2024-11-19T04:59:57,772 Disabling truststore because Python version isn't 3.10+ 2024-11-19T04:59:58,245 Created temporary directory: /tmp/pip-build-tracker-quh_ir_h 2024-11-19T04:59:58,246 Initialized build tracking at /tmp/pip-build-tracker-quh_ir_h 2024-11-19T04:59:58,246 Created build tracker: /tmp/pip-build-tracker-quh_ir_h 2024-11-19T04:59:58,246 Entered build tracker: /tmp/pip-build-tracker-quh_ir_h 2024-11-19T04:59:58,246 Created temporary directory: /tmp/pip-wheel-t7pevsu6 2024-11-19T04:59:58,252 Created temporary directory: /tmp/pip-ephem-wheel-cache-5pl464pn 2024-11-19T04:59:58,294 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-11-19T04:59:58,297 2 location(s) to search for versions of kssdtree: 2024-11-19T04:59:58,297 * https://pypi.org/simple/kssdtree/ 2024-11-19T04:59:58,297 * https://www.piwheels.org/simple/kssdtree/ 2024-11-19T04:59:58,297 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-11-19T04:59:58,298 Getting page https://pypi.org/simple/kssdtree/ 2024-11-19T04:59:58,299 Found index url https://pypi.org/simple/ 2024-11-19T04:59:58,318 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-11-19T04:59:58,321 Found link https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.1 2024-11-19T04:59:58,322 Found link https://files.pythonhosted.org/packages/9a/4c/6516f734f5860e4b30f9091aaac5811663bfae72c4de4ae6566c89192767/kssdtree-1.1.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.2 2024-11-19T04:59:58,322 Found link https://files.pythonhosted.org/packages/a4/cd/f2954686c636e853cc3fda197c459195377b78288874cf7d68218a8bdbf4/kssdtree-1.1.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.3 2024-11-19T04:59:58,322 Found link https://files.pythonhosted.org/packages/20/ea/b0301924e3f7d367cbb7b8da66837dba9af2a332bf56ed35e03a33faee76/kssdtree-1.1.4.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.4 2024-11-19T04:59:58,322 Found link https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.6 2024-11-19T04:59:58,323 Found link https://files.pythonhosted.org/packages/cd/4b/d886cbcc573ff0969da7d9c756049925b86141e60ee6708dfbbe0644d008/kssdtree-1.1.7.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.7 2024-11-19T04:59:58,323 Found link https://files.pythonhosted.org/packages/7e/8a/a62c8adc92df69ab8cb242827ee64a3e2b6d5c89b83425785dd00605af17/kssdtree-1.1.8.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.8 2024-11-19T04:59:58,323 Found link https://files.pythonhosted.org/packages/da/db/e458cca6427752c05428d2378ccdee631d32f760174fdaba65f73125e71b/kssdtree-1.1.9.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.9 2024-11-19T04:59:58,324 Found link https://files.pythonhosted.org/packages/9d/47/017180a30e73e421372377cbe6d01c5e51a5108ea2177f20ccd7d283f8d1/kssdtree-2.0.0.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.0 2024-11-19T04:59:58,324 Found link https://files.pythonhosted.org/packages/ba/39/d443cac955912a0371c93b797311cb9ec3a8d6ee0a5d7673376d826aa6b2/kssdtree-2.0.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.1 2024-11-19T04:59:58,324 Found link https://files.pythonhosted.org/packages/2e/32/e53c0e3735cbc913b2c96b4e0e1c1005fe816a4d71b38b80cdcfb5c67fa8/kssdtree-2.0.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.2 2024-11-19T04:59:58,324 Found link https://files.pythonhosted.org/packages/c0/0f/effc10c8e76dbe3b9a35a4b4d9e65a0a889ee805e10334541c3ca7ae3b94/kssdtree-2.0.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.3 2024-11-19T04:59:58,325 Found link https://files.pythonhosted.org/packages/fc/8d/d3790baa2f2f0a01c913005b94a82dc13ef601e7015e662ccff94bb1b458/kssdtree-2.0.4.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.4 2024-11-19T04:59:58,325 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-11-19T04:59:58,325 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-11-19T04:59:58,326 Found index url https://www.piwheels.org/simple/ 2024-11-19T04:59:58,363 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-11-19T04:59:58,386 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.4-cp311-cp311-linux_armv6l.whl#sha256=97a69f799c2d1b7024a9033b8a1e3fc17af4748a1ed726f52397d884303eb870 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,386 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.4-cp311-cp311-linux_armv7l.whl#sha256=97a69f799c2d1b7024a9033b8a1e3fc17af4748a1ed726f52397d884303eb870 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,386 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.3-cp311-cp311-linux_armv6l.whl#sha256=d70b4b00c6bf4ff5b294b9ad2594aa1e32981df4b9869be9d13aafa0ff614bc3 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,387 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.3-cp311-cp311-linux_armv7l.whl#sha256=d70b4b00c6bf4ff5b294b9ad2594aa1e32981df4b9869be9d13aafa0ff614bc3 