2025-09-07T23:52:25,551 Created temporary directory: /tmp/pip-build-tracker-d6ps39z6 2025-09-07T23:52:25,552 Initialized build tracking at /tmp/pip-build-tracker-d6ps39z6 2025-09-07T23:52:25,552 Created build tracker: /tmp/pip-build-tracker-d6ps39z6 2025-09-07T23:52:25,552 Entered build tracker: /tmp/pip-build-tracker-d6ps39z6 2025-09-07T23:52:25,552 Created temporary directory: /tmp/pip-wheel-uswis55f 2025-09-07T23:52:25,556 Created temporary directory: /tmp/pip-ephem-wheel-cache-2gq7mh92 2025-09-07T23:52:25,614 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T23:52:25,617 2 location(s) to search for versions of scikit-bio: 2025-09-07T23:52:25,617 * https://pypi.org/simple/scikit-bio/ 2025-09-07T23:52:25,617 * https://www.piwheels.org/simple/scikit-bio/ 2025-09-07T23:52:25,617 Fetching project page and analyzing links: https://pypi.org/simple/scikit-bio/ 2025-09-07T23:52:25,617 Getting page https://pypi.org/simple/scikit-bio/ 2025-09-07T23:52:25,618 Found index url https://pypi.org/simple/ 2025-09-07T23:52:25,765 Fetched page https://pypi.org/simple/scikit-bio/ as application/vnd.pypi.simple.v1+json 2025-09-07T23:52:25,773 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 2025-09-07T23:52:25,773 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 2025-09-07T23:52:25,774 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 2025-09-07T23:52:25,774 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 2025-09-07T23:52:25,774 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 2025-09-07T23:52:25,774 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 2025-09-07T23:52:25,775 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 2025-09-07T23:52:25,775 Found link https://files.pythonhosted.org/packages/7b/74/77cf9b45ea0df4d3b8c3adcbd6f59e0b0603d1a3a2fed1b1ae6365232ac6/scikit-bio-0.2.1.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.2.1 2025-09-07T23:52:25,775 Found link https://files.pythonhosted.org/packages/bd/0a/6a5906fd53616c0763c5f445b5dc42907720f344318a1f07627986d22f33/scikit-bio-0.2.2.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.2.2 2025-09-07T23:52:25,775 Found link https://files.pythonhosted.org/packages/8e/70/559566c9dbde9435360058c420a819b4e8ce844f7ebd94daec9836f4be24/scikit-bio-0.2.3.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.2.3 2025-09-07T23:52:25,776 Found link https://files.pythonhosted.org/packages/d9/cb/c4684ce5c521de96411c2b88255feb45077e0b2df7ebbdf946abe5caaf25/scikit-bio-0.4.0.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.4.0 2025-09-07T23:52:25,776 Found link https://files.pythonhosted.org/packages/12/02/81edd2941d892cb4d0144be716c341b9a6fd255046c08d1b7bd6c70a0112/scikit-bio-0.4.1.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.4.1 2025-09-07T23:52:25,776 Found link https://files.pythonhosted.org/packages/a8/87/23635a6a9b6a1abdf78ccfc1e71929570be4c4ab4004eab66da9dd4a5c6a/scikit-bio-0.4.2.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.4.2 2025-09-07T23:52:25,776 Found link https://files.pythonhosted.org/packages/95/60/f4c269a6dfaf9d027adba6a81497e5d238cf5e604f53206b4ea50ed1145f/scikit-bio-0.5.0.zip (from https://pypi.org/simple/scikit-bio/), version: 0.5.0 2025-09-07T23:52:25,777 Found link https://files.pythonhosted.org/packages/e5/7e/cf03a7e53da18ae6a847894384838e9a36a98b48909a3f347ff6077c7304/scikit-bio-0.5.1.tar.gz (from https://pypi.org/simple/scikit-bio/), version: 0.5.1 2025-09-07T23:52:25,777 Found link 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 2025-09-07T23:52:25,777 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 2025-09-07T23:52:25,778 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 2025-09-07T23:52:25,778 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 2025-09-07T23:52:25,778 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 2025-09-07T23:52:25,778 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 2025-09-07T23:52:25,779 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 2025-09-07T23:52:25,779 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 2025-09-07T23:52:25,779 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 2025-09-07T23:52:25,779 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 2025-09-07T23:52:25,780 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 2025-09-07T23:52:25,780 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 2025-09-07T23:52:25,780 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) 2025-09-07T23:52:25,780 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) 2025-09-07T23:52:25,780 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) 2025-09-07T23:52:25,781 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) 2025-09-07T23:52:25,781 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) 2025-09-07T23:52:25,781 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) 2025-09-07T23:52:25,781 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) 2025-09-07T23:52:25,781 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) 2025-09-07T23:52:25,781 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) 2025-09-07T23:52:25,782 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) 2025-09-07T23:52:25,782 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) 2025-09-07T23:52:25,782 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) 2025-09-07T23:52:25,782 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) 2025-09-07T23:52:25,782 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) 2025-09-07T23:52:25,783 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) 2025-09-07T23:52:25,783 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) 2025-09-07T23:52:25,783 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) 2025-09-07T23:52:25,783 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) 2025-09-07T23:52:25,783 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) 2025-09-07T23:52:25,783 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) 2025-09-07T23:52:25,784 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) 2025-09-07T23:52:25,784 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) 2025-09-07T23:52:25,784 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) 2025-09-07T23:52:25,784 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) 