2023-09-18T22:11:50,216 Created temporary directory: /tmp/pip-build-tracker-s_8ewcc3 2023-09-18T22:11:50,217 Initialized build tracking at /tmp/pip-build-tracker-s_8ewcc3 2023-09-18T22:11:50,218 Created build tracker: /tmp/pip-build-tracker-s_8ewcc3 2023-09-18T22:11:50,218 Entered build tracker: /tmp/pip-build-tracker-s_8ewcc3 2023-09-18T22:11:50,219 Created temporary directory: /tmp/pip-wheel-z6x967j1 2023-09-18T22:11:50,222 Created temporary directory: /tmp/pip-ephem-wheel-cache-18hi6wlx 2023-09-18T22:11:50,243 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-18T22:11:50,247 2 location(s) to search for versions of pyfastani: 2023-09-18T22:11:50,247 * https://pypi.org/simple/pyfastani/ 2023-09-18T22:11:50,247 * https://www.piwheels.org/simple/pyfastani/ 2023-09-18T22:11:50,248 Fetching project page and analyzing links: https://pypi.org/simple/pyfastani/ 2023-09-18T22:11:50,248 Getting page https://pypi.org/simple/pyfastani/ 2023-09-18T22:11:50,250 Found index url https://pypi.org/simple/ 2023-09-18T22:11:50,480 Fetched page https://pypi.org/simple/pyfastani/ as application/vnd.pypi.simple.v1+json 2023-09-18T22:11:50,503 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) 2023-09-18T22:11:50,504 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) 2023-09-18T22:11:50,504 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) 2023-09-18T22:11:50,505 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) 2023-09-18T22:11:50,506 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) 2023-09-18T22:11:50,506 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) 2023-09-18T22:11:50,507 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) 2023-09-18T22:11:50,507 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) 2023-09-18T22:11:50,508 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) 2023-09-18T22:11:50,508 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) 2023-09-18T22:11:50,509 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 2023-09-18T22:11:50,511 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) 2023-09-18T22:11:50,511 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) 2023-09-18T22:11:50,512 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) 2023-09-18T22:11:50,512 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) 2023-09-18T22:11:50,513 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 2023-09-18T22:11:50,517 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) 2023-09-18T22:11:50,517 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) 2023-09-18T22:11:50,518 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) 2023-09-18T22:11:50,522 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) 2023-09-18T22:11:50,522 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 2023-09-18T22:11:50,523 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) 2023-09-18T22:11:50,566 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) 2023-09-18T22:11:50,567 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) 2023-09-18T22:11:50,567 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) 2023-09-18T22:11:50,568 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) 2023-09-18T22:11:50,569 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 2023-09-18T22:11:50,569 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/ac/22/02c799ca4f71178de8a99713701ad480ab7a4963761974d2d14f628cd108/pyfastani-0.4.1-cp310-cp310-macosx_10_15_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-18T22:11:50,570 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/af/25/d28216a355b7d06e108c4e991d5071cc2e8bb9c367c101a9d907019643b4/pyfastani-0.4.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-18T22:11:50,571 Skipping link: No binaries permitted for pyfastani: https://files.pythonhosted.org/packages/99/a4/94b396fd5025f73bd50f5043f10528e0b3b06ec0824ad35af77100440d6b/pyfastani-0.4.1-cp310-cp310-manylinux_2_24_x86_64.whl (from https://pypi.org/simple/pyfastani/) (requires-python:>=3.6) 2023-09-18T22:11:50,571 Skipping link: No binaries permitted for pyfastani: 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) 2023-09-18T22:11:50,572 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) 2023-09-18T22:11:50,572 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) 2023-09-18T22:11:50,573 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) 2023-09-18T22:11:50,574 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) 2023-09-18T22:11:50,574 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) 2023-09-18T22:11:50,575 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) 2023-09-18T22:11:50,581 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) 2023-09-18T22:11:50,581 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) 2023-09-18T22:11:50,582 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 2023-09-18T22:11:50,584 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyfastani/ 2023-09-18T22:11:50,584 Getting page https://www.piwheels.org/simple/pyfastani/ 2023-09-18T22:11:50,585 Found index url https://www.piwheels.org/simple/ 2023-09-18T22:11:51,080 Fetched page https://www.piwheels.org/simple/pyfastani/ as text/html 2023-09-18T22:11:51,086 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) 2023-09-18T22:11:51,087 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) 2023-09-18T22:11:51,088 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) 2023-09-18T22:11:51,088 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) 2023-09-18T22:11:51,089 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) 2023-09-18T22:11:51,090 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) 2023-09-18T22:11:51,091 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) 2023-09-18T22:11:51,091 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) 2023-09-18T22:11:51,092 Skipping link: not a file: https://www.piwheels.org/simple/pyfastani/ 2023-09-18T22:11:51,093 Skipping link: not a file: https://pypi.org/simple/pyfastani/ 2023-09-18T22:11:51,130 Given no hashes to check 1 links for project 'pyfastani': discarding no candidates 2023-09-18T22:11:51,164 Collecting pyfastani==0.4.0 2023-09-18T22:11:51,168 Created temporary directory: /tmp/pip-unpack-aq0qr6gc 2023-09-18T22:11:51,968 Downloading pyfastani-0.4.0.tar.gz (4.6 MB) 2023-09-18T22:11:54,904 Added pyfastani==0.4.0 from https://files.pythonhosted.org/packages/04/be/5fa0a7577837e15e03204bdee84493bd46c740f95393cd7e7c84c3796e9d/pyfastani-0.4.0.tar.gz to build tracker '/tmp/pip-build-tracker-s_8ewcc3' 2023-09-18T22:11:54,908 Created temporary directory: /tmp/pip-build-env-ajabz4xq 2023-09-18T22:11:54,913 Installing build dependencies: started 2023-09-18T22:11:54,914 Running command pip subprocess to install build dependencies 