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,387 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.2-cp311-cp311-linux_armv6l.whl#sha256=ae7417e30efd12d8c6800d4167141c94a93f1ce51afd5ae9196cdfb6057ca7d2 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,387 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.2-cp311-cp311-linux_armv7l.whl#sha256=ae7417e30efd12d8c6800d4167141c94a93f1ce51afd5ae9196cdfb6057ca7d2 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,388 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.2-cp39-cp39-linux_armv6l.whl#sha256=599ca3576cae9c0ef5ce475baaee98faa1478f8fd034062ddf88f823c9c91b10 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,388 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.2-cp39-cp39-linux_armv7l.whl#sha256=599ca3576cae9c0ef5ce475baaee98faa1478f8fd034062ddf88f823c9c91b10 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,388 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.1-cp311-cp311-linux_armv6l.whl#sha256=8b8c3190a5a4a010758772e9d53c3c12436541437bc9c503bec9a8f6a007cdcc (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,388 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.1-cp311-cp311-linux_armv7l.whl#sha256=8b8c3190a5a4a010758772e9d53c3c12436541437bc9c503bec9a8f6a007cdcc (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,389 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.0-cp311-cp311-linux_armv6l.whl#sha256=16a2e46376ed2874435371fd57a97405d4b631b35c014b9e395a4528a1e655b8 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,389 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,390 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp311-cp311-linux_armv7l.whl#sha256=d4c397f5fcb0af48dbb11b9fb7d7b399cc180d65355b794a8fcc7327e9a7dde1 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,390 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp39-cp39-linux_armv6l.whl#sha256=ab11dc15aca2923fe0d60bf11deb134bed4df89280b4ce40ca8e9bf3ca46b168 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,391 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp39-cp39-linux_armv7l.whl#sha256=ab11dc15aca2923fe0d60bf11deb134bed4df89280b4ce40ca8e9bf3ca46b168 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,391 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,392 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.7-cp311-cp311-linux_armv6l.whl#sha256=388a8dabd657ea83e6d22b52300337c74e9d84e506806cfd4d2a76eb98777e17 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,392 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.7-cp311-cp311-linux_armv7l.whl#sha256=388a8dabd657ea83e6d22b52300337c74e9d84e506806cfd4d2a76eb98777e17 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,393 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.7-cp39-cp39-linux_armv6l.whl#sha256=e1df896451d30c12e01aceb3eb91f0f7dfe0ee6f16fd66864fdefbc21cc54856 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,393 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,394 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp39-cp39-linux_armv7l.whl#sha256=9defb70b5162efc2c0eb6e415a7e37c604aa9b248a006af86af8f59a3bce5d2b (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,394 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp37-cp37m-linux_armv6l.whl#sha256=ffef4ae0f634dd977cc2ec6798b9f36f73d788aca27bb7199f552d5513c34413 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,395 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp37-cp37m-linux_armv7l.whl#sha256=ffef4ae0f634dd977cc2ec6798b9f36f73d788aca27bb7199f552d5513c34413 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,395 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,396 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp311-cp311-linux_armv6l.whl#sha256=6b76f3b3f532934ad49a829e7bf8176af580f4687f1491c49c3f571bf081f961 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,396 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp311-cp311-linux_armv7l.whl#sha256=6b76f3b3f532934ad49a829e7bf8176af580f4687f1491c49c3f571bf081f961 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,397 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp37-cp37m-linux_armv6l.whl#sha256=d179f6c6c0ad4e0f06950e1609118b065b3476c47446325f6614bdbef5ede0d0 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,397 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp37-cp37m-linux_armv7l.whl#sha256=d179f6c6c0ad4e0f06950e1609118b065b3476c47446325f6614bdbef5ede0d0 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,397 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp39-cp39-linux_armv6l.whl#sha256=6df2298fa80eefa823153fa0b9db67e35da72da7f88c5949f4f637872ff22c3b (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,398 