2025-09-07T23:52:25,784 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) 2025-09-07T23:52:25,785 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 2025-09-07T23:52:25,785 Fetching project page and analyzing links: https://www.piwheels.org/simple/scikit-bio/ 2025-09-07T23:52:25,785 Getting page https://www.piwheels.org/simple/scikit-bio/ 2025-09-07T23:52:25,786 Found index url https://www.piwheels.org/simple/ 2025-09-07T23:52:25,889 Fetched page https://www.piwheels.org/simple/scikit-bio/ as text/html 2025-09-07T23:52:25,895 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.3-cp311-cp311-linux_armv6l.whl#sha256=1377121c66a4fe46966e56e9145ef2a326b3ed4b8a38080cfbe361afafd8e8f2 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,895 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.3-cp311-cp311-linux_armv7l.whl#sha256=1377121c66a4fe46966e56e9145ef2a326b3ed4b8a38080cfbe361afafd8e8f2 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,895 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.3-cp39-cp39-linux_armv6l.whl#sha256=8beed71fd2d4c144f10b9ef761c7a68af8657d4c22e4d37cee45670a40a77a83 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,895 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.3-cp39-cp39-linux_armv7l.whl#sha256=8beed71fd2d4c144f10b9ef761c7a68af8657d4c22e4d37cee45670a40a77a83 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,895 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.2-cp39-cp39-linux_armv6l.whl#sha256=c11cd14b1aa68524f23fa412af6d5139f3023ac63212057c53649ce6a63da7b8 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,896 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.2-cp39-cp39-linux_armv7l.whl#sha256=c11cd14b1aa68524f23fa412af6d5139f3023ac63212057c53649ce6a63da7b8 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,896 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.1-cp311-cp311-linux_armv6l.whl#sha256=7657b22d76cf0c3a508f91d921cbfc5431049f4477456d8b26c9a24a9ebb7190 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,896 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.1-cp311-cp311-linux_armv7l.whl#sha256=7657b22d76cf0c3a508f91d921cbfc5431049f4477456d8b26c9a24a9ebb7190 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,896 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.1-cp37-cp37m-linux_armv6l.whl#sha256=2dfb82a5726354b8f83f298206e3c08373a5c7502bcd2d68eba605d3d7a63398 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,896 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.1-cp37-cp37m-linux_armv7l.whl#sha256=2dfb82a5726354b8f83f298206e3c08373a5c7502bcd2d68eba605d3d7a63398 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,896 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.1-cp39-cp39-linux_armv6l.whl#sha256=e98311cac990697fccc80b97b64ba1e25c17216e95f4ae0608c3c4084a25739d (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,896 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.1-cp39-cp39-linux_armv7l.whl#sha256=e98311cac990697fccc80b97b64ba1e25c17216e95f4ae0608c3c4084a25739d (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,896 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.0-cp311-cp311-linux_armv6l.whl#sha256=3c11c6aec89d859de926ebf1b4a4fb61ce1bcab28c1762427c042704d7ae0c9e (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,897 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.0-cp311-cp311-linux_armv7l.whl#sha256=3c11c6aec89d859de926ebf1b4a4fb61ce1bcab28c1762427c042704d7ae0c9e (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,897 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.0-cp37-cp37m-linux_armv6l.whl#sha256=bfbf0fe68e25c3d128af83db7e51b2f3c100f7cdbda1669dcdf1c51c7f18cd74 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,897 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.0-cp37-cp37m-linux_armv7l.whl#sha256=bfbf0fe68e25c3d128af83db7e51b2f3c100f7cdbda1669dcdf1c51c7f18cd74 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,897 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.0-cp39-cp39-linux_armv6l.whl#sha256=da66a4671abc7db352a7ed3975d364cba1a7adc858a10c82f32d8e6e39d007bd (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,897 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.6.0-cp39-cp39-linux_armv7l.whl#sha256=da66a4671abc7db352a7ed3975d364cba1a7adc858a10c82f32d8e6e39d007bd (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,897 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.9-cp37-cp37m-linux_armv6l.whl#sha256=8fa99b56c44c5c2b18355ef926d00cf7d1d651ab8d0eb367747d3806c4e716dc (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,897 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.9-cp37-cp37m-linux_armv7l.whl#sha256=8fa99b56c44c5c2b18355ef926d00cf7d1d651ab8d0eb367747d3806c4e716dc (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,897 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.9-cp39-cp39-linux_armv6l.whl#sha256=b248a90a5ed7214267889ad197585aa84aeb5ec25dd9bb63ddc064cbda00a971 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,897 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.9-cp39-cp39-linux_armv7l.whl#sha256=b248a90a5ed7214267889ad197585aa84aeb5ec25dd9bb63ddc064cbda00a971 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,898 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.9-cp311-cp311-linux_armv6l.whl#sha256=0d10c6c7922db15dcc5640bac5f192fdd8606fa47facd0f34eb648f9c3e049b2 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,898 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.9-cp311-cp311-linux_armv7l.whl#sha256=0d10c6c7922db15dcc5640bac5f192fdd8606fa47facd0f34eb648f9c3e049b2 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,898 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.8-cp37-cp37m-linux_armv6l.whl#sha256=6569ab2696b41bc41ae4e94547d0acd136512dab7753942df12b06931a5ed810 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,898 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.8-cp37-cp37m-linux_armv7l.whl#sha256=6569ab2696b41bc41ae4e94547d0acd136512dab7753942df12b06931a5ed810 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,898 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.8-cp39-cp39-linux_armv6l.whl#sha256=7692ae74dbd1b55f55796326c6f3ed2e17028eee9e09eecb0f58d7073e534c52 