2023-09-14T00:25:46,331 Created temporary directory: /tmp/pip-build-tracker-5uawhzcf 2023-09-14T00:25:46,332 Initialized build tracking at /tmp/pip-build-tracker-5uawhzcf 2023-09-14T00:25:46,333 Created build tracker: /tmp/pip-build-tracker-5uawhzcf 2023-09-14T00:25:46,333 Entered build tracker: /tmp/pip-build-tracker-5uawhzcf 2023-09-14T00:25:46,334 Created temporary directory: /tmp/pip-wheel-us10m3qj 2023-09-14T00:25:46,337 Created temporary directory: /tmp/pip-ephem-wheel-cache-4vejendo 2023-09-14T00:25:46,358 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-14T00:25:46,362 2 location(s) to search for versions of pyfastani: 2023-09-14T00:25:46,362 * https://pypi.org/simple/pyfastani/ 2023-09-14T00:25:46,362 * https://www.piwheels.org/simple/pyfastani/ 2023-09-14T00:25:46,363 Fetching project page and analyzing links: https://pypi.org/simple/pyfastani/ 2023-09-14T00:25:46,364 Getting page https://pypi.org/simple/pyfastani/ 2023-09-14T00:25:46,365 Found index url https://pypi.org/simple/ 2023-09-14T00:25:46,584 Fetched page https://pypi.org/simple/pyfastani/ as application/vnd.pypi.simple.v1+json 2023-09-14T00:25:46,607 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/18/07/9ed2c77a83ae6bcce41fcfcf98969b25efc6b061ac740bb3bd70fd90de25/pyfastani-0.1.0-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,608 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/31/5a/fb8f4066ef68dd8eba0c289654cd5247244a01c6f6f9d0f91259c89a83f4/pyfastani-0.1.0-cp36-cp36m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,608 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/23/fb/c55d6b960314cb27f162ca010782906e0ccfe8390648cc01e82bab185953/pyfastani-0.1.0-cp37-cp37m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,609 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/7f/e4/6818f273e6990a0e649d236d44db7a3f56a694cbe6cba4b18fa51c517c4f/pyfastani-0.1.0-cp37-cp37m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,609 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/e0/7d/1efdab8fe5f1920cca5fb23d6506a5cb60bff0340b64d73f981466acf38e/pyfastani-0.1.0-cp38-cp38-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,610 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/a8/ea/0daaf8f35f62dcbad48bab59d26e6a811d93def44ebe1585d7c6fc289d0f/pyfastani-0.1.0-cp38-cp38-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,611 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/47/e9/3e6818ce5f4a58f82f4cc4181df9fe99a9626d2743beadfc4799a3961a8c/pyfastani-0.1.0-cp39-cp39-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,612 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/44/d6/d1c43c20d420c44f5944c0ff1b9527f7ad33a51f9263b98bd250a112eea9/pyfastani-0.1.0-cp39-cp39-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,612 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/46/54/84aedc9071fb3f9cc57c3ca1be666d5a2f4b194329ff35e3a496b99e0706/pyfastani-0.1.0-pp37-pypy37_pp73-macosx_10_7_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,613 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/d5/f2/47d4148347c1a2b740ce7b82652069c29b0b13a468e90e421567527906e8/pyfastani-0.1.0-pp37-pypy37_pp73-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,614 Found link https://files.pythonhosted.org/packages/56/e3/8a2309181b801add4dcb4cd5a067892457dc02af9499e2d02e749721faa7/pyfastani-0.1.0.tar.gz (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6), version: 0.1.0 2023-09-14T00:25:46,615 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/b9/09/bb1c3f6818457e9318cfd8fd7d58fc126bfcf7795962fb3b1bc97ccf1c4d/pyfastani-0.1.1-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,615 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/d2/ec/d649375f24497c99a95bf6040b4b279dbfea3afdcb94fa9a98674596cc54/pyfastani-0.1.1-cp36-cp36m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,616 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/92/36/de119b5f1d30d79e9cea593e793c2ea4a1169794965840d546c6acc3a2d2/pyfastani-0.1.1-cp37-cp37m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,616 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/f4/0d/d524205d07cc5c1bccec654008d280b554d659a26f00e84d69078950f22f/pyfastani-0.1.1-cp37-cp37m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,617 Skipping link: No binaries permitted for pyfastani: 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https://files.pythonhosted.org/packages/be/8e/6b1c7e670bc230a51d1a05109d39d6d30d958561b3b9078e0cc4b48fac19/pyfastani-0.1.1.tar.gz (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6), version: 0.1.1 2023-09-14T00:25:46,622 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/a3/e8/88818abf7ba0a0c7e779c303153d463356ea8649c30cf73b075437dd8422/pyfastani-0.1.2-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,623 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/2a/ce/768ca2d25c107afb9f46bce03425dc46b6c26178465c3b4ab530e5960b84/pyfastani-0.1.2-cp36-cp36m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,623 Skipping link: No binaries permitted for pyfastani: 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https://files.pythonhosted.org/packages/9f/d7/412b87b2e89f715e920aeb94eb4872a63ca6482da56315c45599ed77faf5/pyfastani-0.1.2-pp37-pypy37_pp73-macosx_10_7_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,627 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/90/1e/6cb5c74c2f3bad362b8db0450999012cc9eb932f601b2abb84f80eb257de/pyfastani-0.1.2-pp37-pypy37_pp73-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,628 Found link https://files.pythonhosted.org/packages/f1/55/48b109d4a474e7b1fd551971130e4f36bd6552040c831540bb62c680da18/pyfastani-0.1.2.tar.gz (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6), version: 0.1.2 2023-09-14T00:25:46,629 Skipping link: No binaries permitted for pyfastani: 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https://files.pythonhosted.org/packages/a1/97/1fbfad8cf7c1e8403f9510f13e6d286c156fadf3ed4c0bca5bf4177676d1/pyfastani-0.4.0-pp37-pypy37_pp73-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,673 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/87/81/57bf66d3ac27e38fa76e6ad046ee7625ea503b3c0e3dcf0884ae9f0635fa/pyfastani-0.4.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,674 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/3d/24/f25ed2fed2926d20f47624903099367d84a5e6b76f5792542803cf000e14/pyfastani-0.4.0-pp38-pypy38_pp73-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,674 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/d2/52/0058bfa7426635a153289e9493e2f4b19f34bad4caf0dc2455f3c6b701c1/pyfastani-0.4.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,674 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/3b/b3/777e3c36b6020b3d609fa9f4972a2938ca5baca4c2e5b085efc23d9b52a0/pyfastani-0.4.0-pp39-pypy39_pp73-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,675 Found link https://files.pythonhosted.org/packages/04/be/5fa0a7577837e15e03204bdee84493bd46c740f95393cd7e7c84c3796e9d/pyfastani-0.4.0.tar.gz (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6), version: 0.4.0 2023-09-14T00:25:46,676 Skipping link: No binaries permitted for pyfastani: 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https://files.pythonhosted.org/packages/de/59/b293317eab8b69d0898e7bbb194876c2d9f1634d743d38524063e4583693/pyfastani-0.4.1-cp36-cp36m-macosx_10_14_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,678 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/b3/92/ad6796c81324073d74e886cbdf136a26e7f35bd45d88e2a99eecb3e09fd2/pyfastani-0.4.1-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,679 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/6e/ab/b663f64646366a2fdf1045696e0af02b7ecce701739127b6fa4789105825/pyfastani-0.4.1-cp36-cp36m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,679 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/0a/b0/3d7fc40b2a132784eba59032c8790b88094a373290e4964d6b991fefa8fb/pyfastani-0.4.1-cp37-cp37m-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,680 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/d4/05/fe3fee0ad04ab1b43c497050311062f24fe5fd5b51e814ff301d4b627a5d/pyfastani-0.4.1-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,681 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/9f/49/d641f42ea90a29f37034786f5e0571ade532f0f92e561627c3f3337d1a67/pyfastani-0.4.1-cp37-cp37m-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,682 Skipping link: No binaries permitted for pyfastani: 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https://files.pythonhosted.org/packages/76/dd/f1dae6a5352f794d7fd0dcaa678c4433380278eabd659e3f8c4bcdab4328/pyfastani-0.4.1-pp38-pypy38_pp73-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,687 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/24/f5/1e908df6212abb24dda2f2684181c860a769ec21200d93e7953dc4a8aee1/pyfastani-0.4.1-pp39-pypy39_pp73-macosx_10_9_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,687 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/38/7b/6a62ab3c6877f78b78607785b9accc258c4d5ace336d607e2a9a4873882b/pyfastani-0.4.1-pp39-pypy39_pp73-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,688 Found link https://files.pythonhosted.org/packages/b4/c4/30a8e16c9b77b350ef958fdb3d7075fe9a941d82042837a6988126bf04d3/pyfastani-0.4.1.tar.gz (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6), version: 0.4.1 2023-09-14T00:25:46,689 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyfastani/ 2023-09-14T00:25:46,690 Getting page https://www.piwheels.org/simple/pyfastani/ 2023-09-14T00:25:46,691 Found index url https://www.piwheels.org/simple/ 2023-09-14T00:25:46,964 Fetched page https://www.piwheels.org/simple/pyfastani/ as text/html 2023-09-14T00:25:46,969 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.1-cp39-cp39-linux_armv7l.whl#sha256=8e36c818dd9125f4d9a04ba03abc13b820dadffed4cbf96571df4fe0d1272696 (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,969 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.1-cp39-cp39-linux_armv6l.whl#sha256=8e36c818dd9125f4d9a04ba03abc13b820dadffed4cbf96571df4fe0d1272696 (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,970 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.1-cp37-cp37m-linux_armv7l.whl#sha256=9dbdf78ee5e8d2b1190b647a5bd6a8274e533739933a6a919962d378e83bb1ae (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,971 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.1-cp37-cp37m-linux_armv6l.whl#sha256=9dbdf78ee5e8d2b1190b647a5bd6a8274e533739933a6a919962d378e83bb1ae (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,972 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.0-cp39-cp39-linux_armv7l.whl#sha256=7cbb59a8cfe273b488346a51698e3c64954d0273f25bfb12a209d0ef9aba7534 (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,972 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.0-cp39-cp39-linux_armv6l.whl#sha256=7cbb59a8cfe273b488346a51698e3c64954d0273f25bfb12a209d0ef9aba7534 (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,973 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.0-cp37-cp37m-linux_armv7l.whl#sha256=bffd2891ffbb54c0ee53adda7a2ce31642695c5080c5f93631a1a3ff6437ee4f (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,974 Skipping link: No binaries permitted for pyfastani: https://www.piwheels.org/simple/pyfastani/pyfastani-0.4.0-cp37-cp37m-linux_armv6l.whl#sha256=bffd2891ffbb54c0ee53adda7a2ce31642695c5080c5f93631a1a3ff6437ee4f (from https://www.piwheels.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-14T00:25:46,975 Skipping link: not a file: https://www.piwheels.org/simple/pyfastani/ 2023-09-14T00:25:46,976 Skipping link: not a file: https://pypi.org/simple/pyfastani/ 2023-09-14T00:25:47,005 Given no hashes to check 1 links for project 'pyfastani': discarding no candidates 2023-09-14T00:25:47,034 Collecting pyfastani==0.1.0 2023-09-14T00:25:47,037 Created temporary directory: /tmp/pip-unpack-fza_v99a 2023-09-14T00:25:47,718 Downloading pyfastani-0.1.0.tar.gz (18 kB) 2023-09-14T00:25:47,765 Added pyfastani==0.1.0 from https://files.pythonhosted.org/packages/56/e3/8a2309181b801add4dcb4cd5a067892457dc02af9499e2d02e749721faa7/pyfastani-0.