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp39-cp39-linux_armv7l.whl#sha256=6df2298fa80eefa823153fa0b9db67e35da72da7f88c5949f4f637872ff22c3b (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,398 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv6l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,398 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv7l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,398 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv6l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,399 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv7l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,399 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp39-cp39-linux_armv6l.whl#sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,399 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp39-cp39-linux_armv7l.whl#sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,399 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv6l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,400 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv7l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,400 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv6l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,400 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv7l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,401 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv6l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,401 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv7l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T04:59:58,401 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-11-19T04:59:58,402 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-11-19T04:59:58,426 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-11-19T04:59:58,428 Collecting kssdtree==2.0.3 2024-11-19T04:59:58,431 Created temporary directory: /tmp/pip-unpack-qqmxq3jh 2024-11-19T04:59:58,458 Downloading kssdtree-2.0.3.tar.gz (112 kB) 2024-11-19T04:59:58,672 Added kssdtree==2.0.3 from https://files.pythonhosted.org/packages/c0/0f/effc10c8e76dbe3b9a35a4b4d9e65a0a889ee805e10334541c3ca7ae3b94/kssdtree-2.0.3.tar.gz to build tracker '/tmp/pip-build-tracker-quh_ir_h' 2024-11-19T04:59:58,674 Running setup.py (path:/tmp/pip-wheel-t7pevsu6/kssdtree_ea291bd3e3c24e26b57c8f974b4af114/setup.py) egg_info for package kssdtree 2024-11-19T04:59:58,675 Created temporary directory: /tmp/pip-pip-egg-info-am13dqqh 2024-11-19T04:59:58,675 Preparing metadata (setup.py): started 2024-11-19T04:59:58,676 Running command python setup.py egg_info 2024-11-19T05:00:00,062 running egg_info 2024-11-19T05:00:00,090 creating /tmp/pip-pip-egg-info-am13dqqh/kssdtree.egg-info 2024-11-19T05:00:00,091 writing /tmp/pip-pip-egg-info-am13dqqh/kssdtree.egg-info/PKG-INFO 2024-11-19T05:00:00,095 writing dependency_links to /tmp/pip-pip-egg-info-am13dqqh/kssdtree.egg-info/dependency_links.txt 2024-11-19T05:00:00,097 writing requirements to /tmp/pip-pip-egg-info-am13dqqh/kssdtree.egg-info/requires.txt 2024-11-19T05:00:00,098 writing top-level names to /tmp/pip-pip-egg-info-am13dqqh/kssdtree.egg-info/top_level.txt 2024-11-19T05:00:00,099 writing manifest file '/tmp/pip-pip-egg-info-am13dqqh/kssdtree.egg-info/SOURCES.txt' 2024-11-19T05:00:00,212 reading manifest file '/tmp/pip-pip-egg-info-am13dqqh/kssdtree.egg-info/SOURCES.txt' 2024-11-19T05:00:00,214 reading manifest template 'MANIFEST.in' 2024-11-19T05:00:00,234 writing manifest file '/tmp/pip-pip-egg-info-am13dqqh/kssdtree.egg-info/SOURCES.txt' 2024-11-19T05:00:00,324 Preparing metadata (setup.py): finished with status 'done' 2024-11-19T05:00:00,328 Source in /tmp/pip-wheel-t7pevsu6/kssdtree_ea291bd3e3c24e26b57c8f974b4af114 has version 2.0.3, which satisfies requirement kssdtree==2.0.3 from https://files.pythonhosted.org/packages/c0/0f/effc10c8e76dbe3b9a35a4b4d9e65a0a889ee805e10334541c3ca7ae3b94/kssdtree-2.0.3.tar.gz 2024-11-19T05:00:00,329 Removed kssdtree==2.0.3 from https://files.pythonhosted.org/packages/c0/0f/effc10c8e76dbe3b9a35a4b4d9e65a0a889ee805e10334541c3ca7ae3b94/kssdtree-2.0.3.tar.gz from build tracker '/tmp/pip-build-tracker-quh_ir_h' 2024-11-19T05:00:00,336 Created temporary directory: /tmp/pip-unpack-9ilah4_e 2024-11-19T05:00:00,337 Created temporary directory: /tmp/pip-unpack-jr9_2ikq 2024-11-19T05:00:00,337 Building wheels for collected packages: kssdtree 2024-11-19T05:00:00,554 Created temporary directory: /tmp/pip-wheel-gw8zceqg 2024-11-19T05:00:00,554 Building wheel for kssdtree (setup.py): started 2024-11-19T05:00:00,555 Destination directory: /tmp/pip-wheel-gw8zceqg 2024-11-19T05:00:00,555 Running command python setup.py bdist_wheel 2024-11-19T05:00:02,552 