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,898 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.8-cp39-cp39-linux_armv7l.whl#sha256=7692ae74dbd1b55f55796326c6f3ed2e17028eee9e09eecb0f58d7073e534c52 (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,898 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.7-cp35-cp35m-linux_armv6l.whl#sha256=3527865d97cf75cd55785b872d6e479bc2ee03250f6b71b9cc2d4a819d69c64c (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,898 Skipping link: No binaries permitted for scikit-bio: https://archive1.piwheels.org/simple/scikit-bio/scikit_bio-0.5.7-cp35-cp35m-linux_armv7l.whl#sha256=3527865d97cf75cd55785b872d6e479bc2ee03250f6b71b9cc2d4a819d69c64c (from https://www.piwheels.org/simple/scikit-bio/) 2025-09-07T23:52:25,899 Skipping link: No binaries permitted for scikit-bio: 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/) 2025-09-07T23:52:25,899 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/) 2025-09-07T23:52:25,899 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/) 2025-09-07T23:52:25,899 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/) 2025-09-07T23:52:25,899 Skipping link: not a file: https://www.piwheels.org/simple/scikit-bio/ 2025-09-07T23:52:25,899 Skipping link: not a file: https://pypi.org/simple/scikit-bio/ 2025-09-07T23:52:25,928 Given no hashes to check 1 links for project 'scikit-bio': discarding no candidates 2025-09-07T23:52:25,929 Collecting scikit-bio==0.1.0 2025-09-07T23:52:25,931 Created temporary directory: /tmp/pip-unpack-o9rv9jyv 2025-09-07T23:52:26,147 Downloading scikit-bio-0.1.0.tar.gz (335 kB) 2025-09-07T23:52:26,307 Added scikit-bio==0.1.0 from https://files.pythonhosted.org/packages/e0/4f/9e53704ce04a5e60511449a5e16511c6e20219ed0932e4aeea84fe2189fd/scikit-bio-0.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-d6ps39z6' 2025-09-07T23:52:26,308 Running setup.py (path:/tmp/pip-wheel-uswis55f/scikit-bio_1a7ba2bf29784ccf8973522816ec45a9/setup.py) egg_info for package scikit-bio 2025-09-07T23:52:26,308 Created temporary directory: /tmp/pip-pip-egg-info-lfpvt1u0 2025-09-07T23:52:26,308 Preparing metadata (setup.py): started 2025-09-07T23:52:26,309 Running command python setup.py egg_info 2025-09-07T23:52:27,267 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-07T23:52:27,268 warnings.warn(msg) 2025-09-07T23:52:27,665 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:52:27,666 !! 2025-09-07T23:52:27,666 ******************************************************************************** 2025-09-07T23:52:27,666 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:52:27,666 License :: OSI Approved :: BSD License 2025-09-07T23:52:27,666 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:52:27,666 ******************************************************************************** 2025-09-07T23:52:27,667 !! 2025-09-07T23:52:27,667 self._finalize_license_expression() 2025-09-07T23:52:27,739 running egg_info 2025-09-07T23:52:27,810 creating /tmp/pip-pip-egg-info-lfpvt1u0/scikit_bio.egg-info 2025-09-07T23:52:27,810 writing /tmp/pip-pip-egg-info-lfpvt1u0/scikit_bio.egg-info/PKG-INFO 2025-09-07T23:52:27,813 writing dependency_links to /tmp/pip-pip-egg-info-lfpvt1u0/scikit_bio.egg-info/dependency_links.txt 2025-09-07T23:52:27,815 writing requirements to /tmp/pip-pip-egg-info-lfpvt1u0/scikit_bio.egg-info/requires.txt 2025-09-07T23:52:27,816 writing top-level names to /tmp/pip-pip-egg-info-lfpvt1u0/scikit_bio.egg-info/top_level.txt 2025-09-07T23:52:27,816 writing manifest file '/tmp/pip-pip-egg-info-lfpvt1u0/scikit_bio.egg-info/SOURCES.txt' 2025-09-07T23:52:27,896 /usr/local/lib/python3.13/dist-packages/setuptools/command/sdist.py:122: SetuptoolsDeprecationWarning: `build_py` command does not inherit from setuptools' `build_py`. 2025-09-07T23:52:27,897 !! 2025-09-07T23:52:27,897 ******************************************************************************** 2025-09-07T23:52:27,897 Custom 'build_py' does not implement 'get_data_files_without_manifest'. 2025-09-07T23:52:27,897 Please extend command classes from setuptools instead of distutils. 2025-09-07T23:52:27,897 See https://peps.python.org/pep-0632/ for details. 2025-09-07T23:52:27,897 ******************************************************************************** 2025-09-07T23:52:27,897 !! 2025-09-07T23:52:27,897 self._add_data_files(self._safe_data_files(build_py)) 2025-09-07T23:52:28,041 reading manifest file '/tmp/pip-pip-egg-info-lfpvt1u0/scikit_bio.egg-info/SOURCES.txt' 2025-09-07T23:52:28,046 writing manifest file '/tmp/pip-pip-egg-info-lfpvt1u0/scikit_bio.egg-info/SOURCES.txt' 2025-09-07T23:52:28,181 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T23:52:28,186 Source in /tmp/pip-wheel-uswis55f/scikit-bio_1a7ba2bf29784ccf8973522816ec45a9 has version 0.1.0, which satisfies requirement scikit-bio==0.1.0 from https://files.pythonhosted.org/packages/e0/4f/9e53704ce04a5e60511449a5e16511c6e20219ed0932e4aeea84fe2189fd/scikit-bio-0.1.0.tar.gz 2025-09-07T23:52:28,186 Removed scikit-bio==0.1.0 from https://files.pythonhosted.org/packages/e0/4f/9e53704ce04a5e60511449a5e16511c6e20219ed0932e4aeea84fe2189fd/scikit-bio-0.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-d6ps39z6' 2025-09-07T23:52:28,192 Created temporary directory: /tmp/pip-unpack-8jpvul3d 2025-09-07T23:52:28,192 Created temporary directory: /tmp/pip-unpack-izkm6tfw 2025-09-07T23:52:28,192 Building wheels for collected packages: scikit-bio 2025-09-07T23:52:28,194 Created temporary directory: /tmp/pip-wheel-75nm5q6r 2025-09-07T23:52:28,194 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 2025-09-07T23:52:28,195 Building wheel for scikit-bio (setup.py): started 2025-09-07T23:52:28,196 Destination directory: /tmp/pip-wheel-75nm5q6r 2025-09-07T23:52:28,196 Running command python setup.py bdist_wheel 2025-09-07T23:52:29,085 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-07T23:52:29,086 warnings.warn(msg) 2025-09-07T23:52:29,472 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:52:29,472 !! 