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-5uawhzcf' 2023-09-14T00:25:47,769 Created temporary directory: /tmp/pip-build-env-7bzw4irm 2023-09-14T00:25:47,774 Installing build dependencies: started 2023-09-14T00:25:47,775 Running command pip subprocess to install build dependencies 2023-09-14T00:25:48,952 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-14T00:25:49,450 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-14T00:25:51,110 Collecting setuptools>=46.4 2023-09-14T00:25:51,111 Obtaining dependency information for setuptools>=46.4 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata 2023-09-14T00:25:51,116 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-14T00:25:52,501 Collecting cython~=0.29.16 2023-09-14T00:25:52,502 Obtaining dependency information for cython~=0.29.16 from https://files.pythonhosted.org/packages/3f/d6/9eed523aeaca42acbaa3e6d3850edae780dc7f8da9df1bf6a2ceb851839c/Cython-0.29.36-py2.py3-none-any.whl.metadata 2023-09-14T00:25:52,508 Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB) 2023-09-14T00:25:52,682 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-14T00:25:52,720 Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB) 2023-09-14T00:25:55,180 Installing collected packages: setuptools, cython 2023-09-14T00:26:01,759 Creating /tmp/pip-build-env-7bzw4irm/overlay/local/bin 2023-09-14T00:26:01,762 changing mode of /tmp/pip-build-env-7bzw4irm/overlay/local/bin/cygdb to 755 2023-09-14T00:26:01,764 changing mode of /tmp/pip-build-env-7bzw4irm/overlay/local/bin/cython to 755 2023-09-14T00:26:01,767 changing mode of /tmp/pip-build-env-7bzw4irm/overlay/local/bin/cythonize to 755 2023-09-14T00:26:01,789 Successfully installed cython-0.29.36 setuptools-68.2.2 2023-09-14T00:26:02,347 Installing build dependencies: finished with status 'done' 2023-09-14T00:26:02,350 Getting requirements to build wheel: started 2023-09-14T00:26:02,351 Running command Getting requirements to build wheel 2023-09-14T00:26:03,269 Getting requirements to build wheel: finished with status 'done' 2023-09-14T00:26:03,292 Installing backend dependencies: started 2023-09-14T00:26:03,293 Running command pip subprocess to install backend dependencies 2023-09-14T00:26:04,425 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-14T00:26:04,921 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-14T00:26:05,769 Collecting wheel 2023-09-14T00:26:05,790 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-14T00:26:08,262 Installing collected packages: wheel 2023-09-14T00:26:08,787 Creating /tmp/pip-build-env-7bzw4irm/normal/local/bin 2023-09-14T00:26:08,789 changing mode of /tmp/pip-build-env-7bzw4irm/normal/local/bin/wheel to 755 2023-09-14T00:26:08,801 Successfully installed wheel-0.41.2 2023-09-14T00:26:09,532 Installing backend dependencies: finished with status 'done' 2023-09-14T00:26:09,534 Created temporary directory: /tmp/pip-modern-metadata-3oz4sb4x 2023-09-14T00:26:09,536 Preparing metadata (pyproject.toml): started 2023-09-14T00:26:09,537 Running command Preparing metadata (pyproject.toml) 2023-09-14T00:26:10,373 running dist_info 2023-09-14T00:26:10,389 creating /tmp/pip-modern-metadata-3oz4sb4x/pyfastani.egg-info 2023-09-14T00:26:10,394 writing /tmp/pip-modern-metadata-3oz4sb4x/pyfastani.egg-info/PKG-INFO 2023-09-14T00:26:10,398 writing dependency_links to /tmp/pip-modern-metadata-3oz4sb4x/pyfastani.egg-info/dependency_links.txt 2023-09-14T00:26:10,400 writing top-level names to /tmp/pip-modern-metadata-3oz4sb4x/pyfastani.egg-info/top_level.txt 2023-09-14T00:26:10,402 writing manifest file '/tmp/pip-modern-metadata-3oz4sb4x/pyfastani.egg-info/SOURCES.txt' 2023-09-14T00:26:10,430 reading manifest file '/tmp/pip-modern-metadata-3oz4sb4x/pyfastani.egg-info/SOURCES.txt' 2023-09-14T00:26:10,432 adding license file 'COPYING' 2023-09-14T00:26:10,434 writing manifest file '/tmp/pip-modern-metadata-3oz4sb4x/pyfastani.egg-info/SOURCES.txt' 2023-09-14T00:26:10,435 creating '/tmp/pip-modern-metadata-3oz4sb4x/pyfastani-0.1.0.dist-info' 2023-09-14T00:26:10,626 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-14T00:26:10,631 Source in /tmp/pip-wheel-us10m3qj/pyfastani_8e5e5fdafd644d54ad6c69b59174e06d has version 0.1.0, which satisfies requirement pyfastani==0.1.0 from https://files.pythonhosted.org/packages/56/e3/8a2309181b801add4dcb4cd5a067892457dc02af9499e2d02e749721faa7/pyfastani-0.1.0.tar.gz 2023-09-14T00:26:10,632 Removed pyfastani==0.1.0 from https://files.pythonhosted.org/packages/56/e3/8a2309181b801add4dcb4cd5a067892457dc02af9499e2d02e749721faa7/pyfastani-0.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-5uawhzcf' 2023-09-14T00:26:10,638 Created temporary directory: /tmp/pip-unpack-o0g11t6p 2023-09-14T00:26:10,639 Created temporary directory: /tmp/pip-unpack-mic746oo 2023-09-14T00:26:10,643 Building wheels for collected packages: pyfastani 2023-09-14T00:26:10,647 Created temporary directory: /tmp/pip-wheel-h6t22lrk 2023-09-14T00:26:10,647 Destination directory: /tmp/pip-wheel-h6t22lrk 2023-09-14T00:26:10,650 Building wheel for pyfastani (pyproject.toml): started 2023-09-14T00:26:10,651 Running command Building wheel for pyfastani (pyproject.toml) 2023-09-14T00:26:11,494 running bdist_wheel 2023-09-14T00:26:11,521 running build 2023-09-14T00:26:11,521 running build_py 2023-09-14T00:26:11,529 creating build 2023-09-14T00:26:11,529 creating build/lib.linux-armv7l-cpython-311 2023-09-14T00:26:11,530 creating build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-14T00:26:11,531 copying pyfastani/__init__.py -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-14T00:26:11,533 creating build/lib.linux-armv7l-cpython-311/pyfastani/tests 2023-09-14T00:26:11,534 copying pyfastani/tests/test_mapper.py -> build/lib.linux-armv7l-cpython-311/pyfastani/tests 2023-09-14T00:26:11,536 copying pyfastani/tests/__init__.py -> build/lib.linux-armv7l-cpython-311/pyfastani/tests 2023-09-14T00:26:11,537 copying pyfastani/tests/minifasta.py -> build/lib.linux-armv7l-cpython-311/pyfastani/tests 2023-09-14T00:26:11,539 running egg_info 2023-09-14T00:26:11,542 writing pyfastani.egg-info/PKG-INFO 2023-09-14T00:26:11,546 writing dependency_links to pyfastani.egg-info/dependency_links.txt 2023-09-14T00:26:11,548 writing top-level names to pyfastani.egg-info/top_level.txt 2023-09-14T00:26:11,562 reading manifest file 'pyfastani.egg-info/SOURCES.txt' 2023-09-14T00:26:11,564 adding license file 'COPYING' 2023-09-14T00:26:11,566 writing manifest file 'pyfastani.egg-info/SOURCES.txt' 2023-09-14T00:26:11,568 copying pyfastani/_fastani.pyx -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-14T00:26:11,572 copying pyfastani/_utils.cpp -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-14T00:26:11,575 running build_ext 2023-09-14T00:26:12,459 Error compiling Cython file: 2023-09-14T00:26:12,460 ------------------------------------------------------------ 2023-09-14T00:26:12,461 ... 2023-09-14T00:26:12,461 # cython: language_level=3, linetrace=True, language=cpp 2023-09-14T00:26:12,463 # --- C imports -------------------------------------------------------------- 2023-09-14T00:26:12,464 cimport libcpp11.chrono 2023-09-14T00:26:12,464 ^ 2023-09-14T00:26:12,465 ------------------------------------------------------------ 2023-09-14T00:26:12,466 pyfastani/_fastani.pyx:7:8: 'libcpp11/chrono.pxd' not found 2023-09-14T00:26:12,878 Error compiling Cython file: 2023-09-14T00:26:12,878 ------------------------------------------------------------ 2023-09-14T00:26:12,878 ... 2023-09-14T00:26:12,879 from libcpp cimport bool, nullptr 2023-09-14T00:26:12,879 from libcpp.functional cimport function 2023-09-14T00:26:12,880 from libcpp.string cimport string 2023-09-14T00:26:12,881 from libcpp.unordered_map cimport unordered_map 2023-09-14T00:26:12,881 from libcpp.vector cimport vector 2023-09-14T00:26:12,882 from libcpp11.fstream cimport ofstream 2023-09-14T00:26:12,882 ^ 2023-09-14T00:26:12,883 ------------------------------------------------------------ 2023-09-14T00:26:12,884 pyfastani/_fastani.pyx:16:0: 'libcpp11/fstream.pxd' not found 2023-09-14T00:26:12,885 Error compiling Cython file: 2023-09-14T00:26:12,885 ------------------------------------------------------------ 2023-09-14T00:26:12,886 ... 2023-09-14T00:26:12,886 from libcpp cimport bool, nullptr 2023-09-14T00:26:12,886 from libcpp.functional cimport function 2023-09-14T00:26:12,887 from libcpp.string cimport string 2023-09-14T00:26:12,887 from libcpp.unordered_map cimport unordered_map 2023-09-14T00:26:12,887 from libcpp.vector cimport vector 2023-09-14T00:26:12,888 from libcpp11.fstream cimport ofstream 2023-09-14T00:26:12,888 ^ 2023-09-14T00:26:12,889 ------------------------------------------------------------ 2023-09-14T00:26:12,889 pyfastani/_fastani.pyx:16:0: 'libcpp11/fstream/ofstream.pxd' not found 2023-09-14T00:26:12,890 Error compiling Cython file: 2023-09-14T00:26:12,891 ------------------------------------------------------------ 2023-09-14T00:26:12,891 ... 2023-09-14T00:26:12,892 from libcpp.string cimport string 2023-09-14T00:26:12,892 from libcpp.unordered_map cimport unordered_map 2023-09-14T00:26:12,893 from libcpp.vector cimport vector 2023-09-14T00:26:12,893 from libcpp11.fstream cimport ofstream 2023-09-14T00:26:12,894 cimport fastani.map.map_stats 2023-09-14T00:26:12,894 ^ 2023-09-14T00:26:12,895 ------------------------------------------------------------ 2023-09-14T00:26:12,896 pyfastani/_fastani.pyx:18:8: 'fastani/map/map_stats.pxd' not found 2023-09-14T00:26:12,896 Error compiling Cython file: 2023-09-14T00:26:12,897 ------------------------------------------------------------ 2023-09-14T00:26:12,897 ... 2023-09-14T00:26:12,898 from libcpp.unordered_map cimport unordered_map 2023-09-14T00:26:12,898 from libcpp.vector cimport vector 2023-09-14T00:26:12,899 from libcpp11.fstream cimport ofstream 2023-09-14T00:26:12,900 cimport fastani.map.map_stats 2023-09-14T00:26:12,900 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,901 ^ 2023-09-14T00:26:12,902 ------------------------------------------------------------ 2023-09-14T00:26:12,902 pyfastani/_fastani.pyx:19:0: 'kseq.pxd' not found 2023-09-14T00:26:12,904 Error compiling Cython file: 2023-09-14T00:26:12,904 ------------------------------------------------------------ 2023-09-14T00:26:12,905 ... 2023-09-14T00:26:12,905 from libcpp.unordered_map cimport unordered_map 2023-09-14T00:26:12,906 from libcpp.vector cimport vector 2023-09-14T00:26:12,906 from libcpp11.fstream cimport ofstream 2023-09-14T00:26:12,907 cimport fastani.map.map_stats 2023-09-14T00:26:12,908 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,908 ^ 2023-09-14T00:26:12,909 ------------------------------------------------------------ 2023-09-14T00:26:12,910 pyfastani/_fastani.pyx:19:0: 'kseq/kseq_t.pxd' not found 2023-09-14T00:26:12,911 Error compiling Cython file: 2023-09-14T00:26:12,911 ------------------------------------------------------------ 2023-09-14T00:26:12,912 ... 2023-09-14T00:26:12,912 from libcpp.unordered_map cimport unordered_map 2023-09-14T00:26:12,913 from libcpp.vector cimport vector 2023-09-14T00:26:12,913 from libcpp11.fstream cimport ofstream 2023-09-14T00:26:12,914 cimport fastani.map.map_stats 2023-09-14T00:26:12,915 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,915 ^ 2023-09-14T00:26:12,916 ------------------------------------------------------------ 2023-09-14T00:26:12,917 pyfastani/_fastani.pyx:19:0: 'kseq/kstring_t.pxd' not found 2023-09-14T00:26:12,918 Error compiling Cython file: 2023-09-14T00:26:12,918 ------------------------------------------------------------ 2023-09-14T00:26:12,919 ... 2023-09-14T00:26:12,920 from libcpp.vector cimport vector 2023-09-14T00:26:12,920 from libcpp11.fstream cimport ofstream 2023-09-14T00:26:12,921 cimport fastani.map.map_stats 2023-09-14T00:26:12,922 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,922 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,922 ^ 2023-09-14T00:26:12,923 ------------------------------------------------------------ 2023-09-14T00:26:12,924 pyfastani/_fastani.pyx:20:0: 'fastani/cgi/compute_core_identity.pxd' not found 2023-09-14T00:26:12,925 Error compiling Cython file: 2023-09-14T00:26:12,925 ------------------------------------------------------------ 2023-09-14T00:26:12,926 ... 