2023-09-18T22:11:56,528 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-18T22:11:59,089 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-18T22:12:01,220 Collecting setuptools>=46.4 2023-09-18T22:12:01,221 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 2023-09-18T22:12:01,241 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-18T22:12:02,740 Collecting cython~=0.29.16 2023-09-18T22:12:02,742 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 2023-09-18T22:12:02,747 Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB) 2023-09-18T22:12:02,923 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-18T22:12:02,964 Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB) 2023-09-18T22:12:05,451 Installing collected packages: setuptools, cython 2023-09-18T22:12:10,654 Creating /tmp/pip-build-env-ajabz4xq/overlay/local/bin 2023-09-18T22:12:10,657 changing mode of /tmp/pip-build-env-ajabz4xq/overlay/local/bin/cygdb to 755 2023-09-18T22:12:10,659 changing mode of /tmp/pip-build-env-ajabz4xq/overlay/local/bin/cython to 755 2023-09-18T22:12:10,661 changing mode of /tmp/pip-build-env-ajabz4xq/overlay/local/bin/cythonize to 755 2023-09-18T22:12:10,683 Successfully installed cython-0.29.36 setuptools-68.2.2 2023-09-18T22:12:11,293 Installing build dependencies: finished with status 'done' 2023-09-18T22:12:11,297 Getting requirements to build wheel: started 2023-09-18T22:12:11,298 Running command Getting requirements to build wheel 2023-09-18T22:12:12,230 Getting requirements to build wheel: finished with status 'done' 2023-09-18T22:12:12,256 Installing backend dependencies: started 2023-09-18T22:12:12,257 Running command pip subprocess to install backend dependencies 2023-09-18T22:12:13,401 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-18T22:12:13,880 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-18T22:12:14,491 Collecting wheel 2023-09-18T22:12:14,511 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-18T22:12:16,718 Installing collected packages: wheel 2023-09-18T22:12:16,951 Creating /tmp/pip-build-env-ajabz4xq/normal/local/bin 2023-09-18T22:12:16,953 changing mode of /tmp/pip-build-env-ajabz4xq/normal/local/bin/wheel to 755 2023-09-18T22:12:16,965 Successfully installed wheel-0.41.2 2023-09-18T22:12:17,470 Installing backend dependencies: finished with status 'done' 2023-09-18T22:12:17,472 Created temporary directory: /tmp/pip-modern-metadata-dg9w_jb2 2023-09-18T22:12:17,474 Preparing metadata (pyproject.toml): started 2023-09-18T22:12:17,475 Running command Preparing metadata (pyproject.toml) 2023-09-18T22:12:18,314 running dist_info 2023-09-18T22:12:18,330 creating /tmp/pip-modern-metadata-dg9w_jb2/pyfastani.egg-info 2023-09-18T22:12:18,335 writing /tmp/pip-modern-metadata-dg9w_jb2/pyfastani.egg-info/PKG-INFO 2023-09-18T22:12:18,339 writing dependency_links to /tmp/pip-modern-metadata-dg9w_jb2/pyfastani.egg-info/dependency_links.txt 2023-09-18T22:12:18,341 writing top-level names to /tmp/pip-modern-metadata-dg9w_jb2/pyfastani.egg-info/top_level.txt 2023-09-18T22:12:18,342 writing manifest file '/tmp/pip-modern-metadata-dg9w_jb2/pyfastani.egg-info/SOURCES.txt' 2023-09-18T22:12:18,365 reading manifest file '/tmp/pip-modern-metadata-dg9w_jb2/pyfastani.egg-info/SOURCES.txt' 2023-09-18T22:12:18,367 reading manifest template 'MANIFEST.in' 2023-09-18T22:12:18,748 warning: no files found matching '*.ipp' under directory 'vendor/boost-math/include_private' 2023-09-18T22:12:18,846 warning: no previously-included files found matching 'pyfastani/_fastani.cpp' 2023-09-18T22:12:18,847 warning: no previously-included files found matching 'pyfastani/_fasta.c' 2023-09-18T22:12:18,854 adding license file 'COPYING' 2023-09-18T22:12:18,875 writing manifest file '/tmp/pip-modern-metadata-dg9w_jb2/pyfastani.egg-info/SOURCES.txt' 2023-09-18T22:12:18,877 creating '/tmp/pip-modern-metadata-dg9w_jb2/pyfastani-0.4.0.dist-info' 2023-09-18T22:12:19,087 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-18T22:12:19,093 Source in /tmp/pip-wheel-z6x967j1/pyfastani_964a58c0f9ee4b78bbdd67ba9f683bad has version 0.4.0, which satisfies requirement pyfastani==0.4.0 from https://files.pythonhosted.org/packages/04/be/5fa0a7577837e15e03204bdee84493bd46c740f95393cd7e7c84c3796e9d/pyfastani-0.4.0.tar.gz 2023-09-18T22:12:19,094 Removed pyfastani==0.4.0 from https://files.pythonhosted.org/packages/04/be/5fa0a7577837e15e03204bdee84493bd46c740f95393cd7e7c84c3796e9d/pyfastani-0.4.0.tar.gz from build tracker '/tmp/pip-build-tracker-s_8ewcc3' 2023-09-18T22:12:19,101 Created temporary directory: /tmp/pip-unpack-_ij033x8 2023-09-18T22:12:19,102 Created temporary directory: /tmp/pip-unpack-ir0iwiix 2023-09-18T22:12:19,106 Building wheels for collected packages: pyfastani 2023-09-18T22:12:19,111 Created temporary directory: /tmp/pip-wheel-lkklae6m 2023-09-18T22:12:19,111 Destination directory: /tmp/pip-wheel-lkklae6m 2023-09-18T22:12:19,113 Building wheel for pyfastani (pyproject.toml): started 2023-09-18T22:12:19,114 Running command Building wheel for pyfastani (pyproject.toml) 2023-09-18T22:12:19,965 running bdist_wheel 2023-09-18T22:12:19,993 running build 2023-09-18T22:12:19,993 running build_py 2023-09-18T22:12:20,001 creating build 2023-09-18T22:12:20,001 creating build/lib.linux-armv7l-cpython-311 2023-09-18T22:12:20,002 creating build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,003 copying pyfastani/__init__.py -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,005 creating build/lib.linux-armv7l-cpython-311/pyfastani/tests 2023-09-18T22:12:20,006 copying pyfastani/tests/test_ani.py -> build/lib.linux-armv7l-cpython-311/pyfastani/tests 2023-09-18T22:12:20,009 copying pyfastani/tests/test_sketch.py -> build/lib.linux-armv7l-cpython-311/pyfastani/tests 2023-09-18T22:12:20,011 copying pyfastani/tests/__init__.py -> build/lib.linux-armv7l-cpython-311/pyfastani/tests 2023-09-18T22:12:20,013 creating build/lib.linux-armv7l-cpython-311/pyfastani/tests/data 2023-09-18T22:12:20,014 copying pyfastani/tests/data/__init__.py -> build/lib.linux-armv7l-cpython-311/pyfastani/tests/data 2023-09-18T22:12:20,015 running egg_info 2023-09-18T22:12:20,019 writing pyfastani.egg-info/PKG-INFO 2023-09-18T22:12:20,024 writing dependency_links to pyfastani.egg-info/dependency_links.txt 2023-09-18T22:12:20,026 writing top-level names to pyfastani.egg-info/top_level.txt 2023-09-18T22:12:20,036 reading manifest file 'pyfastani.egg-info/SOURCES.txt' 2023-09-18T22:12:20,051 reading manifest template 'MANIFEST.in' 2023-09-18T22:12:20,472 warning: no files found matching '*.ipp' under directory 'vendor/boost-math/include_private' 2023-09-18T22:12:20,565 warning: no previously-included files found matching 'pyfastani/_fastani.cpp' 2023-09-18T22:12:20,566 warning: no previously-included files found matching 'pyfastani/_fasta.c' 2023-09-18T22:12:20,575 adding license file 'COPYING' 2023-09-18T22:12:20,603 writing manifest file 'pyfastani.egg-info/SOURCES.txt' 2023-09-18T22:12:20,608 /tmp/pip-build-env-ajabz4xq/overlay/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pyfastani._sequtils' is absent from the `packages` configuration. 