2025-09-07T23:52:29,472 ******************************************************************************** 2025-09-07T23:52:29,472 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:52:29,472 License :: OSI Approved :: BSD License 2025-09-07T23:52:29,472 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:52:29,473 ******************************************************************************** 2025-09-07T23:52:29,473 !! 2025-09-07T23:52:29,473 self._finalize_license_expression() 2025-09-07T23:52:29,473 running bdist_wheel 2025-09-07T23:52:29,836 running build 2025-09-07T23:52:29,836 running build_py 2025-09-07T23:52:29,838 creating build/lib.linux-armv7l-cpython-313/skbio 2025-09-07T23:52:29,839 copying skbio/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio 2025-09-07T23:52:29,840 creating build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:52:29,840 copying skbio/util/testing.py -> build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:52:29,840 copying skbio/util/sort.py -> build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:52:29,841 copying skbio/util/misc.py -> build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:52:29,841 copying skbio/util/io.py -> build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:52:29,842 copying skbio/util/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/util 2025-09-07T23:52:29,843 creating build/lib.linux-armv7l-cpython-313/skbio/parse 2025-09-07T23:52:29,843 copying skbio/parse/record_finder.py -> build/lib.linux-armv7l-cpython-313/skbio/parse 2025-09-07T23:52:29,844 copying skbio/parse/record.py -> build/lib.linux-armv7l-cpython-313/skbio/parse 2025-09-07T23:52:29,844 copying skbio/parse/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/parse 2025-09-07T23:52:29,845 creating build/lib.linux-armv7l-cpython-313/skbio/math 2025-09-07T23:52:29,845 copying skbio/math/subsample.py -> build/lib.linux-armv7l-cpython-313/skbio/math 2025-09-07T23:52:29,846 copying skbio/math/gradient.py -> build/lib.linux-armv7l-cpython-313/skbio/math 2025-09-07T23:52:29,846 copying skbio/math/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math 2025-09-07T23:52:29,847 creating build/lib.linux-armv7l-cpython-313/skbio/format 2025-09-07T23:52:29,847 copying skbio/format/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/format 2025-09-07T23:52:29,848 creating build/lib.linux-armv7l-cpython-313/skbio/draw 2025-09-07T23:52:29,848 copying skbio/draw/distributions.py -> build/lib.linux-armv7l-cpython-313/skbio/draw 2025-09-07T23:52:29,849 copying skbio/draw/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/draw 2025-09-07T23:52:29,850 creating build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:52:29,850 copying skbio/core/workflow.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:52:29,850 copying skbio/core/warning.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:52:29,851 copying skbio/core/sequence.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:52:29,852 copying skbio/core/genetic_code.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:52:29,852 copying skbio/core/exception.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:52:29,853 copying skbio/core/distance.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:52:29,853 copying skbio/core/alignment.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:52:29,854 copying skbio/core/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core 2025-09-07T23:52:29,855 creating build/lib.linux-armv7l-cpython-313/skbio/app 2025-09-07T23:52:29,855 copying skbio/app/util.py -> build/lib.linux-armv7l-cpython-313/skbio/app 2025-09-07T23:52:29,856 copying skbio/app/parameters.py -> build/lib.linux-armv7l-cpython-313/skbio/app 2025-09-07T23:52:29,856 copying skbio/app/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/app 2025-09-07T23:52:29,857 creating build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:52:29,857 copying skbio/util/tests/test_testing.py -> build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:52:29,858 copying skbio/util/tests/test_sort.py -> build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:52:29,858 copying skbio/util/tests/test_misc.py -> build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:52:29,859 copying skbio/util/tests/test_io.py -> build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:52:29,859 copying skbio/util/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/util/tests 2025-09-07T23:52:29,860 creating build/lib.linux-armv7l-cpython-313/skbio/parse/tests 2025-09-07T23:52:29,860 copying skbio/parse/tests/test_record_finder.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/tests 2025-09-07T23:52:29,861 copying skbio/parse/tests/test_record.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/tests 2025-09-07T23:52:29,861 copying skbio/parse/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/tests 2025-09-07T23:52:29,862 creating build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:52:29,862 copying skbio/parse/sequences/iterator.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:52:29,863 copying skbio/parse/sequences/fastq.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:52:29,863 copying skbio/parse/sequences/fasta.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:52:29,864 copying skbio/parse/sequences/factory.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:52:29,865 copying skbio/parse/sequences/clustal.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:52:29,865 copying skbio/parse/sequences/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences 2025-09-07T23:52:29,866 creating build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:52:29,866 copying skbio/parse/sequences/tests/test_iterator.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:52:29,867 copying skbio/parse/sequences/tests/test_fastq.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:52:29,867 copying skbio/parse/sequences/tests/test_fasta.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:52:29,868 copying skbio/parse/sequences/tests/test_factory.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:52:29,868 copying skbio/parse/sequences/tests/test_clustal.