2023-09-14T00:26:12,926 from libcpp.vector cimport vector 2023-09-14T00:26:12,927 from libcpp11.fstream cimport ofstream 2023-09-14T00:26:12,928 cimport fastani.map.map_stats 2023-09-14T00:26:12,928 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,929 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,930 ^ 2023-09-14T00:26:12,930 ------------------------------------------------------------ 2023-09-14T00:26:12,931 pyfastani/_fastani.pyx:20:0: 'fastani/cgi/compute_core_identity/computeCGI.pxd' not found 2023-09-14T00:26:12,933 Error compiling Cython file: 2023-09-14T00:26:12,933 ------------------------------------------------------------ 2023-09-14T00:26:12,934 ... 2023-09-14T00:26:12,935 from libcpp11.fstream cimport ofstream 2023-09-14T00:26:12,936 cimport fastani.map.map_stats 2023-09-14T00:26:12,937 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,937 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,938 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:12,938 ^ 2023-09-14T00:26:12,939 ------------------------------------------------------------ 2023-09-14T00:26:12,940 pyfastani/_fastani.pyx:21:0: 'fastani/cgi/cgid_types.pxd' not found 2023-09-14T00:26:12,941 Error compiling Cython file: 2023-09-14T00:26:12,941 ------------------------------------------------------------ 2023-09-14T00:26:12,942 ... 2023-09-14T00:26:12,943 from libcpp11.fstream cimport ofstream 2023-09-14T00:26:12,944 cimport fastani.map.map_stats 2023-09-14T00:26:12,945 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,945 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,946 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:12,946 ^ 2023-09-14T00:26:12,947 ------------------------------------------------------------ 2023-09-14T00:26:12,948 pyfastani/_fastani.pyx:21:0: 'fastani/cgi/cgid_types/CGI_Results.pxd' not found 2023-09-14T00:26:12,948 Error compiling Cython file: 2023-09-14T00:26:12,949 ------------------------------------------------------------ 2023-09-14T00:26:12,950 ... 2023-09-14T00:26:12,951 cimport fastani.map.map_stats 2023-09-14T00:26:12,951 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,952 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,952 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:12,952 from fastani.map cimport base_types 2023-09-14T00:26:12,953 ^ 2023-09-14T00:26:12,953 ------------------------------------------------------------ 2023-09-14T00:26:12,954 pyfastani/_fastani.pyx:22:0: 'fastani/map.pxd' not found 2023-09-14T00:26:12,955 Error compiling Cython file: 2023-09-14T00:26:12,956 ------------------------------------------------------------ 2023-09-14T00:26:12,956 ... 2023-09-14T00:26:12,957 cimport fastani.map.map_stats 2023-09-14T00:26:12,958 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,958 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,959 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:12,959 from fastani.map cimport base_types 2023-09-14T00:26:12,960 ^ 2023-09-14T00:26:12,961 ------------------------------------------------------------ 2023-09-14T00:26:12,962 pyfastani/_fastani.pyx:22:0: 'fastani/map/base_types.pxd' not found 2023-09-14T00:26:12,963 Error compiling Cython file: 2023-09-14T00:26:12,963 ------------------------------------------------------------ 2023-09-14T00:26:12,964 ... 2023-09-14T00:26:12,965 cimport fastani.map.map_stats 2023-09-14T00:26:12,965 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,965 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,966 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:12,966 from fastani.map cimport base_types 2023-09-14T00:26:12,967 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:12,967 ^ 2023-09-14T00:26:12,967 ------------------------------------------------------------ 2023-09-14T00:26:12,968 pyfastani/_fastani.pyx:23:0: 'fastani/map/compute_map.pxd' not found 2023-09-14T00:26:12,969 Error compiling Cython file: 2023-09-14T00:26:12,969 ------------------------------------------------------------ 2023-09-14T00:26:12,970 ... 2023-09-14T00:26:12,970 cimport fastani.map.map_stats 2023-09-14T00:26:12,971 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,971 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,971 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:12,972 from fastani.map cimport base_types 2023-09-14T00:26:12,972 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:12,973 ^ 2023-09-14T00:26:12,973 ------------------------------------------------------------ 2023-09-14T00:26:12,974 pyfastani/_fastani.pyx:23:0: 'fastani/map/compute_map/Map.pxd' not found 2023-09-14T00:26:12,975 Error compiling Cython file: 2023-09-14T00:26:12,975 ------------------------------------------------------------ 2023-09-14T00:26:12,976 ... 2023-09-14T00:26:12,976 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,977 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,978 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:12,978 from fastani.map cimport base_types 2023-09-14T00:26:12,979 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:12,980 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:12,980 ^ 2023-09-14T00:26:12,981 ------------------------------------------------------------ 2023-09-14T00:26:12,982 pyfastani/_fastani.pyx:24:0: 'fastani/map/common_func.pxd' not found 2023-09-14T00:26:12,984 Error compiling Cython file: 2023-09-14T00:26:12,984 ------------------------------------------------------------ 2023-09-14T00:26:12,985 ... 2023-09-14T00:26:12,985 from kseq cimport kseq_t, kstring_t 2023-09-14T00:26:12,986 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,987 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:12,987 from fastani.map cimport base_types 2023-09-14T00:26:12,988 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:12,989 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:12,989 ^ 2023-09-14T00:26:12,990 ------------------------------------------------------------ 2023-09-14T00:26:12,991 pyfastani/_fastani.pyx:24:0: 'fastani/map/common_func/addMinimizers.pxd' not found 2023-09-14T00:26:12,992 Error compiling Cython file: 2023-09-14T00:26:12,992 ------------------------------------------------------------ 2023-09-14T00:26:12,993 ... 2023-09-14T00:26:12,993 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:12,994 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:12,995 from fastani.map cimport base_types 2023-09-14T00:26:12,995 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:12,996 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:12,997 from fastani.map.map_parameters cimport Parameters as Parameters_t 2023-09-14T00:26:12,997 ^ 2023-09-14T00:26:12,998 ------------------------------------------------------------ 2023-09-14T00:26:12,999 pyfastani/_fastani.pyx:25:0: 'fastani/map/map_parameters.pxd' not found 2023-09-14T00:26:13,000 Error compiling Cython file: 2023-09-14T00:26:13,001 ------------------------------------------------------------ 2023-09-14T00:26:13,002 ... 2023-09-14T00:26:13,002 from fastani.cgi.compute_core_identity cimport computeCGI 2023-09-14T00:26:13,003 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:13,003 from fastani.map cimport base_types 2023-09-14T00:26:13,003 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:13,004 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:13,004 from fastani.map.map_parameters cimport Parameters as Parameters_t 2023-09-14T00:26:13,005 ^ 2023-09-14T00:26:13,005 ------------------------------------------------------------ 2023-09-14T00:26:13,006 pyfastani/_fastani.pyx:25:0: 'fastani/map/map_parameters/Parameters.pxd' not found 2023-09-14T00:26:13,007 Error compiling Cython file: 2023-09-14T00:26:13,007 ------------------------------------------------------------ 2023-09-14T00:26:13,008 ... 2023-09-14T00:26:13,008 from fastani.cgi.cgid_types cimport CGI_Results 2023-09-14T00:26:13,008 from fastani.map cimport base_types 2023-09-14T00:26:13,009 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:13,009 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:13,010 from fastani.map.map_parameters cimport Parameters as Parameters_t 2023-09-14T00:26:13,010 from fastani.map.map_stats cimport recommendedWindowSize 2023-09-14T00:26:13,010 ^ 2023-09-14T00:26:13,011 ------------------------------------------------------------ 2023-09-14T00:26:13,012 pyfastani/_fastani.pyx:26:0: 'fastani/map/map_stats/recommendedWindowSize.pxd' not found 2023-09-14T00:26:13,012 Error compiling Cython file: 2023-09-14T00:26:13,013 ------------------------------------------------------------ 2023-09-14T00:26:13,013 ... 2023-09-14T00:26:13,014 from fastani.map cimport base_types 2023-09-14T00:26:13,015 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:13,015 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:13,016 from fastani.map.map_parameters cimport Parameters as Parameters_t 2023-09-14T00:26:13,016 from fastani.map.map_stats cimport recommendedWindowSize 2023-09-14T00:26:13,017 from fastani.map.win_sketch cimport Sketch as Sketch_t 2023-09-14T00:26:13,018 ^ 2023-09-14T00:26:13,018 ------------------------------------------------------------ 2023-09-14T00:26:13,020 pyfastani/_fastani.pyx:27:0: 'fastani/map/win_sketch.pxd' not found 2023-09-14T00:26:13,021 Error compiling Cython file: 2023-09-14T00:26:13,021 ------------------------------------------------------------ 2023-09-14T00:26:13,022 ... 2023-09-14T00:26:13,023 from fastani.map cimport base_types 2023-09-14T00:26:13,023 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:13,024 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:13,025 from fastani.map.map_parameters cimport Parameters as Parameters_t 2023-09-14T00:26:13,025 from fastani.map.map_stats cimport recommendedWindowSize 2023-09-14T00:26:13,026 from fastani.map.win_sketch cimport Sketch as Sketch_t 2023-09-14T00:26:13,026 ^ 2023-09-14T00:26:13,027 ------------------------------------------------------------ 2023-09-14T00:26:13,029 pyfastani/_fastani.pyx:27:0: 'fastani/map/win_sketch/Sketch.pxd' not found 2023-09-14T00:26:13,030 Error compiling Cython file: 2023-09-14T00:26:13,031 ------------------------------------------------------------ 2023-09-14T00:26:13,031 ... 2023-09-14T00:26:13,032 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:13,033 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:13,033 from fastani.map.map_parameters cimport Parameters as Parameters_t 2023-09-14T00:26:13,034 from fastani.map.map_stats cimport recommendedWindowSize 2023-09-14T00:26:13,035 from fastani.map.win_sketch cimport Sketch as Sketch_t 2023-09-14T00:26:13,035 from fastani.map.base_types cimport ( 2023-09-14T00:26:13,036 ^ 2023-09-14T00:26:13,036 ------------------------------------------------------------ 2023-09-14T00:26:13,038 pyfastani/_fastani.pyx:28:0: 'fastani/map/base_types/seqno_t.pxd' not found 2023-09-14T00:26:13,039 Error compiling Cython file: 2023-09-14T00:26:13,039 ------------------------------------------------------------ 2023-09-14T00:26:13,040 ... 2023-09-14T00:26:13,040 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:13,041 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:13,041 from fastani.map.map_parameters cimport Parameters as Parameters_t 2023-09-14T00:26:13,041 from fastani.map.map_stats cimport recommendedWindowSize 2023-09-14T00:26:13,042 from fastani.map.win_sketch cimport Sketch as Sketch_t 2023-09-14T00:26:13,042 from fastani.map.base_types cimport ( 2023-09-14T00:26:13,043 ^ 2023-09-14T00:26:13,043 ------------------------------------------------------------ 2023-09-14T00:26:13,044 pyfastani/_fastani.pyx:28:0: 'fastani/map/base_types/ContigInfo.pxd' not found 2023-09-14T00:26:13,045 Error compiling Cython file: 2023-09-14T00:26:13,046 ------------------------------------------------------------ 2023-09-14T00:26:13,046 ... 