2023-09-18T22:12:20,609 !! 2023-09-18T22:12:20,610 ******************************************************************************** 2023-09-18T22:12:20,610 ############################ 2023-09-18T22:12:20,611 # Package would be ignored # 2023-09-18T22:12:20,611 ############################ 2023-09-18T22:12:20,612 Python recognizes 'pyfastani._sequtils' as an importable package[^1], 2023-09-18T22:12:20,612 but it is absent from setuptools' `packages` configuration. 2023-09-18T22:12:20,613 This leads to an ambiguous overall configuration. If you want to distribute this 2023-09-18T22:12:20,613 package, please make sure that 'pyfastani._sequtils' is explicitly added 2023-09-18T22:12:20,614 to the `packages` configuration field. 2023-09-18T22:12:20,614 Alternatively, you can also rely on setuptools' discovery methods 2023-09-18T22:12:20,615 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-09-18T22:12:20,615 instead of `find_packages(...)`/`find:`). 2023-09-18T22:12:20,616 You can read more about "package discovery" on setuptools documentation page: 2023-09-18T22:12:20,617 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-09-18T22:12:20,618 If you don't want 'pyfastani._sequtils' to be distributed and are 2023-09-18T22:12:20,618 already explicitly excluding 'pyfastani._sequtils' via 2023-09-18T22:12:20,618 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-09-18T22:12:20,619 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-09-18T22:12:20,619 combination with a more fine grained `package-data` configuration. 2023-09-18T22:12:20,620 You can read more about "package data files" on setuptools documentation page: 2023-09-18T22:12:20,621 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-09-18T22:12:20,622 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-09-18T22:12:20,622 even if it does not contain any `.py` files. 2023-09-18T22:12:20,623 On the other hand, currently there is no concept of package data 2023-09-18T22:12:20,623 directory, all directories are treated like packages. 2023-09-18T22:12:20,624 ******************************************************************************** 2023-09-18T22:12:20,624 !! 2023-09-18T22:12:20,625 check.warn(importable) 2023-09-18T22:12:20,641 copying pyfastani/_atomic_vector.hpp -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,643 copying pyfastani/_atomic_vector.pxd -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,645 copying pyfastani/_fasta.pyx -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,647 copying pyfastani/_fastani.pyi -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,649 copying pyfastani/_fastani.pyx -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,652 copying pyfastani/_unicode.pxd -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,654 copying pyfastani/_utils.cpp -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,656 copying pyfastani/_utils.hpp -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,658 copying pyfastani/_utils.pxd -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,660 copying pyfastani/omp.cpp -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,662 copying pyfastani/omp.h -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,664 copying pyfastani/py.typed -> build/lib.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:20,665 creating build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils 2023-09-18T22:12:20,666 copying pyfastani/_sequtils/__init__.pxd -> build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils 2023-09-18T22:12:20,668 copying pyfastani/_sequtils/complement.h -> build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils 2023-09-18T22:12:20,670 copying pyfastani/_sequtils/neon.c -> build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils 2023-09-18T22:12:20,672 copying pyfastani/_sequtils/sequtils.cpp -> build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils 2023-09-18T22:12:20,674 copying pyfastani/_sequtils/sequtils.h -> build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils 2023-09-18T22:12:20,676 copying pyfastani/_sequtils/sse2.c -> build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils 2023-09-18T22:12:20,678 copying pyfastani/_sequtils/ssse3.c -> build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils 2023-09-18T22:12:20,680 copying pyfastani/tests/requirements.txt -> build/lib.linux-armv7l-cpython-311/pyfastani/tests 2023-09-18T22:12:20,681 copying pyfastani/tests/data/BGC0001425.faa -> build/lib.linux-armv7l-cpython-311/pyfastani/tests/data 2023-09-18T22:12:20,684 copying pyfastani/tests/data/BGC0001427.faa -> build/lib.linux-armv7l-cpython-311/pyfastani/tests/data 2023-09-18T22:12:20,687 copying pyfastani/tests/data/BGC0001428.faa -> build/lib.linux-armv7l-cpython-311/pyfastani/tests/data 2023-09-18T22:12:20,690 copying pyfastani/tests/data/Escherichia_coli_str_K12_MG1655.fna -> build/lib.linux-armv7l-cpython-311/pyfastani/tests/data 2023-09-18T22:12:20,774 copying pyfastani/tests/data/Shigella_flexneri_2a_01.fna -> build/lib.linux-armv7l-cpython-311/pyfastani/tests/data 2023-09-18T22:12:20,853 running build_clib 2023-09-18T22:12:20,857 creating build/temp.linux-armv7l-cpython-311 2023-09-18T22:12:20,858 generating build/temp.linux-armv7l-cpython-311/libcpu_features.a from vendor/cpu_features/src/filesystem.c, vendor/cpu_features/src/stack_line_reader.c, vendor/cpu_features/src/string_view.c, vendor/cpu_features/src/cpuinfo_aarch64.c, vendor/cpu_features/src/cpuinfo_arm.c, vendor/cpu_features/src/cpuinfo_x86.c 2023-09-18T22:12:20,859 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -g -c build/temp.linux-armv7l-cpython-311/test_dlopen.c -o build/temp.linux-armv7l-cpython-311/test_dlopen.o 2023-09-18T22:12:20,937 found `dlopen` function from 2023-09-18T22:12:20,983 could not find `getauxval` function from 2023-09-18T22:12:20,984 creating build/temp.linux-armv7l-cpython-311/vendor 2023-09-18T22:12:20,984 creating build/temp.linux-armv7l-cpython-311/vendor/cpu_features 2023-09-18T22:12:20,985 creating build/temp.linux-armv7l-cpython-311/vendor/cpu_features/src 2023-09-18T22:12:21,084 failed to compile platform-specific AARCH64 code 2023-09-18T22:12:21,682 successfully built platform-specific ARM code 2023-09-18T22:12:21,768 failed to compile platform-specific X86 code 2023-09-18T22:12:21,769 