running bdist_wheel 2024-11-19T05:00:03,564 running build 2024-11-19T05:00:03,565 running build_py 2024-11-19T05:00:03,598 creating build/lib.linux-armv7l-cpython-39 2024-11-19T05:00:03,599 copying kssdtree.py -> build/lib.linux-armv7l-cpython-39 2024-11-19T05:00:03,603 copying toolutils.py -> build/lib.linux-armv7l-cpython-39 2024-11-19T05:00:03,605 running egg_info 2024-11-19T05:00:03,634 writing kssdtree.egg-info/PKG-INFO 2024-11-19T05:00:03,639 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-11-19T05:00:03,641 writing requirements to kssdtree.egg-info/requires.txt 2024-11-19T05:00:03,643 writing top-level names to kssdtree.egg-info/top_level.txt 2024-11-19T05:00:03,677 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-11-19T05:00:03,689 reading manifest template 'MANIFEST.in' 2024-11-19T05:00:04,190 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-11-19T05:00:04,352 running build_ext 2024-11-19T05:00:08,726 building 'kssd' extension 2024-11-19T05:00:08,754 creating build/temp.linux-armv7l-cpython-39 2024-11-19T05:00:08,767 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c co2mco.c -o build/temp.linux-armv7l-cpython-39/co2mco.o -fopenmp 2024-11-19T05:00:13,202 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-11-19T05:00:13,203 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:13,203 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-11-19T05:00:13,204 | ^ 2024-11-19T05:00:13,208 co2mco.c: In function ‘co2unitllmco’: 2024-11-19T05:00:13,208 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:13,208 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-11-19T05:00:13,209 | ^ 2024-11-19T05:00:14,281 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_composite.c -o build/temp.linux-armv7l-cpython-39/command_composite.o -fopenmp 2024-11-19T05:00:15,657 command_composite.c: In function ‘get_species_abundance’: 2024-11-19T05:00:15,657 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-19T05:00:15,657 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-11-19T05:00:15,657 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,658 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-19T05:00:15,658 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-11-19T05:00:15,658 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,659 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,659 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T05:00:15,659 | ^ 2024-11-19T05:00:15,660 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:15,660 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T05:00:15,660 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,660 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,660 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T05:00:15,660 | ^ 2024-11-19T05:00:15,661 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:15,661 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T05:00:15,661 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,661 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,661 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:15,662 | ^ 2024-11-19T05:00:15,662 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:15,662 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:15,662 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,662 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,663 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T05:00:15,663 | ^ 2024-11-19T05:00:15,663 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:15,663 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T05:00:15,663 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,664 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,664 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:15,664 | ^ 2024-11-19T05:00:15,664 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-11-19T05:00:15,664 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:15,664 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:17,354 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist.c -o build/temp.linux-armv7l-cpython-39/command_dist.o -fopenmp 2024-11-19T05:00:17,600 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-19T05:00:17,600 command_dist.c:677:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-11-19T05:00:17,601 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:17,601 | ~~^ 2024-11-19T05:00:17,601 | | 2024-11-19T05:00:17,601 | long unsigned int 2024-11-19T05:00:17,601 | %u 2024-11-19T05:00:17,601 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:17,601 | ~~~~~~~ 2024-11-19T05:00:17,601 | | 2024-11-19T05:00:17,602 | size_t {aka unsigned int} 2024-11-19T05:00:17,602 command_dist.c:677:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-11-19T05:00:17,602 