2023-09-14T00:26:13,047 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:13,047 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:13,047 from fastani.map.map_parameters cimport Parameters as Parameters_t 2023-09-14T00:26:13,048 from fastani.map.map_stats cimport recommendedWindowSize 2023-09-14T00:26:13,049 from fastani.map.win_sketch cimport Sketch as Sketch_t 2023-09-14T00:26:13,049 from fastani.map.base_types cimport ( 2023-09-14T00:26:13,049 ^ 2023-09-14T00:26:13,050 ------------------------------------------------------------ 2023-09-14T00:26:13,051 pyfastani/_fastani.pyx:28:0: 'fastani/map/base_types/MappingResultsVector_t.pxd' not found 2023-09-14T00:26:13,052 Error compiling Cython file: 2023-09-14T00:26:13,053 ------------------------------------------------------------ 2023-09-14T00:26:13,053 ... 2023-09-14T00:26:13,054 from fastani.map.compute_map cimport Map as Map_t 2023-09-14T00:26:13,054 from fastani.map.common_func cimport addMinimizers 2023-09-14T00:26:13,055 from fastani.map.map_parameters cimport Parameters as Parameters_t 2023-09-14T00:26:13,055 from fastani.map.map_stats cimport recommendedWindowSize 2023-09-14T00:26:13,056 from fastani.map.win_sketch cimport Sketch as Sketch_t 2023-09-14T00:26:13,057 from fastani.map.base_types cimport ( 2023-09-14T00:26:13,057 ^ 2023-09-14T00:26:13,058 ------------------------------------------------------------ 2023-09-14T00:26:13,059 pyfastani/_fastani.pyx:28:0: 'fastani/map/base_types/QueryMetaData.pxd' not found 2023-09-14T00:26:13,060 Error compiling Cython file: 2023-09-14T00:26:13,061 ------------------------------------------------------------ 2023-09-14T00:26:13,062 ... 2023-09-14T00:26:13,062 ) 2023-09-14T00:26:13,063 # HACK: we need kseq_t* as a template argument, which is not supported by 2023-09-14T00:26:13,064 # Cython at the moment, so we just `typedef kseq_t* kseq_ptr_t` in 2023-09-14T00:26:13,064 # an external C++ header to make Cython happy 2023-09-14T00:26:13,065 from _utils cimport kseq_ptr_t 2023-09-14T00:26:13,065 ^ 2023-09-14T00:26:13,066 ------------------------------------------------------------ 2023-09-14T00:26:13,067 pyfastani/_fastani.pyx:38:0: '_utils.pxd' not found 2023-09-14T00:26:13,068 Error compiling Cython file: 2023-09-14T00:26:13,069 ------------------------------------------------------------ 2023-09-14T00:26:13,069 ... 2023-09-14T00:26:13,070 ) 2023-09-14T00:26:13,071 # HACK: we need kseq_t* as a template argument, which is not supported by 2023-09-14T00:26:13,072 # Cython at the moment, so we just `typedef kseq_t* kseq_ptr_t` in 2023-09-14T00:26:13,072 # an external C++ header to make Cython happy 2023-09-14T00:26:13,073 from _utils cimport kseq_ptr_t 2023-09-14T00:26:13,074 ^ 2023-09-14T00:26:13,074 ------------------------------------------------------------ 2023-09-14T00:26:13,075 pyfastani/_fastani.pyx:38:0: '_utils/kseq_ptr_t.pxd' not found 2023-09-14T00:26:14,619 Error compiling Cython file: 2023-09-14T00:26:14,620 ------------------------------------------------------------ 2023-09-14T00:26:14,620 ... 2023-09-14T00:26:14,621 cdef class Mapper: 2023-09-14T00:26:14,621 """A genome mapper using MashMap to compute whole-genome similarity. 2023-09-14T00:26:14,622 """ 2023-09-14T00:26:14,623 cdef size_t _counter 2023-09-14T00:26:14,623 cdef Sketch_t* _sk 2023-09-14T00:26:14,624 ^ 2023-09-14T00:26:14,624 ------------------------------------------------------------ 2023-09-14T00:26:14,625 pyfastani/_fastani.pyx:74:9: 'Sketch_t' is not a type identifier 2023-09-14T00:26:14,632 Error compiling Cython file: 2023-09-14T00:26:14,633 ------------------------------------------------------------ 2023-09-14T00:26:14,633 ... 2023-09-14T00:26:14,634 cdef size_t _counter 2023-09-14T00:26:14,635 cdef Sketch_t* _sk 2023-09-14T00:26:14,635 cdef bool _indexed 2023-09-14T00:26:14,636 cdef vector[uint64_t] _lengths 2023-09-14T00:26:14,636 cdef Parameters_t _param 2023-09-14T00:26:14,636 ^ 2023-09-14T00:26:14,637 ------------------------------------------------------------ 2023-09-14T00:26:14,638 pyfastani/_fastani.pyx:77:9: 'Parameters_t' is not a type identifier 2023-09-14T00:26:14,639 Error compiling Cython file: 2023-09-14T00:26:14,639 ------------------------------------------------------------ 2023-09-14T00:26:14,640 ... 2023-09-14T00:26:14,640 # --- Methods (querying) ------------------------------------------------- 2023-09-14T00:26:14,641 cdef void _query_fragment( 2023-09-14T00:26:14,642 self, 2023-09-14T00:26:14,643 int i, 2023-09-14T00:26:14,644 seqno_t 2023-09-14T00:26:14,644 ^ 2023-09-14T00:26:14,645 ------------------------------------------------------------ 2023-09-14T00:26:14,646 pyfastani/_fastani.pyx:341:8: 'seqno_t' is not a type identifier 2023-09-14T00:26:14,647 Error compiling Cython file: 2023-09-14T00:26:14,648 ------------------------------------------------------------ 2023-09-14T00:26:14,649 ... 2023-09-14T00:26:14,649 int i, 2023-09-14T00:26:14,650 seqno_t 2023-09-14T00:26:14,651 seq_counter, 2023-09-14T00:26:14,651 const unsigned char[::1] seq, 2023-09-14T00:26:14,652 int min_read_length, 2023-09-14T00:26:14,653 Map_t* map, 2023-09-14T00:26:14,653 ^ 2023-09-14T00:26:14,654 ------------------------------------------------------------ 2023-09-14T00:26:14,655 pyfastani/_fastani.pyx:345:8: 'Map_t' is not a type identifier 2023-09-14T00:26:14,656 Error compiling Cython file: 2023-09-14T00:26:14,657 ------------------------------------------------------------ 2023-09-14T00:26:14,657 ... 2023-09-14T00:26:14,658 seqno_t 2023-09-14T00:26:14,658 seq_counter, 2023-09-14T00:26:14,659 const unsigned char[::1] seq, 2023-09-14T00:26:14,659 int min_read_length, 2023-09-14T00:26:14,660 Map_t* map, 2023-09-14T00:26:14,661 kseq_t* kseq, 2023-09-14T00:26:14,661 ^ 2023-09-14T00:26:14,662 ------------------------------------------------------------ 2023-09-14T00:26:14,663 pyfastani/_fastani.pyx:346:8: 'kseq_t' is not a type identifier 2023-09-14T00:26:14,664 Error compiling Cython file: 2023-09-14T00:26:14,665 ------------------------------------------------------------ 2023-09-14T00:26:14,665 ... 2023-09-14T00:26:14,666 seq_counter, 2023-09-14T00:26:14,666 const unsigned char[::1] seq, 2023-09-14T00:26:14,667 int min_read_length, 2023-09-14T00:26:14,668 Map_t* map, 2023-09-14T00:26:14,668 kseq_t* kseq, 2023-09-14T00:26:14,669 ofstream* out, 2023-09-14T00:26:14,669 ^ 2023-09-14T00:26:14,670 ------------------------------------------------------------ 2023-09-14T00:26:14,671 pyfastani/_fastani.pyx:347:8: 'ofstream' is not a type identifier 2023-09-14T00:26:14,672 Error compiling Cython file: 2023-09-14T00:26:14,672 ------------------------------------------------------------ 2023-09-14T00:26:14,673 ... 2023-09-14T00:26:14,673 const unsigned char[::1] seq, 2023-09-14T00:26:14,673 int min_read_length, 2023-09-14T00:26:14,674 Map_t* map, 2023-09-14T00:26:14,674 kseq_t* kseq, 2023-09-14T00:26:14,675 ofstream* out, 2023-09-14T00:26:14,675 MappingResultsVector_t* mappings 2023-09-14T00:26:14,675 ^ 2023-09-14T00:26:14,676 ------------------------------------------------------------ 2023-09-14T00:26:14,677 pyfastani/_fastani.pyx:348:8: 'MappingResultsVector_t' is not a type identifier 2023-09-14T00:26:14,678 Error compiling Cython file: 2023-09-14T00:26:14,678 ------------------------------------------------------------ 2023-09-14T00:26:14,678 ... 2023-09-14T00:26:14,679 cdef class Hit: 2023-09-14T00:26:14,680 """A single hit found when querying the mapper with a genome. 2023-09-14T00:26:14,680 """ 2023-09-14T00:26:14,681 cdef readonly str name 2023-09-14T00:26:14,681 cdef readonly seqno_t matches 2023-09-14T00:26:14,681 ^ 2023-09-14T00:26:14,682 ------------------------------------------------------------ 2023-09-14T00:26:14,683 pyfastani/_fastani.pyx:506:18: 'seqno_t' is not a type identifier 2023-09-14T00:26:14,684 Error compiling Cython file: 2023-09-14T00:26:14,684 ------------------------------------------------------------ 2023-09-14T00:26:14,685 ... 2023-09-14T00:26:14,685 cdef class Hit: 2023-09-14T00:26:14,686 """A single hit found when querying the mapper with a genome. 2023-09-14T00:26:14,686 """ 2023-09-14T00:26:14,687 cdef readonly str name 2023-09-14T00:26:14,687 cdef readonly seqno_t matches 2023-09-14T00:26:14,688 ^ 2023-09-14T00:26:14,689 ------------------------------------------------------------ 2023-09-14T00:26:14,690 pyfastani/_fastani.pyx:506:26: C attribute of type '' cannot be accessed from Python 2023-09-14T00:26:14,691 Error compiling Cython file: 2023-09-14T00:26:14,692 ------------------------------------------------------------ 2023-09-14T00:26:14,692 ... 2023-09-14T00:26:14,693 cdef class Hit: 2023-09-14T00:26:14,694 """A single hit found when querying the mapper with a genome. 2023-09-14T00:26:14,694 """ 2023-09-14T00:26:14,695 cdef readonly str name 2023-09-14T00:26:14,695 cdef readonly seqno_t matches 2023-09-14T00:26:14,696 cdef readonly seqno_t fragments 2023-09-14T00:26:14,697 ^ 2023-09-14T00:26:14,697 ------------------------------------------------------------ 2023-09-14T00:26:14,698 pyfastani/_fastani.pyx:507:18: 'seqno_t' is not a type identifier 2023-09-14T00:26:14,699 Error compiling Cython file: 2023-09-14T00:26:14,700 ------------------------------------------------------------ 2023-09-14T00:26:14,700 ... 2023-09-14T00:26:14,701 cdef class Hit: 2023-09-14T00:26:14,702 """A single hit found when querying the mapper with a genome. 2023-09-14T00:26:14,702 """ 2023-09-14T00:26:14,703 cdef readonly str name 2023-09-14T00:26:14,703 cdef readonly seqno_t matches 2023-09-14T00:26:14,704 cdef readonly seqno_t fragments 2023-09-14T00:26:14,704 ^ 2023-09-14T00:26:14,705 ------------------------------------------------------------ 2023-09-14T00:26:14,706 pyfastani/_fastani.pyx:507:26: C attribute of type '' cannot be accessed from Python 2023-09-14T00:26:14,707 Error compiling Cython file: 2023-09-14T00:26:14,708 ------------------------------------------------------------ 2023-09-14T00:26:14,709 ... 2023-09-14T00:26:14,709 cdef readonly str name 2023-09-14T00:26:14,710 cdef readonly seqno_t matches 2023-09-14T00:26:14,711 cdef readonly seqno_t fragments 2023-09-14T00:26:14,711 cdef readonly float identity 2023-09-14T00:26:14,712 def __init__(self, str name, float identity, seqno_t matches, seqno_t fragments): 2023-09-14T00:26:14,713 ^ 2023-09-14T00:26:14,713 ------------------------------------------------------------ 2023-09-14T00:26:14,714 pyfastani/_fastani.pyx:510:49: 'seqno_t' is not a type identifier 2023-09-14T00:26:14,715 Error compiling Cython file: 2023-09-14T00:26:14,715 ------------------------------------------------------------ 2023-09-14T00:26:14,716 ... 2023-09-14T00:26:14,716 cdef readonly str name 2023-09-14T00:26:14,717 cdef readonly seqno_t matches 2023-09-14T00:26:14,717 cdef readonly seqno_t fragments 2023-09-14T00:26:14,717 cdef readonly float identity 2023-09-14T00:26:14,718 def __init__(self, str name, float identity, seqno_t matches, seqno_t fragments): 2023-09-14T00:26:14,719 ^ 2023-09-14T00:26:14,719 ------------------------------------------------------------ 2023-09-14T00:26:14,720 pyfastani/_fastani.pyx:510:66: 'seqno_t' is not a type identifier 2023-09-14T00:26:14,721 Error compiling Cython file: 2023-09-14T00:26:14,721 ------------------------------------------------------------ 2023-09-14T00:26:14,722 ... 2023-09-14T00:26:14,723 """ 2023-09-14T00:26:14,723 assert self._sk != nullptr 2023-09-14T00:26:14,724 cdef const unsigned char[::1] seq 2023-09-14T00:26:14,724 cdef kseq_t kseq 2023-09-14T00:26:14,725 ^ 2023-09-14T00:26:14,726 ------------------------------------------------------------ 2023-09-14T00:26:14,727 pyfastani/_fastani.pyx:202:13: 'kseq_t' is not a type identifier 2023-09-14T00:26:14,728 Error compiling Cython file: 2023-09-14T00:26:14,728 ------------------------------------------------------------ 2023-09-14T00:26:14,729 ... 2023-09-14T00:26:14,729 """ 2023-09-14T00:26:14,730 assert self._sk != nullptr 2023-09-14T00:26:14,731 cdef const unsigned char[::1] seq 2023-09-14T00:26:14,732 cdef kseq_t kseq 2023-09-14T00:26:14,732 cdef ContigInfo_t info 2023-09-14T00:26:14,733 ^ 2023-09-14T00:26:14,734 ------------------------------------------------------------ 2023-09-14T00:26:14,735 pyfastani/_fastani.pyx:203:13: 'ContigInfo_t' is not a type identifier 2023-09-14T00:26:14,736 Error compiling Cython file: 2023-09-14T00:26:14,737 ------------------------------------------------------------ 2023-09-14T00:26:14,737 ... 