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -DARM_BUILD_SUPPORTED -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-311 -c vendor/cpu_features/src/filesystem.c -o build/temp.linux-armv7l-cpython-311/vendor/cpu_features/src/filesystem.o 2023-09-18T22:12:21,917 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -DARM_BUILD_SUPPORTED -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-311 -c vendor/cpu_features/src/stack_line_reader.c -o build/temp.linux-armv7l-cpython-311/vendor/cpu_features/src/stack_line_reader.o 2023-09-18T22:12:22,105 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -DARM_BUILD_SUPPORTED -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-311 -c vendor/cpu_features/src/string_view.c -o build/temp.linux-armv7l-cpython-311/vendor/cpu_features/src/string_view.o 2023-09-18T22:12:22,476 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DSTACK_LINE_READER_BUFFER_SIZE=1024 -DHAVE_DLFCN_H=1 -DARM_BUILD_SUPPORTED -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-311 -c vendor/cpu_features/src/hwcaps.c -o build/temp.linux-armv7l-cpython-311/vendor/cpu_features/src/hwcaps.o 2023-09-18T22:12:22,679 arm-linux-gnueabihf-gcc-ar rcs build/temp.linux-armv7l-cpython-311/libcpu_features.a build/temp.linux-armv7l-cpython-311/vendor/cpu_features/src/filesystem.o build/temp.linux-armv7l-cpython-311/vendor/cpu_features/src/stack_line_reader.o build/temp.linux-armv7l-cpython-311/vendor/cpu_features/src/string_view.o build/temp.linux-armv7l-cpython-311/vendor/cpu_features/src/hwcaps.o build/temp.linux-armv7l-cpython-311/vendor/cpu_features/src/cpuinfo_arm.o 2023-09-18T22:12:22,736 generating build/temp.linux-armv7l-cpython-311/libsequtils.a from pyfastani/_sequtils/sequtils.cpp, pyfastani/_sequtils/neon.c, pyfastani/_sequtils/sse2.c, pyfastani/_sequtils/ssse3.c 2023-09-18T22:12:22,737 creating build/temp.linux-armv7l-cpython-311/pyfastani 2023-09-18T22:12:22,737 creating build/temp.linux-armv7l-cpython-311/pyfastani/_sequtils 2023-09-18T22:12:22,797 failed to compile platform-specific NEON code 2023-09-18T22:12:22,809 failed to compile platform-specific SSE2 code 2023-09-18T22:12:22,821 failed to compile platform-specific SSSE3 code 2023-09-18T22:12:22,822 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DARM_BUILD_SUPPORTED -Ipyfastani/_sequtils -Ivendor/cpu_features/include -Ibuild/temp.linux-armv7l-cpython-311 -c pyfastani/_sequtils/sequtils.cpp -o build/temp.linux-armv7l-cpython-311/pyfastani/_sequtils/sequtils.o 2023-09-18T22:12:23,027 arm-linux-gnueabihf-gcc-ar rcs build/temp.linux-armv7l-cpython-311/libsequtils.a build/temp.linux-armv7l-cpython-311/pyfastani/_sequtils/sequtils.o 2023-09-18T22:12:23,038 running build_ext 2023-09-18T22:12:23,040 generating build/temp.linux-armv7l-cpython-311/cgi/include/cgid_types.hpp from vendor/FastANI/src/cgi/include/cgid_types.hpp 2023-09-18T22:12:23,040 creating build/temp.linux-armv7l-cpython-311/cgi 2023-09-18T22:12:23,041 creating build/temp.linux-armv7l-cpython-311/cgi/include 2023-09-18T22:12:23,044 generating build/temp.linux-armv7l-cpython-311/cgi/include/computeCoreIdentity.hpp from vendor/FastANI/src/cgi/include/computeCoreIdentity.hpp 2023-09-18T22:12:23,047 generating build/temp.linux-armv7l-cpython-311/common/prettyprint.hpp from vendor/FastANI/src/common/prettyprint.hpp 2023-09-18T22:12:23,047 creating build/temp.linux-armv7l-cpython-311/common 2023-09-18T22:12:23,050 generating build/temp.linux-armv7l-cpython-311/common/kseq.h from vendor/FastANI/src/common/kseq.h 2023-09-18T22:12:23,052 generating build/temp.linux-armv7l-cpython-311/common/memcpyLink.h from vendor/FastANI/src/common/memcpyLink.h 2023-09-18T22:12:23,054 generating build/temp.linux-armv7l-cpython-311/common/murmur3.h from vendor/FastANI/src/common/murmur3.h 2023-09-18T22:12:23,056 generating build/temp.linux-armv7l-cpython-311/common/clipp.h from vendor/FastANI/src/common/clipp.h 2023-09-18T22:12:23,070 generating build/temp.linux-armv7l-cpython-311/map/include/parseCmdArgs.hpp from vendor/FastANI/src/map/include/parseCmdArgs.hpp 2023-09-18T22:12:23,071 creating build/temp.linux-armv7l-cpython-311/map 2023-09-18T22:12:23,071 creating build/temp.linux-armv7l-cpython-311/map/include 2023-09-18T22:12:23,074 generating build/temp.linux-armv7l-cpython-311/map/include/MIIteratorL2.hpp from vendor/FastANI/src/map/include/MIIteratorL2.hpp 2023-09-18T22:12:23,076 generating build/temp.linux-armv7l-cpython-311/map/include/map_stats.hpp from vendor/FastANI/src/map/include/map_stats.hpp 2023-09-18T22:12:23,078 generating build/temp.linux-armv7l-cpython-311/map/include/winSketch.hpp from vendor/FastANI/src/map/include/winSketch.hpp 2023-09-18T22:12:23,080 generating build/temp.linux-armv7l-cpython-311/map/include/slidingMap.hpp from vendor/FastANI/src/map/include/slidingMap.hpp 2023-09-18T22:12:23,082 generating build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp from vendor/FastANI/src/map/include/commonFunc.hpp 2023-09-18T22:12:23,085 generating build/temp.linux-armv7l-cpython-311/map/include/base_types.hpp from vendor/FastANI/src/map/include/base_types.hpp 2023-09-18T22:12:23,086 generating build/temp.linux-armv7l-cpython-311/map/include/map_parameters.hpp from vendor/FastANI/src/map/include/map_parameters.hpp 2023-09-18T22:12:23,088 generating build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp from vendor/FastANI/src/map/include/computeMap.hpp 2023-09-18T22:12:34,457 Compiling pyfastani/_fastani.pyx because it changed. 2023-09-18T22:12:34,457 Compiling pyfastani/_fasta.pyx because it changed. 2023-09-18T22:12:34,458 [1/2] Cythonizing pyfastani/_fasta.pyx 2023-09-18T22:12:34,458 [2/2] Cythonizing pyfastani/_fastani.pyx 2023-09-18T22:12:34,459 building 'pyfastani._fastani' extension 2023-09-18T22:12:34,459 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_BOOST=1 -DBOOST_NO_EXCEPTIONS=1 -DBOOST_IF_CONSTEXPR=if -DCYTHON_WITHOUT_ASSERTIONS=1 -Ipyfastani -Ipyfastani/_sequtils -Iinclude -Ivendor/cpu_features/include -Ivendor/boost-math/include -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c pyfastani/_fastani.cpp -o build/temp.linux-armv7l-cpython-311/pyfastani/_fastani.o -std=c++11 2023-09-18T22:12:40,573 In file included from build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:25, 2023-09-18T22:12:40,574 from pyfastani/_fastani.cpp:859: 2023-09-18T22:12:40,574 build/temp.linux-armv7l-cpython-311/map/include/MIIteratorL2.hpp: In constructor ‘skch::MIIteratorL2::MIIteratorL2(MIIter_t, MIIter_t, skch::offset_t)’: 2023-09-18T22:12:40,575 build/temp.linux-armv7l-cpython-311/map/include/MIIteratorL2.hpp:49:16: warning: ‘skch::MIIteratorL2::sw_end’ will be initialized after [-Wreorder] 2023-09-18T22:12:40,575 49 | MIIter_t sw_end; 2023-09-18T22:12:40,576 | ^~~~~~ 2023-09-18T22:12:40,577 