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:52:29,869 copying skbio/parse/sequences/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/parse/sequences/tests 2025-09-07T23:52:29,869 creating build/lib.linux-armv7l-cpython-313/skbio/math/tests 2025-09-07T23:52:29,870 copying skbio/math/tests/test_subsample.py -> build/lib.linux-armv7l-cpython-313/skbio/math/tests 2025-09-07T23:52:29,870 copying skbio/math/tests/test_gradient.py -> build/lib.linux-armv7l-cpython-313/skbio/math/tests 2025-09-07T23:52:29,871 copying skbio/math/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/tests 2025-09-07T23:52:29,872 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats 2025-09-07T23:52:29,872 copying skbio/math/stats/spatial.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats 2025-09-07T23:52:29,873 copying skbio/math/stats/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats 2025-09-07T23:52:29,873 creating build/lib.linux-armv7l-cpython-313/skbio/math/diversity 2025-09-07T23:52:29,873 copying skbio/math/diversity/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity 2025-09-07T23:52:29,874 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/tests 2025-09-07T23:52:29,874 copying skbio/math/stats/tests/test_spatial.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/tests 2025-09-07T23:52:29,875 copying skbio/math/stats/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/tests 2025-09-07T23:52:29,876 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:52:29,876 copying skbio/math/stats/ordination/utils.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:52:29,877 copying skbio/math/stats/ordination/redundancy_analysis.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:52:29,877 copying skbio/math/stats/ordination/principal_coordinate_analysis.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:52:29,878 copying skbio/math/stats/ordination/correspondence_analysis.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:52:29,878 copying skbio/math/stats/ordination/canonical_correspondence_analysis.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:52:29,879 copying skbio/math/stats/ordination/base.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:52:29,879 copying skbio/math/stats/ordination/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination 2025-09-07T23:52:29,880 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:52:29,880 copying skbio/math/stats/distance/permanova.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:52:29,881 copying skbio/math/stats/distance/base.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:52:29,881 copying skbio/math/stats/distance/anosim.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:52:29,882 copying skbio/math/stats/distance/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance 2025-09-07T23:52:29,883 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests 2025-09-07T23:52:29,883 copying skbio/math/stats/ordination/tests/test_ordination.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests 2025-09-07T23:52:29,884 copying skbio/math/stats/ordination/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/ordination/tests 2025-09-07T23:52:29,884 creating build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:52:29,885 copying skbio/math/stats/distance/tests/test_permanova.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:52:29,885 copying skbio/math/stats/distance/tests/test_base.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:52:29,886 copying skbio/math/stats/distance/tests/test_anosim.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:52:29,886 copying skbio/math/stats/distance/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/stats/distance/tests 2025-09-07T23:52:29,887 creating build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:52:29,887 copying skbio/math/diversity/alpha/lladser.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:52:29,888 copying skbio/math/diversity/alpha/gini.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:52:29,888 copying skbio/math/diversity/alpha/chao1.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:52:29,889 copying skbio/math/diversity/alpha/base.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:52:29,889 copying skbio/math/diversity/alpha/ace.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:52:29,890 copying skbio/math/diversity/alpha/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha 2025-09-07T23:52:29,891 creating build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:52:29,891 copying skbio/math/diversity/alpha/tests/test_lladser.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:52:29,891 copying skbio/math/diversity/alpha/tests/test_gini.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:52:29,892 copying skbio/math/diversity/alpha/tests/test_chao1.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:52:29,893 copying skbio/math/diversity/alpha/tests/test_base.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:52:29,893 copying skbio/math/diversity/alpha/tests/test_ace.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:52:29,894 copying skbio/math/diversity/alpha/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/math/diversity/alpha/tests 2025-09-07T23:52:29,894 creating build/lib.linux-armv7l-cpython-313/skbio/format/tests 2025-09-07T23:52:29,894 copying skbio/format/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/format/tests 2025-09-07T23:52:29,895 creating build/lib.linux-armv7l-cpython-313/skbio/format/sequences 2025-09-07T23:52:29,895 copying skbio/format/sequences/fastq.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences 2025-09-07T23:52:29,896 copying skbio/format/sequences/fasta.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences 2025-09-07T23:52:29,896 copying skbio/format/sequences/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences 2025-09-07T23:52:29,897 creating build/lib.linux-armv7l-cpython-313/skbio/format/sequences/tests 2025-09-07T23:52:29,897 copying skbio/format/sequences/tests/test_fastq.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences/tests 2025-09-07T23:52:29,898 copying skbio/format/sequences/tests/test_fasta.