2023-09-14T00:26:14,738 cdef const unsigned char[::1] seq 2023-09-14T00:26:14,739 cdef kseq_t kseq 2023-09-14T00:26:14,739 cdef ContigInfo_t info 2023-09-14T00:26:14,740 cdef size_t seql_total = 0 2023-09-14T00:26:14,740 cdef Parameters_t* param = &self._param 2023-09-14T00:26:14,741 ^ 2023-09-14T00:26:14,742 ------------------------------------------------------------ 2023-09-14T00:26:14,743 pyfastani/_fastani.pyx:205:13: 'Parameters_t' is not a type identifier 2023-09-14T00:26:14,744 Error compiling Cython file: 2023-09-14T00:26:14,744 ------------------------------------------------------------ 2023-09-14T00:26:14,745 ... 2023-09-14T00:26:14,745 Map_t* map, 2023-09-14T00:26:14,746 kseq_t* kseq, 2023-09-14T00:26:14,746 ofstream* out, 2023-09-14T00:26:14,747 MappingResultsVector_t* mappings 2023-09-14T00:26:14,748 ) nogil: 2023-09-14T00:26:14,748 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:14,749 ^ 2023-09-14T00:26:14,749 ------------------------------------------------------------ 2023-09-14T00:26:14,750 pyfastani/_fastani.pyx:350:13: 'QueryMetaData_t' is not a type identifier 2023-09-14T00:26:14,752 Error compiling Cython file: 2023-09-14T00:26:14,752 ------------------------------------------------------------ 2023-09-14T00:26:14,752 ... 2023-09-14T00:26:14,753 """ 2023-09-14T00:26:14,754 assert self._sk != nullptr 2023-09-14T00:26:14,755 cdef int i # fragment counter 2023-09-14T00:26:14,755 cdef kseq_t kseq # 2023-09-14T00:26:14,755 ^ 2023-09-14T00:26:14,756 ------------------------------------------------------------ 2023-09-14T00:26:14,757 pyfastani/_fastani.pyx:371:13: 'kseq_t' is not a type identifier 2023-09-14T00:26:14,757 Error compiling Cython file: 2023-09-14T00:26:14,758 ------------------------------------------------------------ 2023-09-14T00:26:14,758 ... 2023-09-14T00:26:14,759 """ 2023-09-14T00:26:14,759 assert self._sk != nullptr 2023-09-14T00:26:14,760 cdef int i # fragment counter 2023-09-14T00:26:14,760 cdef kseq_t kseq # 2023-09-14T00:26:14,761 cdef Map_t* map 2023-09-14T00:26:14,762 ^ 2023-09-14T00:26:14,762 ------------------------------------------------------------ 2023-09-14T00:26:14,763 pyfastani/_fastani.pyx:372:13: 'Map_t' is not a type identifier 2023-09-14T00:26:14,764 Error compiling Cython file: 2023-09-14T00:26:14,764 ------------------------------------------------------------ 2023-09-14T00:26:14,765 ... 2023-09-14T00:26:14,765 assert self._sk != nullptr 2023-09-14T00:26:14,766 cdef int i # fragment counter 2023-09-14T00:26:14,767 cdef kseq_t kseq # 2023-09-14T00:26:14,767 cdef Map_t* map 2023-09-14T00:26:14,768 cdef MappingResultsVector_t final_mappings 2023-09-14T00:26:14,768 ^ 2023-09-14T00:26:14,769 ------------------------------------------------------------ 2023-09-14T00:26:14,770 pyfastani/_fastani.pyx:373:13: 'MappingResultsVector_t' is not a type identifier 2023-09-14T00:26:14,771 Error compiling Cython file: 2023-09-14T00:26:14,772 ------------------------------------------------------------ 2023-09-14T00:26:14,773 ... 2023-09-14T00:26:14,774 cdef int i # fragment counter 2023-09-14T00:26:14,775 cdef kseq_t kseq # 2023-09-14T00:26:14,775 cdef Map_t* map 2023-09-14T00:26:14,776 cdef MappingResultsVector_t final_mappings 2023-09-14T00:26:14,777 cdef vector[CGI_Results] results 2023-09-14T00:26:14,777 ^ 2023-09-14T00:26:14,778 ------------------------------------------------------------ 2023-09-14T00:26:14,779 pyfastani/_fastani.pyx:374:31: unknown type in template argument 2023-09-14T00:26:14,780 Error compiling Cython file: 2023-09-14T00:26:14,781 ------------------------------------------------------------ 2023-09-14T00:26:14,781 ... 2023-09-14T00:26:14,782 cdef const unsigned char[::1] seq 2023-09-14T00:26:14,782 cdef uint64_t seql 2023-09-14T00:26:14,783 cdef int fragment_count = 0 2023-09-14T00:26:14,784 cdef int seq_counter = 0 2023-09-14T00:26:14,784 cdef uint64_t total_fragments = 0 2023-09-14T00:26:14,785 cdef Parameters_t p = self._param 2023-09-14T00:26:14,785 ^ 2023-09-14T00:26:14,786 ------------------------------------------------------------ 2023-09-14T00:26:14,787 pyfastani/_fastani.pyx:381:13: 'Parameters_t' is not a type identifier 2023-09-14T00:26:14,788 Error compiling Cython file: 2023-09-14T00:26:14,789 ------------------------------------------------------------ 2023-09-14T00:26:14,790 ... 2023-09-14T00:26:14,791 cdef int fragment_count = 0 2023-09-14T00:26:14,791 cdef int seq_counter = 0 2023-09-14T00:26:14,791 cdef uint64_t total_fragments = 0 2023-09-14T00:26:14,792 cdef Parameters_t p = self._param 2023-09-14T00:26:14,792 cdef list hits = [] 2023-09-14T00:26:14,793 cdef ofstream out = ofstream() 2023-09-14T00:26:14,793 ^ 2023-09-14T00:26:14,794 ------------------------------------------------------------ 2023-09-14T00:26:14,795 pyfastani/_fastani.pyx:383:13: 'ofstream' is not a type identifier 2023-09-14T00:26:14,795 Error compiling Cython file: 2023-09-14T00:26:14,796 ------------------------------------------------------------ 2023-09-14T00:26:14,796 ... 2023-09-14T00:26:14,797 self._param.threads = 1 2023-09-14T00:26:14,797 self._param.reportAll = True 2023-09-14T00:26:14,798 self._param.visualize = False 2023-09-14T00:26:14,798 self._param.matrixOutput = False 2023-09-14T00:26:14,799 # create a new Sketch with the parameters 2023-09-14T00:26:14,799 self._sk = new Sketch_t(self._param) 2023-09-14T00:26:14,800 ^ 2023-09-14T00:26:14,800 ------------------------------------------------------------ 2023-09-14T00:26:14,801 pyfastani/_fastani.pyx:90:23: 'Sketch_t' is not a type identifier 2023-09-14T00:26:14,802 Error compiling Cython file: 2023-09-14T00:26:14,802 ------------------------------------------------------------ 2023-09-14T00:26:14,803 ... 2023-09-14T00:26:14,803 self._param.threads = 1 2023-09-14T00:26:14,804 self._param.reportAll = True 2023-09-14T00:26:14,805 self._param.visualize = False 2023-09-14T00:26:14,806 self._param.matrixOutput = False 2023-09-14T00:26:14,806 # create a new Sketch with the parameters 2023-09-14T00:26:14,807 self._sk = new Sketch_t(self._param) 2023-09-14T00:26:14,807 ^ 2023-09-14T00:26:14,808 ------------------------------------------------------------ 2023-09-14T00:26:14,809 pyfastani/_fastani.pyx:90:23: new operator can only be applied to a C++ class 2023-09-14T00:26:14,810 Error compiling Cython file: 2023-09-14T00:26:14,811 ------------------------------------------------------------ 2023-09-14T00:26:14,812 ... 2023-09-14T00:26:14,812 self._param.p_value = p_value 2023-09-14T00:26:14,813 self._param.percentageIdentity = percentage_identity 2023-09-14T00:26:14,814 self._param.referenceSize = reference_size 2023-09-14T00:26:14,816 # compute the recommended window size 2023-09-14T00:26:14,816 self._param.windowSize = fastani.map.map_stats.recommendedWindowSize( 2023-09-14T00:26:14,817 ^ 2023-09-14T00:26:14,818 ------------------------------------------------------------ 2023-09-14T00:26:14,819 pyfastani/_fastani.pyx:148:54: cimported module has no attribute 'recommendedWindowSize' 2023-09-14T00:26:14,820 Error compiling Cython file: 2023-09-14T00:26:14,821 ------------------------------------------------------------ 2023-09-14T00:26:14,821 ... 2023-09-14T00:26:14,822 # reinitialize bookkeeping values 2023-09-14T00:26:14,822 self._indexed = True 2023-09-14T00:26:14,823 self._counter = 0 2023-09-14T00:26:14,824 def __dealloc__(self): 2023-09-14T00:26:14,825 del self._sk 2023-09-14T00:26:14,825 ^ 2023-09-14T00:26:14,826 ------------------------------------------------------------ 2023-09-14T00:26:14,829 pyfastani/_fastani.pyx:162:16: Deletion of non-Python, non-C++ object 2023-09-14T00:26:14,831 Error compiling Cython file: 2023-09-14T00:26:14,831 ------------------------------------------------------------ 2023-09-14T00:26:14,832 ... 2023-09-14T00:26:14,833 # advance that the sequence is already uppercase. 2023-09-14T00:26:14,833 kseq.seq.l = kseq.seq.m = seq.shape[0] 2023-09-14T00:26:14,833 kseq.seq.s = &seq[0] 2023-09-14T00:26:14,834 # compute the minimizers 2023-09-14T00:26:14,834 with nogil: 2023-09-14T00:26:14,835 addMinimizers( 2023-09-14T00:26:14,835 ^ 2023-09-14T00:26:14,836 ------------------------------------------------------------ 2023-09-14T00:26:14,836 pyfastani/_fastani.pyx:241:20: 'addMinimizers' is not a constant, variable or function identifier 2023-09-14T00:26:14,837 Error compiling Cython file: 2023-09-14T00:26:14,837 ------------------------------------------------------------ 2023-09-14T00:26:14,838 ... 2023-09-14T00:26:14,838 kseq_t* kseq, 2023-09-14T00:26:14,839 ofstream* out, 2023-09-14T00:26:14,839 MappingResultsVector_t* mappings 2023-09-14T00:26:14,839 ) nogil: 2023-09-14T00:26:14,840 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:14,840 query.kseq = kseq 2023-09-14T00:26:14,841 ^ 2023-09-14T00:26:14,841 ------------------------------------------------------------ 2023-09-14T00:26:14,842 pyfastani/_fastani.pyx:351:13: Assignment of Python object not allowed without gil 2023-09-14T00:26:14,843 Error compiling Cython file: 2023-09-14T00:26:14,843 ------------------------------------------------------------ 2023-09-14T00:26:14,844 ... 2023-09-14T00:26:14,844 ofstream* out, 2023-09-14T00:26:14,845 MappingResultsVector_t* mappings 2023-09-14T00:26:14,845 ) nogil: 2023-09-14T00:26:14,846 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:14,846 query.kseq = kseq 2023-09-14T00:26:14,847 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:14,848 ^ 2023-09-14T00:26:14,848 ------------------------------------------------------------ 2023-09-14T00:26:14,849 pyfastani/_fastani.pyx:352:22: Assignment of Python object not allowed without gil 2023-09-14T00:26:14,851 Error compiling Cython file: 2023-09-14T00:26:14,851 ------------------------------------------------------------ 2023-09-14T00:26:14,852 ... 2023-09-14T00:26:14,853 MappingResultsVector_t* mappings 2023-09-14T00:26:14,853 ) nogil: 2023-09-14T00:26:14,854 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:14,855 query.kseq = kseq 2023-09-14T00:26:14,855 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:14,856 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:14,856 ^ 2023-09-14T00:26:14,857 ------------------------------------------------------------ 2023-09-14T00:26:14,858 pyfastani/_fastani.pyx:353:22: Assignment of Python object not allowed without gil 2023-09-14T00:26:14,859 Error compiling Cython file: 2023-09-14T00:26:14,859 ------------------------------------------------------------ 2023-09-14T00:26:14,860 ... 2023-09-14T00:26:14,861 MappingResultsVector_t* mappings 2023-09-14T00:26:14,861 ) nogil: 2023-09-14T00:26:14,862 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:14,862 query.kseq = kseq 2023-09-14T00:26:14,863 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:14,863 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:14,864 ^ 2023-09-14T00:26:14,864 ------------------------------------------------------------ 2023-09-14T00:26:14,866 pyfastani/_fastani.pyx:353:41: Assignment of Python object not allowed without gil 2023-09-14T00:26:14,867 Error compiling Cython file: 2023-09-14T00:26:14,868 ------------------------------------------------------------ 2023-09-14T00:26:14,868 ... 2023-09-14T00:26:14,869 ) nogil: 2023-09-14T00:26:14,869 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:14,870 query.kseq = kseq 2023-09-14T00:26:14,870 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:14,871 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:14,871 query.seqCounter = seq_counter + i 2023-09-14T00:26:14,872 ^ 2023-09-14T00:26:14,872 ------------------------------------------------------------ 2023-09-14T00:26:14,873 pyfastani/_fastani.pyx:354:13: Assignment of Python object not allowed without gil 2023-09-14T00:26:14,874 Error compiling Cython file: 2023-09-14T00:26:14,874 ------------------------------------------------------------ 2023-09-14T00:26:14,874 ... 