23:58:51,434 skbio/math/_subsample.c:2912:29: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-07T23:58:51,434 2912 | if (unlikely(__pyx_v_descr->names == Py_None)) { 2025-09-07T23:58:51,434 | ^~ 2025-09-07T23:58:51,435 skbio/math/_subsample.c:511:45: note: in definition of macro ‘unlikely’ 2025-09-07T23:58:51,435 511 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-07T23:58:51,435 | ^ 2025-09-07T23:58:51,437 skbio/math/_subsample.c:2916:28: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-07T23:58:51,437 2916 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; 2025-09-07T23:58:51,437 | ^~ 2025-09-07T23:58:51,440 skbio/math/_subsample.c:2934:47: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-07T23:58:51,440 2934 | __pyx_t_3 = PyObject_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; 2025-09-07T23:58:51,440 | ^~ 2025-09-07T23:58:51,447 skbio/math/_subsample.c:3112:81: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’ 2025-09-07T23:58:51,447 3112 | (__pyx_v_offset[__pyx_t_10]) = ((__pyx_v_offset[__pyx_t_10]) + __pyx_v_child->elsize); 2025-09-07T23:58:51,448 | ^~ 2025-09-07T23:58:51,460 skbio/math/_subsample.c: In function ‘__Pyx_InitCachedConstants’: 2025-09-07T23:58:51,464 skbio/math/_subsample.c:3858:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-07T23:58:51,464 3858 | __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(3, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jrideout_virtualenvs_sciki, __pyx_n_s_subsample_without_replacement, 17, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T23:58:51,464 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,464 In file included from /usr/include/python3.13/Python.h:101, 2025-09-07T23:58:51,464 from skbio/math/_subsample.c:16: 2025-09-07T23:58:51,464 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:58:51,465 213 | PyCode_New( 2025-09-07T23:58:51,465 | ^~~~~~~~~~ 2025-09-07T23:58:51,468 skbio/math/_subsample.c:3858:262: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T23:58:51,468 3858 | __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(3, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jrideout_virtualenvs_sciki, __pyx_n_s_subsample_without_replacement, 17, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T23:58:51,468 | ^~ 2025-09-07T23:58:51,469 | | 2025-09-07T23:58:51,469 | int 2025-09-07T23:58:51,469 skbio/math/_subsample.c:124:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:58:51,469 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:58:51,469 | ^~~~~ 2025-09-07T23:58:51,469 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-07T23:58:51,469 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:58:51,469 | ~~~~~~~~~~^ 2025-09-07T23:58:51,472 skbio/math/_subsample.c:3858:266: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-07T23:58:51,472 3858 | __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(3, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jrideout_virtualenvs_sciki, __pyx_n_s_subsample_without_replacement, 17, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T23:58:51,472 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,473 | | 2025-09-07T23:58:51,473 | PyObject * {aka struct _object *} 2025-09-07T23:58:51,473 skbio/math/_subsample.c:124:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:58:51,473 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:58:51,473 | ^~~~ 2025-09-07T23:58:51,473 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-07T23:58:51,473 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:58:51,473 | ~~~~^ 2025-09-07T23:58:51,476 skbio/math/_subsample.c:124:11: error: too few arguments to function ‘PyCode_New’ 2025-09-07T23:58:51,476 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:58:51,477 | ^~~~~~~~~~ 2025-09-07T23:58:51,477 skbio/math/_subsample.c:3858:33: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:58:51,477 3858 | __pyx_codeobj__8 = (PyObject*)__Pyx_PyCode_New(3, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__7, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jrideout_virtualenvs_sciki, __pyx_n_s_subsample_without_replacement, 17, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T23:58:51,477 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,477 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:58:51,477 213 | PyCode_New( 2025-09-07T23:58:51,477 | ^~~~~~~~~~ 2025-09-07T23:58:51,501 skbio/math/_subsample.c: In function ‘__Pyx_ParseOptionalKeywords’: 2025-09-07T23:58:51,506 skbio/math/_subsample.c:4145:22: error: implicit declaration of function ‘PyUnicode_GET_SIZE’; did you mean ‘PyDict_GET_SIZE’? [-Wimplicit-function-declaration] 2025-09-07T23:58:51,507 4145 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-07T23:58:51,507 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,507 | PyDict_GET_SIZE 2025-09-07T23:58:51,551 skbio/math/_subsample.c: In function ‘__Pyx_ErrRestore’: 2025-09-07T23:58:51,555 skbio/math/_subsample.c:4932:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:58:51,555 4932 | tmp_type = tstate->curexc_type; 2025-09-07T23:58:51,555 | ^~ 2025-09-07T23:58:51,560 skbio/math/_subsample.c:4933:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:58:51,560 4933 | tmp_value = tstate->curexc_value; 2025-09-07T23:58:51,560 | ^~ 2025-09-07T23:58:51,564 skbio/math/_subsample.c:4934:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:58:51,565 4934 | tmp_tb = tstate->curexc_traceback; 2025-09-07T23:58:51,565 | ^~ 