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences/tests 2025-09-07T23:52:29,898 copying skbio/format/sequences/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/format/sequences/tests 2025-09-07T23:52:29,899 creating build/lib.linux-armv7l-cpython-313/skbio/draw/tests 2025-09-07T23:52:29,899 copying skbio/draw/tests/test_distributions.py -> build/lib.linux-armv7l-cpython-313/skbio/draw/tests 2025-09-07T23:52:29,900 copying skbio/draw/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/draw/tests 2025-09-07T23:52:29,901 creating build/lib.linux-armv7l-cpython-313/skbio/core/tree 2025-09-07T23:52:29,901 copying skbio/core/tree/trie.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree 2025-09-07T23:52:29,902 copying skbio/core/tree/tree.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree 2025-09-07T23:52:29,902 copying skbio/core/tree/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tree 2025-09-07T23:52:29,903 creating build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:52:29,903 copying skbio/core/tests/test_workflow.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:52:29,904 copying skbio/core/tests/test_sequence.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:52:29,905 copying skbio/core/tests/test_genetic_code.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:52:29,905 copying skbio/core/tests/test_distance.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:52:29,906 copying skbio/core/tests/test_alignment.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:52:29,906 copying skbio/core/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core/tests 2025-09-07T23:52:29,907 creating build/lib.linux-armv7l-cpython-313/skbio/core/ssw 2025-09-07T23:52:29,907 copying skbio/core/ssw/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/core/ssw 2025-09-07T23:52:29,908 creating build/lib.linux-armv7l-cpython-313/skbio/app/tests 2025-09-07T23:52:29,908 copying skbio/app/tests/test_util.py -> build/lib.linux-armv7l-cpython-313/skbio/app/tests 2025-09-07T23:52:29,909 copying skbio/app/tests/test_parameters.py -> build/lib.linux-armv7l-cpython-313/skbio/app/tests 2025-09-07T23:52:29,910 copying skbio/app/tests/__init__.py -> build/lib.linux-armv7l-cpython-313/skbio/app/tests 2025-09-07T23:52:29,917 running build_ext 2025-09-07T23:52:30,246 building 'skbio.math._subsample' extension 2025-09-07T23:52:30,247 creating build/temp.linux-armv7l-cpython-313/skbio/math 2025-09-07T23:52:30,247 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 2025-09-07T23:52:30,701 skbio/math/_subsample.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-07T23:52:30,703 skbio/math/_subsample.c:1869:52: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-07T23:52:30,704 1869 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); 2025-09-07T23:52:30,704 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,704 | PyBUF_C_CONTIGUOUS 2025-09-07T23:52:30,704 skbio/math/_subsample.c:1869:52: note: each undeclared identifier is reported only once for each function it appears in 2025-09-07T23:52:30,727 skbio/math/_subsample.c:1907:52: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-07T23:52:30,727 1907 | __pyx_t_1 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); 2025-09-07T23:52:30,727 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,727 | PyBUF_F_CONTIGUOUS 2025-09-07T23:52:30,735 skbio/math/_subsample.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-07T23:52:30,738 skbio/math/_subsample.c:2912:29: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-07T23:52:30,738 2912 | if (unlikely(__pyx_v_descr->names == Py_None)) { 2025-09-07T23:52:30,738 | ^~ 2025-09-07T23:52:30,738 skbio/math/_subsample.c:511:45: note: in definition of macro ‘unlikely’ 2025-09-07T23:52:30,738 511 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-07T23:52:30,738 | ^ 2025-09-07T23:52:30,741 skbio/math/_subsample.c:2916:28: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-07T23:52:30,741 2916 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; 2025-09-07T23:52:30,741 | ^~ 2025-09-07T23:52:30,745 skbio/math/_subsample.c:2934:47: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-07T23:52:30,745 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;}; 2025-09-07T23:52:30,745 | ^~ 2025-09-07T23:52:30,752 skbio/math/_subsample.c:3112:81: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’ 2025-09-07T23:52:30,752 3112 | (__pyx_v_offset[__pyx_t_10]) = ((__pyx_v_offset[__pyx_t_10]) + __pyx_v_child->elsize); 2025-09-07T23:52:30,753 | ^~ 2025-09-07T23:52:30,766 skbio/math/_subsample.c: In function ‘__Pyx_InitCachedConstants’: 2025-09-07T23:52:30,769 skbio/math/_subsample.c:3858:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-07T23:52:30,770 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;} 2025-09-07T23:52:30,770 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,770 In file included from /usr/include/python3.13/Python.h:101, 2025-09-07T23:52:30,771 from skbio/math/_subsample.c:16: 2025-09-07T23:52:30,771 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:52:30,771 213 | PyCode_New( 2025-09-07T23:52:30,771 | ^~~~~~~~~~ 2025-09-07T23:52:30,775 skbio/math/_subsample.c:3858:262: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T23:52:30,775 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;} 2025-09-07T23:52:30,775 | ^~ 2025-09-07T23:52:30,775 | | 2025-09-07T23:52:30,776 | int 2025-09-07T23:52:30,776 skbio/math/_subsample.c:124:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:30,776 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:30,776 | ^~~~~ 2025-09-07T23:52:30,776 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-07T23:52:30,776 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:52:30,776 | ~~~~~~~~~~^ 2025-09-07T23:52:30,780 skbio/math/_subsample.c:3858:266: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-07T23:52:30,781 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;} 2025-09-07T23:52:30,781 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,781 | | 2025-09-07T23:52:30,781 | PyObject * {aka struct _object *} 2025-09-07T23:52:30,781 skbio/math/_subsample.c:124:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:30,781 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:30,781 | ^~~~ 2025-09-07T23:52:30,781 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-07T23:52:30,781 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:52:30,782 | ~~~~^ 2025-09-07T23:52:30,786 skbio/math/_subsample.c:124:11: error: too few arguments