2023-09-14T00:26:14,875 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:14,875 query.kseq = kseq 2023-09-14T00:26:14,876 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:14,876 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:14,876 query.seqCounter = seq_counter + i 2023-09-14T00:26:14,877 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:14,877 ^ 2023-09-14T00:26:14,878 ------------------------------------------------------------ 2023-09-14T00:26:14,878 pyfastani/_fastani.pyx:355:30: 'QueryMetaData_t' is not a constant, variable or function identifier 2023-09-14T00:26:14,879 Error compiling Cython file: 2023-09-14T00:26:14,880 ------------------------------------------------------------ 2023-09-14T00:26:14,881 ... 2023-09-14T00:26:14,881 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:14,882 query.kseq = kseq 2023-09-14T00:26:14,882 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:14,883 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:14,883 query.seqCounter = seq_counter + i 2023-09-14T00:26:14,884 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:14,885 ^ 2023-09-14T00:26:14,885 ------------------------------------------------------------ 2023-09-14T00:26:14,887 pyfastani/_fastani.pyx:355:46: 'kseq_ptr_t' is not a constant, variable or function identifier 2023-09-14T00:26:14,888 Error compiling Cython file: 2023-09-14T00:26:14,888 ------------------------------------------------------------ 2023-09-14T00:26:14,889 ... 2023-09-14T00:26:14,890 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:14,891 query.kseq = kseq 2023-09-14T00:26:14,892 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:14,893 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:14,894 query.seqCounter = seq_counter + i 2023-09-14T00:26:14,894 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:14,895 ^ 2023-09-14T00:26:14,896 ------------------------------------------------------------ 2023-09-14T00:26:14,898 pyfastani/_fastani.pyx:355:63: cimported module has no attribute 'MinVec_Type' 2023-09-14T00:26:14,900 Error compiling Cython file: 2023-09-14T00:26:14,901 ------------------------------------------------------------ 2023-09-14T00:26:14,902 ... 2023-09-14T00:26:14,903 cdef int fragment_count = 0 2023-09-14T00:26:14,904 cdef int seq_counter = 0 2023-09-14T00:26:14,904 cdef uint64_t total_fragments = 0 2023-09-14T00:26:14,905 cdef Parameters_t p = self._param 2023-09-14T00:26:14,906 cdef list hits = [] 2023-09-14T00:26:14,907 cdef ofstream out = ofstream() 2023-09-14T00:26:14,908 ^ 2023-09-14T00:26:14,908 ------------------------------------------------------------ 2023-09-14T00:26:14,910 pyfastani/_fastani.pyx:383:56: 'ofstream' is not a constant, variable or function identifier 2023-09-14T00:26:14,911 Error compiling Cython file: 2023-09-14T00:26:14,912 ------------------------------------------------------------ 2023-09-14T00:26:14,912 ... 2023-09-14T00:26:14,913 cdef Parameters_t p = self._param 2023-09-14T00:26:14,914 cdef list hits = [] 2023-09-14T00:26:14,914 cdef ofstream out = ofstream() 2023-09-14T00:26:14,916 # create a new mapper with the given mapping result vector 2023-09-14T00:26:14,916 map = new Map_t(p, self._sk[0], total_fragments, 0) 2023-09-14T00:26:14,917 ^ 2023-09-14T00:26:14,918 ------------------------------------------------------------ 2023-09-14T00:26:14,919 pyfastani/_fastani.pyx:386:18: 'Map_t' is not a type identifier 2023-09-14T00:26:14,920 Error compiling Cython file: 2023-09-14T00:26:14,921 ------------------------------------------------------------ 2023-09-14T00:26:14,922 ... 2023-09-14T00:26:14,922 cdef Parameters_t p = self._param 2023-09-14T00:26:14,923 cdef list hits = [] 2023-09-14T00:26:14,924 cdef ofstream out = ofstream() 2023-09-14T00:26:14,925 # create a new mapper with the given mapping result vector 2023-09-14T00:26:14,926 map = new Map_t(p, self._sk[0], total_fragments, 0) 2023-09-14T00:26:14,927 ^ 2023-09-14T00:26:14,928 ------------------------------------------------------------ 2023-09-14T00:26:14,929 pyfastani/_fastani.pyx:386:18: new operator can only be applied to a C++ class 2023-09-14T00:26:14,931 Error compiling Cython file: 2023-09-14T00:26:14,932 ------------------------------------------------------------ 2023-09-14T00:26:14,933 ... 2023-09-14T00:26:14,934 "Mapper received a short sequence relative to parameters, " 2023-09-14T00:26:14,935 "mapping will not be computed." 2023-09-14T00:26:14,936 )) 2023-09-14T00:26:14,938 # compute core genomic identity after successful mapping 2023-09-14T00:26:14,938 computeCGI( 2023-09-14T00:26:14,939 ^ 2023-09-14T00:26:14,940 ------------------------------------------------------------ 2023-09-14T00:26:14,942 pyfastani/_fastani.pyx:432:8: 'computeCGI' is not a constant, variable or function identifier 2023-09-14T00:26:14,943 Error compiling Cython file: 2023-09-14T00:26:14,944 ------------------------------------------------------------ 2023-09-14T00:26:14,945 ... 2023-09-14T00:26:14,946 0, # queryFileNo, only used for visualization, ignored 2023-09-14T00:26:14,946 string(), # fileName, only used for reporting, ignored 2023-09-14T00:26:14,947 results, 2023-09-14T00:26:14,948 ) 2023-09-14T00:26:14,949 # free the map 2023-09-14T00:26:14,949 del map 2023-09-14T00:26:14,950 ^ 2023-09-14T00:26:14,951 ------------------------------------------------------------ 2023-09-14T00:26:14,953 pyfastani/_fastani.pyx:443:12: Deletion of non-Python, non-C++ object 2023-09-14T00:26:15,009 Error compiling Cython file: 2023-09-14T00:26:15,009 ------------------------------------------------------------ 2023-09-14T00:26:15,010 ... 2023-09-14T00:26:15,010 # advance that the sequence is already uppercase. 2023-09-14T00:26:15,011 kseq.seq.l = kseq.seq.m = seq.shape[0] 2023-09-14T00:26:15,012 kseq.seq.s = &seq[0] 2023-09-14T00:26:15,012 # compute the minimizers 2023-09-14T00:26:15,013 with nogil: 2023-09-14T00:26:15,013 addMinimizers( 2023-09-14T00:26:15,013 ^ 2023-09-14T00:26:15,014 ------------------------------------------------------------ 2023-09-14T00:26:15,014 pyfastani/_fastani.pyx:241:33: Discarding owned Python object not allowed without gil 2023-09-14T00:26:15,015 Error compiling Cython file: 2023-09-14T00:26:15,016 ------------------------------------------------------------ 2023-09-14T00:26:15,016 ... 2023-09-14T00:26:15,016 # advance that the sequence is already uppercase. 2023-09-14T00:26:15,017 kseq.seq.l = kseq.seq.m = seq.shape[0] 2023-09-14T00:26:15,017 kseq.seq.s = &seq[0] 2023-09-14T00:26:15,018 # compute the minimizers 2023-09-14T00:26:15,018 with nogil: 2023-09-14T00:26:15,019 addMinimizers( 2023-09-14T00:26:15,019 ^ 2023-09-14T00:26:15,019 ------------------------------------------------------------ 2023-09-14T00:26:15,020 pyfastani/_fastani.pyx:241:33: Calling gil-requiring function not allowed without gil 2023-09-14T00:26:15,021 Error compiling Cython file: 2023-09-14T00:26:15,022 ------------------------------------------------------------ 2023-09-14T00:26:15,022 ... 2023-09-14T00:26:15,023 # advance that the sequence is already uppercase. 2023-09-14T00:26:15,023 kseq.seq.l = kseq.seq.m = seq.shape[0] 2023-09-14T00:26:15,024 kseq.seq.s = &seq[0] 2023-09-14T00:26:15,025 # compute the minimizers 2023-09-14T00:26:15,025 with nogil: 2023-09-14T00:26:15,025 addMinimizers( 2023-09-14T00:26:15,026 ^ 2023-09-14T00:26:15,026 ------------------------------------------------------------ 2023-09-14T00:26:15,028 pyfastani/_fastani.pyx:241:20: Accessing Python global or builtin not allowed without gil 2023-09-14T00:26:15,029 Error compiling Cython file: 2023-09-14T00:26:15,029 ------------------------------------------------------------ 2023-09-14T00:26:15,030 ... 2023-09-14T00:26:15,031 # advance that the sequence is already uppercase. 2023-09-14T00:26:15,032 kseq.seq.l = kseq.seq.m = seq.shape[0] 2023-09-14T00:26:15,032 kseq.seq.s = &seq[0] 2023-09-14T00:26:15,033 # compute the minimizers 2023-09-14T00:26:15,033 with nogil: 2023-09-14T00:26:15,034 addMinimizers( 2023-09-14T00:26:15,034 ^ 2023-09-14T00:26:15,035 ------------------------------------------------------------ 2023-09-14T00:26:15,036 pyfastani/_fastani.pyx:241:33: Constructing Python tuple not allowed without gil 2023-09-14T00:26:15,037 Error compiling Cython file: 2023-09-14T00:26:15,037 ------------------------------------------------------------ 2023-09-14T00:26:15,038 ... 2023-09-14T00:26:15,038 kseq.seq.l = kseq.seq.m = seq.shape[0] 2023-09-14T00:26:15,039 kseq.seq.s = &seq[0] 2023-09-14T00:26:15,039 # compute the minimizers 2023-09-14T00:26:15,040 with nogil: 2023-09-14T00:26:15,040 addMinimizers( 2023-09-14T00:26:15,041 self._sk.minimizerIndex, 2023-09-14T00:26:15,042 ^ 2023-09-14T00:26:15,042 ------------------------------------------------------------ 2023-09-14T00:26:15,043 pyfastani/_fastani.pyx:242:32: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,045 Error compiling Cython file: 2023-09-14T00:26:15,045 ------------------------------------------------------------ 2023-09-14T00:26:15,046 ... 2023-09-14T00:26:15,046 kseq.seq.s = &seq[0] 2023-09-14T00:26:15,047 # compute the minimizers 2023-09-14T00:26:15,047 with nogil: 2023-09-14T00:26:15,047 addMinimizers( 2023-09-14T00:26:15,048 self._sk.minimizerIndex, 2023-09-14T00:26:15,048 &kseq, 2023-09-14T00:26:15,049 ^ 2023-09-14T00:26:15,049 ------------------------------------------------------------ 2023-09-14T00:26:15,050 pyfastani/_fastani.pyx:243:24: Converting to Python object not allowed without gil 2023-09-14T00:26:15,051 Error compiling Cython file: 2023-09-14T00:26:15,051 ------------------------------------------------------------ 2023-09-14T00:26:15,051 ... 2023-09-14T00:26:15,052 # compute the minimizers 2023-09-14T00:26:15,052 with nogil: 2023-09-14T00:26:15,053 addMinimizers( 2023-09-14T00:26:15,053 self._sk.minimizerIndex, 2023-09-14T00:26:15,054 &kseq, 2023-09-14T00:26:15,054 param.kmerSize, 2023-09-14T00:26:15,054 ^ 2023-09-14T00:26:15,055 ------------------------------------------------------------ 2023-09-14T00:26:15,056 pyfastani/_fastani.pyx:244:29: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,057 Error compiling Cython file: 2023-09-14T00:26:15,057 ------------------------------------------------------------ 2023-09-14T00:26:15,058 ... 2023-09-14T00:26:15,059 with nogil: 2023-09-14T00:26:15,059 addMinimizers( 2023-09-14T00:26:15,060 self._sk.minimizerIndex, 2023-09-14T00:26:15,060 &kseq, 2023-09-14T00:26:15,061 param.kmerSize, 2023-09-14T00:26:15,062 param.windowSize, 2023-09-14T00:26:15,062 ^ 2023-09-14T00:26:15,063 ------------------------------------------------------------ 2023-09-14T00:26:15,064 pyfastani/_fastani.pyx:245:29: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,065 Error compiling Cython file: 2023-09-14T00:26:15,066 ------------------------------------------------------------ 2023-09-14T00:26:15,067 ... 2023-09-14T00:26:15,067 addMinimizers( 2023-09-14T00:26:15,068 self._sk.minimizerIndex, 2023-09-14T00:26:15,068 &kseq, 2023-09-14T00:26:15,069 param.kmerSize, 2023-09-14T00:26:15,069 param.windowSize, 2023-09-14T00:26:15,070 param.alphabetSize, 2023-09-14T00:26:15,070 ^ 2023-09-14T00:26:15,071 ------------------------------------------------------------ 2023-09-14T00:26:15,072 pyfastani/_fastani.pyx:246:29: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,073 Error compiling Cython file: 2023-09-14T00:26:15,074 ------------------------------------------------------------ 2023-09-14T00:26:15,074 ... 2023-09-14T00:26:15,075 self._sk.minimizerIndex, 2023-09-14T00:26:15,076 &kseq, 2023-09-14T00:26:15,076 param.kmerSize, 2023-09-14T00:26:15,077 param.windowSize, 2023-09-14T00:26:15,077 param.alphabetSize, 2023-09-14T00:26:15,078 self._counter 2023-09-14T00:26:15,078 ^ 2023-09-14T00:26:15,079 ------------------------------------------------------------ 2023-09-14T00:26:15,080 pyfastani/_fastani.pyx:247:28: Converting to Python object not allowed without gil 2023-09-14T00:26:15,082 Error compiling Cython file: 2023-09-14T00:26:15,082 ------------------------------------------------------------ 2023-09-14T00:26:15,083 ... 