2025-09-07T23:58:51,569 skbio/math/_subsample.c:4935:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:58:51,569 4935 | tstate->curexc_type = type; 2025-09-07T23:58:51,569 | ^~ 2025-09-07T23:58:51,574 skbio/math/_subsample.c:4936:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:58:51,574 4936 | tstate->curexc_value = value; 2025-09-07T23:58:51,574 | ^~ 2025-09-07T23:58:51,578 skbio/math/_subsample.c:4937:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:58:51,578 4937 | tstate->curexc_traceback = tb; 2025-09-07T23:58:51,579 | ^~ 2025-09-07T23:58:51,579 skbio/math/_subsample.c: In function ‘__Pyx_ErrFetch’: 2025-09-07T23:58:51,583 skbio/math/_subsample.c:4948:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:58:51,583 4948 | *type = tstate->curexc_type; 2025-09-07T23:58:51,583 | ^~ 2025-09-07T23:58:51,588 skbio/math/_subsample.c:4949:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:58:51,588 4949 | *value = tstate->curexc_value; 2025-09-07T23:58:51,588 | ^~ 2025-09-07T23:58:51,593 skbio/math/_subsample.c:4950:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:58:51,593 4950 | *tb = tstate->curexc_traceback; 2025-09-07T23:58:51,593 | ^~ 2025-09-07T23:58:51,597 skbio/math/_subsample.c:4951:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:58:51,597 4951 | tstate->curexc_type = 0; 2025-09-07T23:58:51,597 | ^~ 2025-09-07T23:58:51,602 skbio/math/_subsample.c:4952:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:58:51,602 4952 | tstate->curexc_value = 0; 2025-09-07T23:58:51,602 | ^~ 2025-09-07T23:58:51,607 skbio/math/_subsample.c:4953:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:58:51,607 4953 | tstate->curexc_traceback = 0; 2025-09-07T23:58:51,607 | ^~ 2025-09-07T23:58:51,618 skbio/math/_subsample.c: In function ‘__Pyx_Raise’: 2025-09-07T23:58:51,623 skbio/math/_subsample.c:5111:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:58:51,623 5111 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-07T23:58:51,623 | ^~ 2025-09-07T23:58:51,628 skbio/math/_subsample.c:5114:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:58:51,628 5114 | tstate->curexc_traceback = tb; 2025-09-07T23:58:51,628 | ^~ 2025-09-07T23:58:51,636 skbio/math/_subsample.c: In function ‘__Pyx_PyInt_As_Py_intptr_t’: 2025-09-07T23:58:51,641 skbio/math/_subsample.c:5434:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-07T23:58:51,641 5434 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-07T23:58:51,641 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,641 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-07T23:58:51,641 from /usr/include/python3.13/Python.h:81: 2025-09-07T23:58:51,641 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-07T23:58:51,641 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-07T23:58:51,641 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,646 skbio/math/_subsample.c: In function ‘__Pyx_PyInt_As_int’: 2025-09-07T23:58:51,651 skbio/math/_subsample.c:5800:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-07T23:58:51,651 5800 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-07T23:58:51,651 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,651 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-07T23:58:51,651 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-07T23:58:51,651 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,655 skbio/math/_subsample.c: In function ‘__Pyx_PyInt_As_long’: 2025-09-07T23:58:51,660 skbio/math/_subsample.c:5926:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-07T23:58:51,660 5926 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-07T23:58:51,660 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,660 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-07T23:58:51,661 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-07T23:58:51,661 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,675 skbio/math/_subsample.c: In function ‘__Pyx_CreateCodeObjectForTraceback’: 2025-09-07T23:58:51,681 skbio/math/_subsample.c:6159:5: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-07T23:58:51,681 6159 | py_code = __Pyx_PyCode_New( 2025-09-07T23:58:51,681 | ^~~~~~~ 2025-09-07T23:58:51,681 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:58:51,682 213 | PyCode_New( 2025-09-07T23:58:51,682 | ^~~~~~~~~~ 2025-09-07T23:58:51,687 skbio/math/_subsample.c:6173:9: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T23:58:51,687 6173 | py_line, /*int firstlineno,*/ 2025-09-07T23:58:51,687 | ^~~~~~~ 2025-09-07T23:58:51,687 | | 2025-09-07T23:58:51,687 | int 2025-09-07T23:58:51,687 skbio/math/_subsample.c:124:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:58:51,688 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:58:51,688 | ^~~~~ 2025-09-07T23:58:51,688 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-07T23:58:51,688 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:58:51,688 | ~~~~~~~~~~^ 2025-09-07T23:58:51,694 skbio/math/_subsample.c:6174:9: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-07T23:58:51,694 6174 | __pyx_empty_bytes /*PyObject *lnotab*/ 2025-09-07T23:58:51,694 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,694 | | 2025-09-07T23:58:51,694 | PyObject * {aka struct _object *} 2025-09-07T23:58:51,694 skbio/math/_subsample.c:124:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:58:51,694 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:58:51,694 | ^~~~ 2025-09-07T23:58:51,694 