to function ‘PyCode_New’ 2025-09-07T23:52:30,786 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:30,786 | ^~~~~~~~~~ 2025-09-07T23:52:30,786 skbio/math/_subsample.c:3858:33: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:30,786 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;} 2025-09-07T23:52:30,786 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,786 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:52:30,786 213 | PyCode_New( 2025-09-07T23:52:30,786 | ^~~~~~~~~~ 2025-09-07T23:52:30,811 skbio/math/_subsample.c: In function ‘__Pyx_ParseOptionalKeywords’: 2025-09-07T23:52:30,817 skbio/math/_subsample.c:4145:22: error: implicit declaration of function ‘PyUnicode_GET_SIZE’; did you mean ‘PyDict_GET_SIZE’? [-Wimplicit-function-declaration] 2025-09-07T23:52:30,817 4145 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-07T23:52:30,817 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,817 | PyDict_GET_SIZE 2025-09-07T23:52:30,862 skbio/math/_subsample.c: In function ‘__Pyx_ErrRestore’: 2025-09-07T23:52:30,866 skbio/math/_subsample.c:4932:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:52:30,867 4932 | tmp_type = tstate->curexc_type; 2025-09-07T23:52:30,867 | ^~ 2025-09-07T23:52:30,871 skbio/math/_subsample.c:4933:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:52:30,872 4933 | tmp_value = tstate->curexc_value; 2025-09-07T23:52:30,872 | ^~ 2025-09-07T23:52:30,876 skbio/math/_subsample.c:4934:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:30,877 4934 | tmp_tb = tstate->curexc_traceback; 2025-09-07T23:52:30,877 | ^~ 2025-09-07T23:52:30,881 skbio/math/_subsample.c:4935:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:52:30,882 4935 | tstate->curexc_type = type; 2025-09-07T23:52:30,882 | ^~ 2025-09-07T23:52:30,887 skbio/math/_subsample.c:4936:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:52:30,887 4936 | tstate->curexc_value = value; 2025-09-07T23:52:30,887 | ^~ 2025-09-07T23:52:30,892 skbio/math/_subsample.c:4937:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:30,892 4937 | tstate->curexc_traceback = tb; 2025-09-07T23:52:30,892 | ^~ 2025-09-07T23:52:30,892 skbio/math/_subsample.c: In function ‘__Pyx_ErrFetch’: 2025-09-07T23:52:30,897 skbio/math/_subsample.c:4948:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:52:30,897 4948 | *type = tstate->curexc_type; 2025-09-07T23:52:30,897 | ^~ 2025-09-07T23:52:30,902 skbio/math/_subsample.c:4949:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:52:30,902 4949 | *value = tstate->curexc_value; 2025-09-07T23:52:30,902 | ^~ 2025-09-07T23:52:30,907 skbio/math/_subsample.c:4950:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:30,907 4950 | *tb = tstate->curexc_traceback; 2025-09-07T23:52:30,908 | ^~ 2025-09-07T23:52:30,912 skbio/math/_subsample.c:4951:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:52:30,912 4951 | tstate->curexc_type = 0; 2025-09-07T23:52:30,913 | ^~ 2025-09-07T23:52:30,917 skbio/math/_subsample.c:4952:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:52:30,917 4952 | tstate->curexc_value = 0; 2025-09-07T23:52:30,918 | ^~ 2025-09-07T23:52:30,922 skbio/math/_subsample.c:4953:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:30,923 4953 | tstate->curexc_traceback = 0; 2025-09-07T23:52:30,923 | ^~ 2025-09-07T23:52:30,934 skbio/math/_subsample.c: In function ‘__Pyx_Raise’: 2025-09-07T23:52:30,939 skbio/math/_subsample.c:5111:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:30,939 5111 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-07T23:52:30,939 | ^~ 2025-09-07T23:52:30,944 skbio/math/_subsample.c:5114:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:30,945 5114 | tstate->curexc_traceback = tb; 2025-09-07T23:52:30,945 | ^~ 2025-09-07T23:52:30,953 skbio/math/_subsample.c: In function ‘__Pyx_PyInt_As_Py_intptr_t’: 2025-09-07T23:52:30,958 skbio/math/_subsample.c:5434:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-07T23:52:30,958 5434 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-07T23:52:30,958 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,959 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-07T23:52:30,959 from /usr/include/python3.13/Python.h:81: 2025-09-07T23:52:30,959 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-07T23:52:30,959 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-07T23:52:30,960 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,964 skbio/math/_subsample.c: In function ‘__Pyx_PyInt_As_int’: 2025-09-07T23:52:30,970 skbio/math/_subsample.c:5800:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-07T23:52:30,970 5800 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-07T23:52:30,970 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,970 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-07T23:52:30,970 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-07T23:52:30,971 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,974 skbio/math/_subsample.c: In function ‘__Pyx_PyInt_As_long’: 2025-09-07T23:52:30,980 skbio/math/_subsample.c:5926:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-07T23:52:30,980 5926 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-07T23:52:30,980 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,980 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-07T23:52:30,981 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-07T23:52:30,981 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:30,997 skbio/math/_subsample.c: In function ‘__Pyx_CreateCodeObjectForTraceback’: 2025-09-07T23:52:31,003 skbio/math/_subsample.c:6159:5: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-07T23:52:31,003 6159 | py_code = __Pyx_PyCode_New( 2025-09-07T23:52:31,003 | ^~~~~~~ 2025-09-07T23:52:31,003 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:52:31,003 213 | PyCode_New( 2025-09-07T23:52:31,003 | ^~~~~~~~~~ 2025-09-07T23:52:31,009 skbio/math/_subsample.c:6173:9: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T23:52:31,009 6173 | py_line, /*int firstlineno,*/ 2025-09-07T23:52:31,009 | ^~~~~~~ 2025-09-07T23:52:31,009 | | 2025-09-07T23:52:31,010 | int 2025-09-07T23:52:31,010 skbio/math/_subsample.c:124:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:31,010 