2023-09-14T00:26:15,083 kseq_t* kseq, 2023-09-14T00:26:15,084 ofstream* out, 2023-09-14T00:26:15,084 MappingResultsVector_t* mappings 2023-09-14T00:26:15,084 ) nogil: 2023-09-14T00:26:15,085 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,085 query.kseq = kseq 2023-09-14T00:26:15,086 ^ 2023-09-14T00:26:15,086 ------------------------------------------------------------ 2023-09-14T00:26:15,087 pyfastani/_fastani.pyx:351:13: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,088 Error compiling Cython file: 2023-09-14T00:26:15,088 ------------------------------------------------------------ 2023-09-14T00:26:15,089 ... 2023-09-14T00:26:15,089 kseq_t* kseq, 2023-09-14T00:26:15,089 ofstream* out, 2023-09-14T00:26:15,090 MappingResultsVector_t* mappings 2023-09-14T00:26:15,090 ) nogil: 2023-09-14T00:26:15,091 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,091 query.kseq = kseq 2023-09-14T00:26:15,092 ^ 2023-09-14T00:26:15,092 ------------------------------------------------------------ 2023-09-14T00:26:15,093 pyfastani/_fastani.pyx:351:21: Converting to Python object not allowed without gil 2023-09-14T00:26:15,094 Error compiling Cython file: 2023-09-14T00:26:15,094 ------------------------------------------------------------ 2023-09-14T00:26:15,095 ... 2023-09-14T00:26:15,095 ofstream* out, 2023-09-14T00:26:15,096 MappingResultsVector_t* mappings 2023-09-14T00:26:15,096 ) nogil: 2023-09-14T00:26:15,097 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,098 query.kseq = kseq 2023-09-14T00:26:15,098 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,099 ^ 2023-09-14T00:26:15,100 ------------------------------------------------------------ 2023-09-14T00:26:15,101 pyfastani/_fastani.pyx:352:22: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,102 Error compiling Cython file: 2023-09-14T00:26:15,103 ------------------------------------------------------------ 2023-09-14T00:26:15,103 ... 2023-09-14T00:26:15,104 ofstream* out, 2023-09-14T00:26:15,104 MappingResultsVector_t* mappings 2023-09-14T00:26:15,105 ) nogil: 2023-09-14T00:26:15,106 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,106 query.kseq = kseq 2023-09-14T00:26:15,107 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,107 ^ 2023-09-14T00:26:15,108 ------------------------------------------------------------ 2023-09-14T00:26:15,109 pyfastani/_fastani.pyx:352:18: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,110 Error compiling Cython file: 2023-09-14T00:26:15,111 ------------------------------------------------------------ 2023-09-14T00:26:15,111 ... 2023-09-14T00:26:15,112 ofstream* out, 2023-09-14T00:26:15,112 MappingResultsVector_t* mappings 2023-09-14T00:26:15,113 ) nogil: 2023-09-14T00:26:15,113 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,114 query.kseq = kseq 2023-09-14T00:26:15,114 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,115 ^ 2023-09-14T00:26:15,116 ------------------------------------------------------------ 2023-09-14T00:26:15,117 pyfastani/_fastani.pyx:352:13: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,118 Error compiling Cython file: 2023-09-14T00:26:15,119 ------------------------------------------------------------ 2023-09-14T00:26:15,119 ... 2023-09-14T00:26:15,120 ofstream* out, 2023-09-14T00:26:15,121 MappingResultsVector_t* mappings 2023-09-14T00:26:15,121 ) nogil: 2023-09-14T00:26:15,122 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,122 query.kseq = kseq 2023-09-14T00:26:15,122 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,123 ^ 2023-09-14T00:26:15,123 ------------------------------------------------------------ 2023-09-14T00:26:15,124 pyfastani/_fastani.pyx:352:27: Converting to Python object not allowed without gil 2023-09-14T00:26:15,125 Error compiling Cython file: 2023-09-14T00:26:15,125 ------------------------------------------------------------ 2023-09-14T00:26:15,125 ... 2023-09-14T00:26:15,126 MappingResultsVector_t* mappings 2023-09-14T00:26:15,126 ) nogil: 2023-09-14T00:26:15,127 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,127 query.kseq = kseq 2023-09-14T00:26:15,127 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,128 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,128 ^ 2023-09-14T00:26:15,129 ------------------------------------------------------------ 2023-09-14T00:26:15,130 pyfastani/_fastani.pyx:353:22: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,130 Error compiling Cython file: 2023-09-14T00:26:15,131 ------------------------------------------------------------ 2023-09-14T00:26:15,131 ... 2023-09-14T00:26:15,132 MappingResultsVector_t* mappings 2023-09-14T00:26:15,132 ) nogil: 2023-09-14T00:26:15,133 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,133 query.kseq = kseq 2023-09-14T00:26:15,134 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,134 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,135 ^ 2023-09-14T00:26:15,136 ------------------------------------------------------------ 2023-09-14T00:26:15,137 pyfastani/_fastani.pyx:353:18: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,138 Error compiling Cython file: 2023-09-14T00:26:15,139 ------------------------------------------------------------ 2023-09-14T00:26:15,139 ... 2023-09-14T00:26:15,140 MappingResultsVector_t* mappings 2023-09-14T00:26:15,141 ) nogil: 2023-09-14T00:26:15,141 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,142 query.kseq = kseq 2023-09-14T00:26:15,143 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,143 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,144 ^ 2023-09-14T00:26:15,144 ------------------------------------------------------------ 2023-09-14T00:26:15,145 pyfastani/_fastani.pyx:353:13: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,146 Error compiling Cython file: 2023-09-14T00:26:15,147 ------------------------------------------------------------ 2023-09-14T00:26:15,147 ... 2023-09-14T00:26:15,148 MappingResultsVector_t* mappings 2023-09-14T00:26:15,149 ) nogil: 2023-09-14T00:26:15,149 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,150 query.kseq = kseq 2023-09-14T00:26:15,150 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,151 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,152 ^ 2023-09-14T00:26:15,152 ------------------------------------------------------------ 2023-09-14T00:26:15,153 pyfastani/_fastani.pyx:353:41: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,154 Error compiling Cython file: 2023-09-14T00:26:15,155 ------------------------------------------------------------ 2023-09-14T00:26:15,156 ... 2023-09-14T00:26:15,156 MappingResultsVector_t* mappings 2023-09-14T00:26:15,157 ) nogil: 2023-09-14T00:26:15,157 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,158 query.kseq = kseq 2023-09-14T00:26:15,158 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,158 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,159 ^ 2023-09-14T00:26:15,159 ------------------------------------------------------------ 2023-09-14T00:26:15,161 pyfastani/_fastani.pyx:353:37: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,162 Error compiling Cython file: 2023-09-14T00:26:15,163 ------------------------------------------------------------ 2023-09-14T00:26:15,163 ... 2023-09-14T00:26:15,164 MappingResultsVector_t* mappings 2023-09-14T00:26:15,164 ) nogil: 2023-09-14T00:26:15,165 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,165 query.kseq = kseq 2023-09-14T00:26:15,166 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,166 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,166 ^ 2023-09-14T00:26:15,167 ------------------------------------------------------------ 2023-09-14T00:26:15,168 pyfastani/_fastani.pyx:353:32: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,169 Error compiling Cython file: 2023-09-14T00:26:15,169 ------------------------------------------------------------ 2023-09-14T00:26:15,170 ... 2023-09-14T00:26:15,171 MappingResultsVector_t* mappings 2023-09-14T00:26:15,171 ) nogil: 2023-09-14T00:26:15,172 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,172 query.kseq = kseq 2023-09-14T00:26:15,173 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,174 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,174 ^ 2023-09-14T00:26:15,175 ------------------------------------------------------------ 2023-09-14T00:26:15,176 pyfastani/_fastani.pyx:353:46: Converting to Python object not allowed without gil 2023-09-14T00:26:15,177 Error compiling Cython file: 2023-09-14T00:26:15,178 ------------------------------------------------------------ 2023-09-14T00:26:15,179 ... 2023-09-14T00:26:15,179 ) nogil: 2023-09-14T00:26:15,180 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,181 query.kseq = kseq 2023-09-14T00:26:15,181 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,182 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,182 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,183 ^ 2023-09-14T00:26:15,183 ------------------------------------------------------------ 2023-09-14T00:26:15,184 pyfastani/_fastani.pyx:354:13: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,186 Error compiling Cython file: 2023-09-14T00:26:15,186 ------------------------------------------------------------ 2023-09-14T00:26:15,187 ... 2023-09-14T00:26:15,187 ) nogil: 2023-09-14T00:26:15,188 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,188 query.kseq = kseq 2023-09-14T00:26:15,189 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,189 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,190 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,191 ^ 2023-09-14T00:26:15,191 ------------------------------------------------------------ 2023-09-14T00:26:15,193 pyfastani/_fastani.pyx:354:39: Converting to Python object not allowed without gil 2023-09-14T00:26:15,194 Error compiling Cython file: 2023-09-14T00:26:15,194 ------------------------------------------------------------ 2023-09-14T00:26:15,194 ... 2023-09-14T00:26:15,195 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,195 query.kseq = kseq 2023-09-14T00:26:15,196 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,196 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,196 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,197 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,197 ^ 2023-09-14T00:26:15,198 ------------------------------------------------------------ 2023-09-14T00:26:15,198 pyfastani/_fastani.pyx:355:77: Discarding owned Python object not allowed without gil 2023-09-14T00:26:15,199 Error compiling Cython file: 2023-09-14T00:26:15,200 ------------------------------------------------------------ 2023-09-14T00:26:15,200 ... 2023-09-14T00:26:15,201 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,201 query.kseq = kseq 2023-09-14T00:26:15,202 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,202 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,202 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,203 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,203 ^ 2023-09-14T00:26:15,204 ------------------------------------------------------------ 2023-09-14T00:26:15,205 pyfastani/_fastani.pyx:355:77: Calling gil-requiring function not allowed without gil 2023-09-14T00:26:15,206 Error compiling Cython file: 2023-09-14T00:26:15,207 ------------------------------------------------------------ 2023-09-14T00:26:15,207 ... 2023-09-14T00:26:15,208 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,209 query.kseq = kseq 2023-09-14T00:26:15,209 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,210 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,211 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,211 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,212 ^ 2023-09-14T00:26:15,212 ------------------------------------------------------------ 2023-09-14T00:26:15,213 pyfastani/_fastani.pyx:355:29: Indexing Python object not allowed without gil 2023-09-14T00:26:15,214 Error compiling Cython file: 2023-09-14T00:26:15,215 ------------------------------------------------------------ 2023-09-14T00:26:15,216 ... 2023-09-14T00:26:15,216 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,217 query.kseq = kseq 2023-09-14T00:26:15,217 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,218 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,218 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,219 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,219 ^ 2023-09-14T00:26:15,220 ------------------------------------------------------------ 2023-09-14T00:26:15,221 pyfastani/_fastani.pyx:355:11: Accessing Python attribute not allowed without gil 2023-09-14T00:26:15,222 Error compiling Cython file: 2023-09-14T00:26:15,223 ------------------------------------------------------------ 2023-09-14T00:26:15,224 ... 