build/temp.linux-armv7l-cpython-311/map/include/MIIteratorL2.hpp:40:16: warning: ‘skch::offset_t skch::MIIteratorL2::countMinimizerWindows’ [-Wreorder] 2023-09-18T22:12:40,577 40 | offset_t countMinimizerWindows; 2023-09-18T22:12:40,578 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:12:40,578 build/temp.linux-armv7l-cpython-311/map/include/MIIteratorL2.hpp:56:7: warning: when initialized here [-Wreorder] 2023-09-18T22:12:40,579 56 | MIIteratorL2( MIIter_t firstSuperWindowRangeStart, 2023-09-18T22:12:40,580 | ^~~~~~~~~~~~ 2023-09-18T22:12:40,698 In file included from pyfastani/_fastani.cpp:860: 2023-09-18T22:12:40,698 build/temp.linux-armv7l-cpython-311/cgi/include/computeCoreIdentity.hpp: In function ‘void cgi::outputVisualizationFile(skch::Parameters&, std::vector&, skch::Map&, skch::Sketch&, uint64_t, std::string&)’: 2023-09-18T22:12:40,699 build/temp.linux-armv7l-cpython-311/cgi/include/computeCoreIdentity.hpp:116:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-18T22:12:40,700 116 | for(int i = 0; i < mapper.metadata.size(); i++) 2023-09-18T22:12:40,700 | ~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:12:40,701 build/temp.linux-armv7l-cpython-311/cgi/include/computeCoreIdentity.hpp:124:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-18T22:12:40,701 124 | for(int i = 0; i < refSketch.metadata.size(); i++) 2023-09-18T22:12:40,702 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:12:40,889 build/temp.linux-armv7l-cpython-311/cgi/include/computeCoreIdentity.hpp: In function ‘void cgi::splitReferenceGenomes(skch::Parameters&, std::vector&)’: 2023-09-18T22:12:40,890 build/temp.linux-armv7l-cpython-311/cgi/include/computeCoreIdentity.hpp:465:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-18T22:12:40,890 465 | for (int j = 0; j < parameters.refSequences.size(); j++) 2023-09-18T22:12:40,891 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:12:41,521 pyfastani/_fastani.cpp: In function ‘void __pyx_f_9pyfastani_8_fastani_6Mapper__do_l1_mappings(skch::Map&, int, const void*, Py_ssize_t, skch::QueryMetaData >&, std::vector&)’: 2023-09-18T22:12:41,522 pyfastani/_fastani.cpp:10905:54: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-18T22:12:41,522 10905 | __pyx_t_1 = ((__pyx_v_hit_position_list.size() < __pyx_v_map.refSketch.getFreqThreshold()) != 0); 2023-09-18T22:12:41,523 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:12:43,856 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp: In instantiation of ‘void skch::Map::computeL1CandidateRegions(Q_Info&, Vec1&, int, Vec2&) [with Q_Info = skch::QueryMetaData >; Vec1 = std::vector; Vec2 = std::vector]’: 2023-09-18T22:12:43,857 pyfastani/_fastani.cpp:10977:42: required from here 2023-09-18T22:12:43,857 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:328:66: warning: comparison of integer expressions of different signedness: ‘skch::offset_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-18T22:12:43,858 328 | if(it2->seqId == it->seqId && it2->wpos - it->wpos < Q.kseq->seq.l) 2023-09-18T22:12:43,858 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2023-09-18T22:12:43,954 In file included from build/temp.linux-armv7l-cpython-311/map/include/winSketch.hpp:19, 2023-09-18T22:12:43,955 from pyfastani/_fastani.cpp:858: 2023-09-18T22:12:43,956 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp: In instantiation of ‘void skch::CommonFunc::makeUpperCase(KSEQ) [with KSEQ = kseq_t*]’: 2023-09-18T22:12:43,956 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp:104:22: required from ‘void skch::CommonFunc::addMinimizers(std::vector&, KSEQ, int, int, int, skch::seqno_t) [with T = skch::MinimizerInfo; KSEQ = kseq_t*; skch::seqno_t = int]’ 2023-09-18T22:12:43,957 build/temp.linux-armv7l-cpython-311/map/include/winSketch.hpp:155:46: required from here 2023-09-18T22:12:43,958 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp:59:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-18T22:12:43,958 59 | for ( int i = 0; i < kseq->seq.l; i++ ) 2023-09-18T22:12:43,959 | ~~^~~~~~~~~~~~~ 2023-09-18T22:12:44,013 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp: In instantiation of ‘void skch::Map::doL1Mapping(Q_Info&, Vec&) [with Q_Info = skch::QueryMetaData >; Vec = std::vector]’: 2023-09-18T22:12:44,014 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:212:22: required from ‘void skch::Map::mapSingleQuerySeq(Q_Info&, skch::MappingResultsVector_t&, std::ofstream&) [with Q_Info = skch::QueryMetaData >; skch::MappingResultsVector_t = std::vector; std::ofstream = std::basic_ofstream]’ 2023-09-18T22:12:44,014 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:177:34: required from here 2023-09-18T22:12:44,015 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:289:41: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2023-09-18T22:12:44,016 289 | if(hitPositionList.size() < refSketch.getFreqThreshold()) 2023-09-18T22:12:44,016 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:12:44,017 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:277:15: warning: unused variable ‘totalMinimizersPicked’ [-Wunused-variable] 2023-09-18T22:12:44,017 277 | int totalMinimizersPicked = 0; 2023-09-18T22:12:44,018 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:13:20,241 In function ‘skch::hash_t skch::CommonFunc::getHash(const char*, int)’, 2023-09-18T22:13:20,242 inlined from ‘int __pyx_f_9pyfastani_8_fastani__add_minimizers_nucl(std::vector&, int, const void*, Py_ssize_t, int, int, skch::seqno_t)’ at pyfastani/_fastani.cpp:4076:49: 2023-09-18T22:13:20,242 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp:78:12: warning: ‘data’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-18T22:13:20,243 78 | hash = *((hash_t *)data); 2023-09-18T22:13:20,243 | ~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-18T22:13:20,244 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp: In function ‘int __pyx_f_9pyfastani_8_fastani__add_minimizers_nucl(std::vector&, int, const void*, Py_ssize_t, int, int, skch::seqno_t)’: 2023-09-18T22:13:20,244 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp:73:12: note: ‘data’ declared here 2023-09-18T22:13:20,245 73 | char data[16]; 2023-09-18T22:13:20,246 | ^~~~ 2023-09-18T22:13:20,246 In function ‘skch::hash_t skch::CommonFunc::getHash(const char*, int)’, 2023-09-18T22:13:20,247 inlined from ‘int __pyx_f_9pyfastani_8_fastani__add_minimizers_nucl(std::vector&, int, const void*, Py_ssize_t, int, int, skch::seqno_t)’ at pyfastani/_fastani.cpp:4086:49: 2023-09-18T22:13:20,248 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp:78:12: warning: ‘data’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-18T22:13:20,248 78 | hash = *((hash_t *)data); 2023-09-18T22:13:20,249 | ~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-18T22:13:20,250 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp: In function ‘int __pyx_f_9pyfastani_8_fastani__add_minimizers_nucl(std::vector&, int, const void*, Py_ssize_t, int, int, skch::seqno_t)’: 2023-09-18T22:13:20,250 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp:73:12: note: ‘data’ declared here 2023-09-18T22:13:20,251 73 | char data[16]; 2023-09-18T22:13:20,252 | ^~~~ 2023-09-18T22:13:20,441 In function ‘skch::hash_t skch::CommonFunc::getHash(const char*, int)’, 2023-09-18T22:13:20,442 inlined from ‘int __pyx_f_9pyfastani_8_fastani__add_minimizers_prot(std::vector&, int, const void*, Py_ssize_t, int, int, skch::seqno_t)’ at pyfastani/_fastani.cpp:4659:53: 2023-09-18T22:13:20,442 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp:78:12: warning: ‘data’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-18T22:13:20,443 78 | hash = *((hash_t *)data); 2023-09-18T22:13:20,443 | ~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-18T22:13:20,444 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp: In function ‘int __pyx_f_9pyfastani_8_fastani__add_minimizers_prot(std::vector&, int, const void*, Py_ssize_t, int, int, skch::seqno_t)’: 2023-09-18T22:13:20,444 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp:73:12: note: ‘data’ declared here 2023-09-18T22:13:20,445 73 | char data[16]; 2023-09-18T22:13:20,446 | ^~~~ 2023-09-18T22:13:22,364 In file included from /usr/include/c++/12/vector:70, 2023-09-18T22:13:22,364 from pyfastani/_fastani.cpp:846: 2023-09-18T22:13:22,365 /usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’: 2023-09-18T22:13:22,365 /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-09-18T22:13:22,366 439 | vector<_Tp, _Alloc>:: 2023-09-18T22:13:22,367 | ^~~~~~~~~~~~~~~~~~~ 2023-09-18T22:13:22,503 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’, 2023-09-18T22:13:22,503 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-18T22:13:22,504 inlined from ‘std::vector __pyx_convert_vector_from_py_uint64_t(PyObject*)’ at pyfastani/_fastani.cpp:18820:24: 2023-09-18T22:13:22,504 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-18T22:13:22,505 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-18T22:13:22,506 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:13:22,878 pyfastani/_fastani.cpp: In function ‘int __pyx_f_9pyfastani_8_fastani_6Sketch__add_draft(__pyx_obj_9pyfastani_8_fastani_Sketch*, PyObject*, PyObject*)’: 2023-09-18T22:13:22,879 pyfastani/_fastani.cpp:8601:76: warning: ‘__pyx_v_data’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-18T22:13:22,879 8601 | __pyx_t_7 = __pyx_f_9pyfastani_8_fastani__add_minimizers_nucl(__pyx_v_self->_sk->minimizerIndex, __pyx_v_kind, __pyx_v_data, __pyx_v_slen, __pyx_v_param->kmerSize, __pyx_v_param->windowSize, __pyx_v_self->_counter); if (unlikely(__pyx_t_7 == ((int)1))) __PYX_ERR(0, 627, __pyx_L13_error) 2023-09-18T22:13:22,880 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:13:22,881 pyfastani/_fastani.cpp:8308:9: note: ‘__pyx_v_data’ was declared here 2023-09-18T22:13:22,881 8308 | void *__pyx_v_data; 2023-09-18T22:13:22,882 | ^~~~~~~~~~~~ 2023-09-18T22:13:22,890 In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]’, 2023-09-18T22:13:22,891 inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21, 2023-09-18T22:13:22,892 inlined from ‘int __pyx_f_9pyfastani_8_fastani_6Sketch__add_draft(__pyx_obj_9pyfastani_8_fastani_Sketch*, PyObject*, PyObject*)’ at pyfastani/_fastani.cpp:8757:37: 2023-09-18T22:13:22,892 /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-09-18T22:13:22,893 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-09-18T22:13:22,894 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:13:31,438 pyfastani/_fastani.cpp: In function ‘PyObject* __pyx_f_9pyfastani_8_fastani_6Mapper__query_draft(__pyx_obj_9pyfastani_8_fastani_Mapper*, PyObject*, __pyx_opt_args_9pyfastani_8_fastani_6Mapper__query_draft*)’: 2023-09-18T22:13:31,439 pyfastani/_fastani.cpp:12232:48: warning: ‘__pyx_v_data’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-18T22:13:31,439 12232 | __pyx_t_5 = PyMemoryView_FromMemory(((char *)__pyx_v_data), (__pyx_v_slen * __pyx_cur_scope->__pyx_v_stride), PyBUF_READ); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 1074, __pyx_L11_error) 2023-09-18T22:13:31,439 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-18T22:13:31,440 pyfastani/_fastani.cpp:11506:9: note: ‘__pyx_v_data’ was declared here 2023-09-18T22:13:31,440 11506 | void *__pyx_v_data; 2023-09-18T22:13:31,441 | ^~~~~~~~~~~~ 2023-09-18T22:13:36,825 In file included from pyfastani/_fastani.cpp:850: 2023-09-18T22:13:36,825 build/temp.linux-armv7l-cpython-311/map/include/map_stats.hpp: In function ‘int skch::Stat::recommendedWindowSize(double, int, int, float, int, uint64_t)’: 2023-09-18T22:13:36,826 build/temp.linux-armv7l-cpython-311/map/include/map_stats.hpp:252:33: warning: ‘optimalSketchSize’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-18T22:13:36,826 252 | int w = 2.0 * lengthQuery/optimalSketchSize; 2023-09-18T22:13:36,827 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2023-09-18T22:13:36,827 build/temp.linux-armv7l-cpython-311/map/include/map_stats.hpp:237:11: note: ‘optimalSketchSize’ was declared here 2023-09-18T22:13:36,828 237 | int optimalSketchSize; 2023-09-18T22:13:36,829 | ^~~~~~~~~~~~~~~~~ 2023-09-18T22:13:39,188 In member function ‘void skch::Map::computeL2MappedRegions(Q_Info&, L1_candidateLocus_t&, L2_mapLocus_t&) [with Q_Info = skch::QueryMetaData >]’, 2023-09-18T22:13:39,189 inlined from ‘bool skch::Map::doL2Mapping(Q_Info&, VecIn&, VecOut&) [with Q_Info = skch::QueryMetaData >; VecIn = std::vector; VecOut = atomic_vector]’ at build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:368:35, 2023-09-18T22:13:39,189 inlined from ‘void __pyx_f_9pyfastani_8_fastani_6Mapper__query_fragment(__pyx_obj_9pyfastani_8_fastani_Mapper*, __pyx_obj_9pyfastani_8_fastani__Map*, int, skch::seqno_t, PyObject*, int, int, __pyx_obj_9pyfastani_8_fastani__FinalMappings*, int)’ at pyfastani/_fastani.cpp:11202:41: 2023-09-18T22:13:39,190 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:492:52: warning: ‘lastOptimalPos’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-18T22:13:39,191 492 | l2_out.meanOptimalPos = (beginOptimalPos + lastOptimalPos)/2; 2023-09-18T22:13:39,191 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-18T22:13:39,192 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp: In function ‘void __pyx_f_9pyfastani_8_fastani_6Mapper__query_fragment(__pyx_obj_9pyfastani_8_fastani_Mapper*, __pyx_obj_9pyfastani_8_fastani__Map*, int, skch::seqno_t, PyObject*, int, int, __pyx_obj_9pyfastani_8_fastani__FinalMappings*, int)’: 