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-07T23:58:51,694 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:58:51,695 | ~~~~^ 2025-09-07T23:58:51,700 skbio/math/_subsample.c:124:11: error: too few arguments to function ‘PyCode_New’ 2025-09-07T23:58:51,700 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:58:51,700 | ^~~~~~~~~~ 2025-09-07T23:58:51,700 skbio/math/_subsample.c:6159:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:58:51,700 6159 | py_code = __Pyx_PyCode_New( 2025-09-07T23:58:51,701 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:58:51,701 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:58:51,701 213 | PyCode_New( 2025-09-07T23:58:51,701 | ^~~~~~~~~~ 2025-09-07T23:58:51,705 skbio/math/_subsample.c: In function ‘__Pyx_AddTraceback’: 2025-09-07T23:58:51,710 skbio/math/_subsample.c:6205:13: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-07T23:58:51,711 6205 | py_frame->f_lineno = py_line; 2025-09-07T23:58:51,711 | ^~ 2025-09-07T23:58:51,755 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-07T23:58:51,926 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T23:58:51,938 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T23:58:51,938 exec(compile('"'"''"'"''"'"' 2025-09-07T23:58:51,938 # This is -- a caller that pip uses to run setup.py 2025-09-07T23:58:51,938 # 2025-09-07T23:58:51,938 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T23:58:51,938 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T23:58:51,938 # - It provides a clear error message when setuptools is not installed. 2025-09-07T23:58:51,938 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T23:58:51,938 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T23:58:51,938 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T23:58:51,938 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T23:58:51,938 import os, sys, tokenize, traceback 2025-09-07T23:58:51,938 2025-09-07T23:58:51,938 try: 2025-09-07T23:58:51,938 import setuptools 2025-09-07T23:58:51,938 except ImportError: 2025-09-07T23:58:51,938 print( 2025-09-07T23:58:51,938 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T23:58:51,938 "the build environment with exception:", 2025-09-07T23:58:51,938 file=sys.stderr, 2025-09-07T23:58:51,938 ) 2025-09-07T23:58:51,938 traceback.print_exc() 2025-09-07T23:58:51,938 sys.exit(1) 2025-09-07T23:58:51,938 2025-09-07T23:58:51,938 __file__ = %r 2025-09-07T23:58:51,938 sys.argv[0] = __file__ 2025-09-07T23:58:51,938 2025-09-07T23:58:51,938 if os.path.exists(__file__): 2025-09-07T23:58:51,938 filename = __file__ 2025-09-07T23:58:51,938 with tokenize.open(__file__) as f: 2025-09-07T23:58:51,938 setup_py_code = f.read() 2025-09-07T23:58:51,938 else: 2025-09-07T23:58:51,938 filename = "" 2025-09-07T23:58:51,938 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T23:58:51,938 2025-09-07T23:58:51,938 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T23:58:51,938 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-wq2ynixx/scikit-bio_3914b064406a4be0b52bb926f44abf99/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-agn0oa6_[/] 2025-09-07T23:58:51,938 [bold magenta]cwd[/]: /tmp/pip-wheel-wq2ynixx/scikit-bio_3914b064406a4be0b52bb926f44abf99/ 2025-09-07T23:58:51,938 Building wheel for scikit-bio (setup.py): finished with status 'error' 2025-09-07T23:58:51,939 ERROR: Failed building wheel for scikit-bio 2025-09-07T23:58:51,940 Running setup.py clean for scikit-bio 2025-09-07T23:58:51,941 Running command python setup.py clean 2025-09-07T23:58:52,833 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-07T23:58:52,833 warnings.warn(msg) 2025-09-07T23:58:53,219 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:58:53,220 !! 2025-09-07T23:58:53,220 ******************************************************************************** 2025-09-07T23:58:53,220 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:58:53,220 License :: OSI Approved :: BSD License 2025-09-07T23:58:53,220 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:58:53,220 ******************************************************************************** 2025-09-07T23:58:53,221 !! 2025-09-07T23:58:53,221 self._finalize_license_expression() 2025-09-07T23:58:53,294 running clean 2025-09-07T23:58:53,443 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:58:53,443 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:58:53,452 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T23:58:53,452 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T23:58:53,452 removing 'build' 2025-09-07T23:58:53,592 Failed to build scikit-bio 2025-09-07T23:58:53,593 ERROR: Failed to build one or more wheels 2025-09-07T23:58:53,594 Exception information: 2025-09-07T23:58:53,594 Traceback (most recent call last): 2025-09-07T23:58:53,594 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T23:58:53,594 status = _inner_run() 2025-09-07T23:58:53,594 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T23:58:53,594 return self.run(options, args) 2025-09-07T23:58:53,594 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T23:58:53,594 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T23:58:53,594 return func(self, options, args) 2025-09-07T23:58:53,594 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T23:58:53,594 raise CommandError("Failed to build one or more wheels") 2025-09-07T23:58:53,594 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T23:58:53,599 Removed build tracker: '/tmp/pip-build-tracker-fanm2dd_'