2023-09-14T00:26:15,225 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,225 query.kseq = kseq 2023-09-14T00:26:15,225 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,226 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,226 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,227 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,227 ^ 2023-09-14T00:26:15,227 ------------------------------------------------------------ 2023-09-14T00:26:15,228 pyfastani/_fastani.pyx:355:45: Indexing Python object not allowed without gil 2023-09-14T00:26:15,229 Error compiling Cython file: 2023-09-14T00:26:15,229 ------------------------------------------------------------ 2023-09-14T00:26:15,230 ... 2023-09-14T00:26:15,230 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,231 query.kseq = kseq 2023-09-14T00:26:15,231 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,231 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,232 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,232 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,233 ^ 2023-09-14T00:26:15,233 ------------------------------------------------------------ 2023-09-14T00:26:15,234 pyfastani/_fastani.pyx:355:30: Accessing Python global or builtin not allowed without gil 2023-09-14T00:26:15,235 Error compiling Cython file: 2023-09-14T00:26:15,235 ------------------------------------------------------------ 2023-09-14T00:26:15,236 ... 2023-09-14T00:26:15,236 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,237 query.kseq = kseq 2023-09-14T00:26:15,238 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,238 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,239 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,240 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,240 ^ 2023-09-14T00:26:15,241 ------------------------------------------------------------ 2023-09-14T00:26:15,242 pyfastani/_fastani.pyx:355:45: Constructing Python tuple not allowed without gil 2023-09-14T00:26:15,243 Error compiling Cython file: 2023-09-14T00:26:15,244 ------------------------------------------------------------ 2023-09-14T00:26:15,245 ... 2023-09-14T00:26:15,245 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,246 query.kseq = kseq 2023-09-14T00:26:15,246 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,247 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,247 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,248 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,248 ^ 2023-09-14T00:26:15,249 ------------------------------------------------------------ 2023-09-14T00:26:15,250 pyfastani/_fastani.pyx:355:46: Accessing Python global or builtin not allowed without gil 2023-09-14T00:26:15,251 Error compiling Cython file: 2023-09-14T00:26:15,252 ------------------------------------------------------------ 2023-09-14T00:26:15,252 ... 2023-09-14T00:26:15,253 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,254 query.kseq = kseq 2023-09-14T00:26:15,254 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,255 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,256 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,256 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,256 ^ 2023-09-14T00:26:15,257 ------------------------------------------------------------ 2023-09-14T00:26:15,258 pyfastani/_fastani.pyx:355:63: Converting to Python object not allowed without gil 2023-09-14T00:26:15,258 Error compiling Cython file: 2023-09-14T00:26:15,259 ------------------------------------------------------------ 2023-09-14T00:26:15,259 ... 2023-09-14T00:26:15,260 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,260 query.kseq = kseq 2023-09-14T00:26:15,260 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,261 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,261 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,262 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,262 ^ 2023-09-14T00:26:15,263 ------------------------------------------------------------ 2023-09-14T00:26:15,263 pyfastani/_fastani.pyx:355:77: Constructing Python tuple not allowed without gil 2023-09-14T00:26:15,264 Error compiling Cython file: 2023-09-14T00:26:15,265 ------------------------------------------------------------ 2023-09-14T00:26:15,265 ... 2023-09-14T00:26:15,266 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,266 query.kseq = kseq 2023-09-14T00:26:15,267 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,268 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,268 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,269 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,269 ^ 2023-09-14T00:26:15,270 ------------------------------------------------------------ 2023-09-14T00:26:15,271 pyfastani/_fastani.pyx:355:78: Converting to Python object not allowed without gil 2023-09-14T00:26:15,273 Error compiling Cython file: 2023-09-14T00:26:15,273 ------------------------------------------------------------ 2023-09-14T00:26:15,274 ... 2023-09-14T00:26:15,274 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,275 query.kseq = kseq 2023-09-14T00:26:15,276 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,276 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,277 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,277 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,278 ^ 2023-09-14T00:26:15,278 ------------------------------------------------------------ 2023-09-14T00:26:15,279 pyfastani/_fastani.pyx:355:93: Converting to Python object not allowed without gil 2023-09-14T00:26:15,280 Error compiling Cython file: 2023-09-14T00:26:15,281 ------------------------------------------------------------ 2023-09-14T00:26:15,281 ... 2023-09-14T00:26:15,282 cdef QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type] query 2023-09-14T00:26:15,282 query.kseq = kseq 2023-09-14T00:26:15,283 query.kseq.seq.s = &seq[i * min_read_length] 2023-09-14T00:26:15,284 query.kseq.seq.l = query.kseq.seq.m = min_read_length 2023-09-14T00:26:15,284 query.seqCounter = seq_counter + i 2023-09-14T00:26:15,285 map.mapSingleQuerySeq[QueryMetaData_t[kseq_ptr_t, Map_t.MinVec_Type]](query, mappings[0], out[0]) 2023-09-14T00:26:15,286 ^ 2023-09-14T00:26:15,286 ------------------------------------------------------------ 2023-09-14T00:26:15,287 pyfastani/_fastani.pyx:355:101: Converting to Python object not allowed without gil 2023-09-14T00:26:16,577 Compiling pyfastani/_fastani.pyx because it changed. 2023-09-14T00:26:16,578 [1/1] Cythonizing pyfastani/_fastani.pyx 2023-09-14T00:26:16,578 Traceback (most recent call last): 2023-09-14T00:26:16,579 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in 2023-09-14T00:26:16,579 main() 2023-09-14T00:26:16,580 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main 2023-09-14T00:26:16,580 json_out['return_val'] = hook(**hook_input['kwargs']) 2023-09-14T00:26:16,581 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-14T00:26:16,581 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel 2023-09-14T00:26:16,582 return _build_backend().build_wheel(wheel_directory, config_settings, 2023-09-14T00:26:16,582 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-14T00:26:16,583 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 434, in build_wheel 2023-09-14T00:26:16,583 return self._build_with_temp_dir( 2023-09-14T00:26:16,583 ^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-14T00:26:16,584 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 419, in _build_with_temp_dir 2023-09-14T00:26:16,584 self.run_setup() 2023-09-14T00:26:16,585 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 341, in run_setup 2023-09-14T00:26:16,585 exec(code, locals()) 2023-09-14T00:26:16,586 File "", line 248, in 2023-09-14T00:26:16,586 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/__init__.py", line 103, in setup 2023-09-14T00:26:16,587 return distutils.core.setup(**attrs) 2023-09-14T00:26:16,587 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-14T00:26:16,588 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/core.py", line 185, in setup 2023-09-14T00:26:16,589 return run_commands(dist) 2023-09-14T00:26:16,589 ^^^^^^^^^^^^^^^^^^ 2023-09-14T00:26:16,590 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/core.py", line 201, in run_commands 2023-09-14T00:26:16,590 dist.run_commands() 2023-09-14T00:26:16,591 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 969, in run_commands 2023-09-14T00:26:16,591 self.run_command(cmd) 2023-09-14T00:26:16,592 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py", line 989, in run_command 2023-09-14T00:26:16,593 super().run_command(command) 2023-09-14T00:26:16,593 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-09-14T00:26:16,594 cmd_obj.run() 2023-09-14T00:26:16,594 File "/tmp/pip-build-env-7bzw4irm/normal/local/lib/python3.11/dist-packages/wheel/bdist_wheel.py", line 364, in run 2023-09-14T00:26:16,595 self.run_command("build") 2023-09-14T00:26:16,595 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command 2023-09-14T00:26:16,596 self.distribution.run_command(command) 2023-09-14T00:26:16,597 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py", line 989, in run_command 2023-09-14T00:26:16,598 super().run_command(command) 2023-09-14T00:26:16,599 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-09-14T00:26:16,600 cmd_obj.run() 2023-09-14T00:26:16,601 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/command/build.py", line 131, in run 2023-09-14T00:26:16,601 self.run_command(cmd_name) 2023-09-14T00:26:16,602 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command 2023-09-14T00:26:16,603 self.distribution.run_command(command) 2023-09-14T00:26:16,604 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py", line 989, in run_command 2023-09-14T00:26:16,604 super().run_command(command) 2023-09-14T00:26:16,605 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-09-14T00:26:16,606 cmd_obj.run() 2023-09-14T00:26:16,606 File "", line 177, in run 2023-09-14T00:26:16,607 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1115, in cythonize 2023-09-14T00:26:16,608 cythonize_one(*args) 2023-09-14T00:26:16,609 File "/tmp/pip-build-env-7bzw4irm/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1238, in cythonize_one 2023-09-14T00:26:16,610 raise CompileError(None, pyx_file) 2023-09-14T00:26:16,611 Cython.Compiler.Errors.CompileError: pyfastani/_fastani.pyx 2023-09-14T00:26:17,004 ERROR: [present-rich] Building wheel for pyfastani (pyproject.toml) exited with 1 2023-09-14T00:26:17,018 [bold magenta]full command[/]: [blue]/usr/bin/python3 /usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmpxxnwnyak[/] 2023-09-14T00:26:17,019 [bold magenta]cwd[/]: /tmp/pip-wheel-us10m3qj/pyfastani_8e5e5fdafd644d54ad6c69b59174e06d 2023-09-14T00:26:17,019 Building wheel for pyfastani (pyproject.toml): finished with status 'error' 2023-09-14T00:26:17,022 ERROR: Failed building wheel for pyfastani 2023-09-14T00:26:17,024 Failed to build pyfastani 2023-09-14T00:26:17,025 ERROR: Failed to build one or more wheels 2023-09-14T00:26:17,026 Exception information: 2023-09-14T00:26:17,026 Traceback (most recent call last): 2023-09-14T00:26:17,026 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-14T00:26:17,026 status = run_func(*args) 2023-09-14T00:26:17,026 ^^^^^^^^^^^^^^^ 2023-09-14T00:26:17,026 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-14T00:26:17,026 return func(self, options, args) 2023-09-14T00:26:17,026 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-14T00:26:17,026 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-14T00:26:17,026 raise CommandError("Failed to build one or more wheels") 2023-09-14T00:26:17,026 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-14T00:26:17,030 Removed build tracker: '/tmp/pip-build-tracker-5uawhzcf'