2023-09-18T22:13:39,193 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:449:32: note: ‘lastOptimalPos’ was declared here 2023-09-18T22:13:39,193 449 | int beginOptimalPos, lastOptimalPos; 2023-09-18T22:13:39,194 | ^~~~~~~~~~~~~~ 2023-09-18T22:13:39,195 In member function ‘void skch::Map::computeL2MappedRegions(Q_Info&, L1_candidateLocus_t&, L2_mapLocus_t&) [with Q_Info = skch::QueryMetaData >]’, 2023-09-18T22:13:39,196 inlined from ‘bool skch::Map::doL2Mapping(Q_Info&, VecIn&, VecOut&) [with Q_Info = skch::QueryMetaData >; VecIn = std::vector; VecOut = atomic_vector]’ at build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:368:35, 2023-09-18T22:13:39,196 inlined from ‘void __pyx_f_9pyfastani_8_fastani_6Mapper__query_fragment(__pyx_obj_9pyfastani_8_fastani_Mapper*, __pyx_obj_9pyfastani_8_fastani__Map*, int, skch::seqno_t, PyObject*, int, int, __pyx_obj_9pyfastani_8_fastani__FinalMappings*, int)’ at pyfastani/_fastani.cpp:11202:41: 2023-09-18T22:13:39,197 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:492:52: warning: ‘beginOptimalPos’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-18T22:13:39,197 492 | l2_out.meanOptimalPos = (beginOptimalPos + lastOptimalPos)/2; 2023-09-18T22:13:39,198 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2023-09-18T22:13:39,198 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp: In function ‘void __pyx_f_9pyfastani_8_fastani_6Mapper__query_fragment(__pyx_obj_9pyfastani_8_fastani_Mapper*, __pyx_obj_9pyfastani_8_fastani__Map*, int, skch::seqno_t, PyObject*, int, int, __pyx_obj_9pyfastani_8_fastani__FinalMappings*, int)’: 2023-09-18T22:13:39,199 build/temp.linux-armv7l-cpython-311/map/include/computeMap.hpp:449:15: note: ‘beginOptimalPos’ was declared here 2023-09-18T22:13:39,199 449 | int beginOptimalPos, lastOptimalPos; 2023-09-18T22:13:39,200 | ^~~~~~~~~~~~~~~ 2023-09-18T22:13:46,015 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_BOOST=1 -DBOOST_NO_EXCEPTIONS=1 -DBOOST_IF_CONSTEXPR=if -DCYTHON_WITHOUT_ASSERTIONS=1 -Ipyfastani -Ipyfastani/_sequtils -Iinclude -Ivendor/cpu_features/include -Ivendor/boost-math/include -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c pyfastani/_utils.cpp -o build/temp.linux-armv7l-cpython-311/pyfastani/_utils.o -std=c++11 2023-09-18T22:13:48,907 In file included from build/temp.linux-armv7l-cpython-311/map/include/winSketch.hpp:19, 2023-09-18T22:13:48,908 from pyfastani/_utils.hpp:14, 2023-09-18T22:13:48,908 from pyfastani/_utils.cpp:2: 2023-09-18T22:13:48,909 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp: In instantiation of ‘void skch::CommonFunc::makeUpperCase(KSEQ) [with KSEQ = kseq_t*]’: 2023-09-18T22:13:48,909 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp:104:22: required from ‘void skch::CommonFunc::addMinimizers(std::vector&, KSEQ, int, int, int, skch::seqno_t) [with T = skch::MinimizerInfo; KSEQ = kseq_t*; skch::seqno_t = int]’ 2023-09-18T22:13:48,910 build/temp.linux-armv7l-cpython-311/map/include/winSketch.hpp:155:46: required from here 2023-09-18T22:13:48,911 build/temp.linux-armv7l-cpython-311/map/include/commonFunc.hpp:59:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-09-18T22:13:48,911 59 | for ( int i = 0; i < kseq->seq.l; i++ ) 2023-09-18T22:13:48,912 | ~~^~~~~~~~~~~~~ 2023-09-18T22:13:49,418 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DUSE_BOOST=1 -DBOOST_NO_EXCEPTIONS=1 -DBOOST_IF_CONSTEXPR=if -DCYTHON_WITHOUT_ASSERTIONS=1 -Ipyfastani -Ipyfastani/_sequtils -Iinclude -Ivendor/cpu_features/include -Ivendor/boost-math/include -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c pyfastani/omp.cpp -o build/temp.linux-armv7l-cpython-311/pyfastani/omp.o -std=c++11 2023-09-18T22:13:49,495 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pyfastani/_fastani.o build/temp.linux-armv7l-cpython-311/pyfastani/_utils.o build/temp.linux-armv7l-cpython-311/pyfastani/omp.o build/temp.linux-armv7l-cpython-311/libsequtils.a -L/usr/lib/arm-linux-gnueabihf -Lbuild/temp.linux-armv7l-cpython-311 -lsequtils -lcpu_features -lsequtils -o build/lib.linux-armv7l-cpython-311/pyfastani/_fastani.cpython-311-arm-linux-gnueabihf.so -std=c++11 2023-09-18T22:13:49,984 building 'pyfastani._fasta' extension 2023-09-18T22:13:49,985 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DCYTHON_WITHOUT_ASSERTIONS=1 -Ipyfastani/_sequtils -Iinclude -Ipyfastani -Ivendor/cpu_features/include -Ipyfastani/simd -Ibuild/temp.linux-armv7l-cpython-311 -I/usr/include/python3.11 -c pyfastani/_fasta.c -o build/temp.linux-armv7l-cpython-311/pyfastani/_fasta.o 2023-09-18T22:13:54,120 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/pyfastani/_fasta.o build/temp.linux-armv7l-cpython-311/libsequtils.a -L/usr/lib/arm-linux-gnueabihf -Lbuild/temp.linux-armv7l-cpython-311 -lsequtils -lcpu_features -lsequtils -o build/lib.linux-armv7l-cpython-311/pyfastani/_fasta.cpython-311-arm-linux-gnueabihf.so 2023-09-18T22:13:54,247 installing to build/bdist.linux-armv7l/wheel 2023-09-18T22:13:54,248 running install 2023-09-18T22:13:54,272 running install_lib 2023-09-18T22:13:54,279 creating build/bdist.linux-armv7l 2023-09-18T22:13:54,280 creating build/bdist.linux-armv7l/wheel 2023-09-18T22:13:54,282 creating build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,284 creating build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2023-09-18T22:13:54,285 copying build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils/sequtils.h -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2023-09-18T22:13:54,287 copying build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils/complement.h -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2023-09-18T22:13:54,289 copying build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils/__init__.pxd -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2023-09-18T22:13:54,291 copying build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils/neon.c -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2023-09-18T22:13:54,293 copying build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils/ssse3.c -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2023-09-18T22:13:54,296 copying build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils/sse2.c -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2023-09-18T22:13:54,298 copying build/lib.linux-armv7l-cpython-311/pyfastani/_sequtils/sequtils.cpp -> build/bdist.linux-armv7l/wheel/pyfastani/_sequtils 2023-09-18T22:13:54,300 copying build/lib.linux-armv7l-cpython-311/pyfastani/_utils.cpp -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,302 creating build/bdist.linux-armv7l/wheel/pyfastani/tests 2023-09-18T22:13:54,304 copying build/lib.linux-armv7l-cpython-311/pyfastani/tests/requirements.txt -> build/bdist.linux-armv7l/wheel/pyfastani/tests 2023-09-18T22:13:54,306 copying build/lib.linux-armv7l-cpython-311/pyfastani/tests/test_ani.py -> build/bdist.linux-armv7l/wheel/pyfastani/tests 2023-09-18T22:13:54,309 creating build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2023-09-18T22:13:54,310 copying build/lib.linux-armv7l-cpython-311/pyfastani/tests/data/BGC0001428.faa -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2023-09-18T22:13:54,314 copying build/lib.linux-armv7l-cpython-311/pyfastani/tests/data/Shigella_flexneri_2a_01.fna -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2023-09-18T22:13:54,390 copying build/lib.linux-armv7l-cpython-311/pyfastani/tests/data/Escherichia_coli_str_K12_MG1655.fna -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2023-09-18T22:13:54,459 copying build/lib.linux-armv7l-cpython-311/pyfastani/tests/data/BGC0001425.faa -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2023-09-18T22:13:54,462 copying build/lib.linux-armv7l-cpython-311/pyfastani/tests/data/BGC0001427.faa -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2023-09-18T22:13:54,465 copying build/lib.linux-armv7l-cpython-311/pyfastani/tests/data/__init__.py -> build/bdist.linux-armv7l/wheel/pyfastani/tests/data 2023-09-18T22:13:54,467 copying build/lib.linux-armv7l-cpython-311/pyfastani/tests/test_sketch.py -> build/bdist.linux-armv7l/wheel/pyfastani/tests 2023-09-18T22:13:54,470 copying build/lib.linux-armv7l-cpython-311/pyfastani/tests/__init__.py -> build/bdist.linux-armv7l/wheel/pyfastani/tests 2023-09-18T22:13:54,472 copying build/lib.linux-armv7l-cpython-311/pyfastani/_fasta.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,481 copying build/lib.linux-armv7l-cpython-311/pyfastani/_fastani.pyi -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,483 copying build/lib.linux-armv7l-cpython-311/pyfastani/_fastani.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,573 copying build/lib.linux-armv7l-cpython-311/pyfastani/_utils.pxd -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,575 copying build/lib.linux-armv7l-cpython-311/pyfastani/_fastani.pyx -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,578 copying build/lib.linux-armv7l-cpython-311/pyfastani/_atomic_vector.pxd -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,579 copying build/lib.linux-armv7l-cpython-311/pyfastani/omp.cpp -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,581 copying build/lib.linux-armv7l-cpython-311/pyfastani/_unicode.pxd -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,583 copying build/lib.linux-armv7l-cpython-311/pyfastani/omp.h -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,585 copying build/lib.linux-armv7l-cpython-311/pyfastani/_atomic_vector.hpp -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,586 copying build/lib.linux-armv7l-cpython-311/pyfastani/py.typed -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,588 copying build/lib.linux-armv7l-cpython-311/pyfastani/_fasta.pyx -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,590 copying build/lib.linux-armv7l-cpython-311/pyfastani/_utils.hpp -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,592 copying build/lib.linux-armv7l-cpython-311/pyfastani/__init__.py -> build/bdist.linux-armv7l/wheel/pyfastani 2023-09-18T22:13:54,593 running install_egg_info 2023-09-18T22:13:54,604 Copying pyfastani.egg-info to build/bdist.linux-armv7l/wheel/pyfastani-0.4.0-py3.11.egg-info 2023-09-18T22:13:54,616 running install_scripts 2023-09-18T22:13:54,664 creating build/bdist.linux-armv7l/wheel/pyfastani-0.4.0.dist-info/WHEEL 2023-09-18T22:13:54,666 creating '/tmp/pip-wheel-lkklae6m/.tmp-y097lkcn/pyfastani-0.4.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-18T22:13:54,669 adding 'pyfastani/__init__.py' 2023-09-18T22:13:54,670 adding 'pyfastani/_atomic_vector.hpp' 2023-09-18T22:13:54,671 adding 'pyfastani/_atomic_vector.pxd' 2023-09-18T22:13:54,739 adding 'pyfastani/_fasta.cpython-311-arm-linux-gnueabihf.so' 2023-09-18T22:13:54,743 adding 'pyfastani/_fasta.pyx' 2023-09-18T22:13:55,541 adding 'pyfastani/_fastani.cpython-311-arm-linux-gnueabihf.so' 2023-09-18T22:13:55,580 adding 'pyfastani/_fastani.pyi' 2023-09-18T22:13:55,586 adding 'pyfastani/_fastani.pyx' 2023-09-18T22:13:55,589 adding 'pyfastani/_unicode.pxd' 2023-09-18T22:13:55,590 adding 'pyfastani/_utils.cpp' 2023-09-18T22:13:55,591 adding 'pyfastani/_utils.hpp' 2023-09-18T22:13:55,592 adding 'pyfastani/_utils.pxd' 2023-09-18T22:13:55,593 adding 'pyfastani/omp.cpp' 2023-09-18T22:13:55,595 adding 'pyfastani/omp.h' 2023-09-18T22:13:55,596 adding 'pyfastani/py.typed' 2023-09-18T22:13:55,597 adding 'pyfastani/_sequtils/__init__.pxd' 2023-09-18T22:13:55,599 adding 'pyfastani/_sequtils/complement.h' 2023-09-18T22:13:55,600 adding 'pyfastani/_sequtils/neon.c' 2023-09-18T22:13:55,601 adding 'pyfastani/_sequtils/sequtils.cpp' 2023-09-18T22:13:55,602 adding 'pyfastani/_sequtils/sequtils.h' 2023-09-18T22:13:55,604 adding 'pyfastani/_sequtils/sse2.c' 2023-09-18T22:13:55,605 adding 'pyfastani/_sequtils/ssse3.c' 2023-09-18T22:13:55,606 adding 'pyfastani/tests/__init__.py' 2023-09-18T22:13:55,607 adding 'pyfastani/tests/requirements.txt' 2023-09-18T22:13:55,609 adding 'pyfastani/tests/test_ani.py' 2023-09-18T22:13:55,610 adding 'pyfastani/tests/test_sketch.py' 2023-09-18T22:13:55,613 adding 'pyfastani/tests/data/BGC0001425.faa' 2023-09-18T22:13:55,616 adding 'pyfastani/tests/data/BGC0001427.faa' 2023-09-18T22:13:55,619 adding 'pyfastani/tests/data/BGC0001428.faa' 2023-09-18T22:13:58,296 adding 'pyfastani/tests/data/Escherichia_coli_str_K12_MG1655.fna' 2023-09-18T22:14:01,111 adding 'pyfastani/tests/data/Shigella_flexneri_2a_01.fna' 2023-09-18T22:14:01,152 adding 'pyfastani/tests/data/__init__.py' 2023-09-18T22:14:01,154 adding 'pyfastani-0.4.0.dist-info/COPYING' 2023-09-18T22:14:01,156 adding 'pyfastani-0.4.0.dist-info/METADATA' 2023-09-18T22:14:01,157 adding 'pyfastani-0.4.0.dist-info/WHEEL' 2023-09-18T22:14:01,157 adding 'pyfastani-0.4.0.dist-info/top_level.txt' 2023-09-18T22:14:01,158 adding 'pyfastani-0.4.0.dist-info/RECORD' 2023-09-18T22:14:01,222 removing build/bdist.linux-armv7l/wheel 2023-09-18T22:14:01,874 Building wheel for pyfastani (pyproject.toml): finished with status 'done' 2023-09-18T22:14:01,992 Created wheel for pyfastani: filename=pyfastani-0.4.0-cp311-cp311-linux_armv7l.whl size=4812353 sha256=cb1e29cdc434665017f29f0a1c59540a70b1583a862cadf55db472bc7066ac9f 2023-09-18T22:14:01,994 Stored in directory: /tmp/pip-ephem-wheel-cache-18hi6wlx/wheels/d6/23/5d/3866dc0c23bcfb924a007013513003e5ba21b210c457c88951 2023-09-18T22:14:02,010 Successfully built pyfastani 2023-09-18T22:14:02,138 Removed build tracker: '/tmp/pip-build-tracker-s_8ewcc3'