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:31,010 | ^~~~~ 2025-09-07T23:52:31,010 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-07T23:52:31,010 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:52:31,010 | ~~~~~~~~~~^ 2025-09-07T23:52:31,017 skbio/math/_subsample.c:6174:9: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-07T23:52:31,017 6174 | __pyx_empty_bytes /*PyObject *lnotab*/ 2025-09-07T23:52:31,017 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:52:31,017 | | 2025-09-07T23:52:31,017 | PyObject * {aka struct _object *} 2025-09-07T23:52:31,018 skbio/math/_subsample.c:124:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:31,018 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:31,018 | ^~~~ 2025-09-07T23:52:31,018 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-07T23:52:31,018 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:52:31,018 | ~~~~^ 2025-09-07T23:52:31,025 skbio/math/_subsample.c:124:11: error: too few arguments to function ‘PyCode_New’ 2025-09-07T23:52:31,025 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:31,025 | ^~~~~~~~~~ 2025-09-07T23:52:31,025 skbio/math/_subsample.c:6159:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:31,025 6159 | py_code = __Pyx_PyCode_New( 2025-09-07T23:52:31,025 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:52:31,025 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:52:31,026 213 | PyCode_New( 2025-09-07T23:52:31,026 | ^~~~~~~~~~ 2025-09-07T23:52:31,030 skbio/math/_subsample.c: In function ‘__Pyx_AddTraceback’: 2025-09-07T23:52:31,036 skbio/math/_subsample.c:6205:13: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-07T23:52:31,036 6205 | py_frame->f_lineno = py_line; 2025-09-07T23:52:31,037 | ^~ 2025-09-07T23:52:31,080 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-07T23:52:31,250 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T23:52:31,263 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T23:52:31,263 exec(compile('"'"''"'"''"'"' 2025-09-07T23:52:31,263 # This is -- a caller that pip uses to run setup.py 2025-09-07T23:52:31,263 # 2025-09-07T23:52:31,263 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T23:52:31,263 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T23:52:31,263 # - It provides a clear error message when setuptools is not installed. 2025-09-07T23:52:31,263 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T23:52:31,263 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T23:52:31,263 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T23:52:31,263 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T23:52:31,263 import os, sys, tokenize, traceback 2025-09-07T23:52:31,263 2025-09-07T23:52:31,263 try: 2025-09-07T23:52:31,263 import setuptools 2025-09-07T23:52:31,263 except ImportError: 2025-09-07T23:52:31,263 print( 2025-09-07T23:52:31,263 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T23:52:31,263 "the build environment with exception:", 2025-09-07T23:52:31,263 file=sys.stderr, 2025-09-07T23:52:31,263 ) 2025-09-07T23:52:31,263 traceback.print_exc() 2025-09-07T23:52:31,263 sys.exit(1) 2025-09-07T23:52:31,263 2025-09-07T23:52:31,263 __file__ = %r 2025-09-07T23:52:31,263 sys.argv[0] = __file__ 2025-09-07T23:52:31,263 2025-09-07T23:52:31,263 if os.path.exists(__file__): 2025-09-07T23:52:31,263 filename = __file__ 2025-09-07T23:52:31,263 with tokenize.open(__file__) as f: 2025-09-07T23:52:31,263 setup_py_code = f.read() 2025-09-07T23:52:31,263 else: 2025-09-07T23:52:31,263 filename = "" 2025-09-07T23:52:31,263 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T23:52:31,263 2025-09-07T23:52:31,263 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T23:52:31,263 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-uswis55f/scikit-bio_1a7ba2bf29784ccf8973522816ec45a9/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-75nm5q6r[/] 2025-09-07T23:52:31,263 [bold magenta]cwd[/]: /tmp/pip-wheel-uswis55f/scikit-bio_1a7ba2bf29784ccf8973522816ec45a9/ 2025-09-07T23:52:31,263 Building wheel for scikit-bio (setup.py): finished with status 'error' 2025-09-07T23:52:31,264 ERROR: Failed building wheel for scikit-bio 2025-09-07T23:52:31,265 Running setup.py clean for scikit-bio 2025-09-07T23:52:31,265 Running command python setup.py clean 2025-09-07T23:52:32,161 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-07T23:52:32,161 warnings.warn(msg) 2025-09-07T23:52:32,553 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:52:32,554 !! 2025-09-07T23:52:32,554 ******************************************************************************** 2025-09-07T23:52:32,554 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:52:32,554 License :: OSI Approved :: BSD License 2025-09-07T23:52:32,554 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:52:32,554 ******************************************************************************** 2025-09-07T23:52:32,554 !! 2025-09-07T23:52:32,555 self._finalize_license_expression() 2025-09-07T23:52:32,627 running clean 2025-09-07T23:52:32,773 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:52:32,773 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:52:32,779 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T23:52:32,779 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T23:52:32,779 removing 'build' 2025-09-07T23:52:32,914 Failed to build scikit-bio 2025-09-07T23:52:32,915 ERROR: Failed to build one or more wheels 2025-09-07T23:52:32,916 Exception information: 2025-09-07T23:52:32,916 Traceback (most recent call last): 2025-09-07T23:52:32,916 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T23:52:32,916 status = _inner_run() 2025-09-07T23:52:32,916 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T23:52:32,916 return self.run(options, args) 2025-09-07T23:52:32,916 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T23:52:32,916 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T23:52:32,916 return func(self, options, args) 2025-09-07T23:52:32,916 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T23:52:32,916 raise CommandError("Failed to build one or more wheels") 2025-09-07T23:52:32,916 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T23:52:32,920 Removed build tracker: '/tmp/pip-build-tracker-d6ps39z6'