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:17,602 | ~~^ 2024-11-19T05:00:17,602 | | 2024-11-19T05:00:17,602 | long unsigned int 2024-11-19T05:00:17,602 | %u 2024-11-19T05:00:17,602 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:17,603 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:17,603 | ~~~~~~~~~ 2024-11-19T05:00:17,603 | | 2024-11-19T05:00:17,603 | size_t {aka unsigned int} 2024-11-19T05:00:17,603 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T05:00:17,603 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:17,603 | ~~^ 2024-11-19T05:00:17,603 | | 2024-11-19T05:00:17,604 | long unsigned int 2024-11-19T05:00:17,604 | %u 2024-11-19T05:00:17,604 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:17,604 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:17,604 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:17,604 | | 2024-11-19T05:00:17,604 | unsigned int 2024-11-19T05:00:17,605 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T05:00:17,605 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-11-19T05:00:17,606 | ^ 2024-11-19T05:00:17,612 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-19T05:00:17,613 command_dist.c:863:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-11-19T05:00:17,613 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T05:00:17,613 | ~~^ ~~~~~~~ 2024-11-19T05:00:17,613 | | | 2024-11-19T05:00:17,613 | long unsigned int size_t {aka unsigned int} 2024-11-19T05:00:17,613 | %u 2024-11-19T05:00:17,614 command_dist.c:863:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-11-19T05:00:17,614 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T05:00:17,614 | ~~^ 2024-11-19T05:00:17,615 | | 2024-11-19T05:00:17,615 | long unsigned int 2024-11-19T05:00:17,615 | %u 2024-11-19T05:00:17,615 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-19T05:00:17,615 | ~~~~~~~~~ 2024-11-19T05:00:17,615 | | 2024-11-19T05:00:17,615 | size_t {aka unsigned int} 2024-11-19T05:00:17,616 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T05:00:17,616 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T05:00:17,616 | ~~^ 2024-11-19T05:00:17,616 | | 2024-11-19T05:00:17,616 | long unsigned int 2024-11-19T05:00:17,616 | %u 2024-11-19T05:00:17,616 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-19T05:00:17,617 865 | (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:17,617 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:17,617 | | 2024-11-19T05:00:17,617 | unsigned int 2024-11-19T05:00:17,618 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-11-19T05:00:17,618 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-11-19T05:00:17,618 | ^~~~~~~ 2024-11-19T05:00:17,618 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-11-19T05:00:17,618 809 | struct stat cbd_fcode_stat; 2024-11-19T05:00:17,618 | ^~~~~~~~~~~~~~ 2024-11-19T05:00:17,619 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-11-19T05:00:17,619 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-19T05:00:17,619 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:17,619 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-11-19T05:00:17,619 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-19T05:00:17,620 | ^~~~~~~~~~~~~~~~~ 2024-11-19T05:00:17,625 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-19T05:00:17,626 command_dist.c:1018:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-11-19T05:00:17,626 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:17,627 | ~~^ 2024-11-19T05:00:17,627 | | 2024-11-19T05:00:17,627 | long unsigned int 2024-11-19T05:00:17,627 | %u 2024-11-19T05:00:17,627 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:17,627 | ~~~~~~~ 2024-11-19T05:00:17,627 | | 2024-11-19T05:00:17,627 | size_t {aka unsigned int} 2024-11-19T05:00:17,628 command_dist.c:1018:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-11-19T05:00:17,628 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:17,628 | ~~^ 2024-11-19T05:00:17,628 | | 2024-11-19T05:00:17,628 | long unsigned int 2024-11-19T05:00:17,629 | %u 2024-11-19T05:00:17,629 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:17,629 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:17,629 | ~~~~~~~~~ 2024-11-19T05:00:17,629 | | 2024-11-19T05:00:17,629 | size_t {aka unsigned int} 2024-11-19T05:00:17,630 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T05:00:17,630 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:17,630 | ~~^ 2024-11-19T05:00:17,630 | | 2024-11-19T05:00:17,630 | long unsigned int 2024-11-19T05:00:17,630 | %u 2024-11-19T05:00:17,631 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:17,631 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:17,631 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:17,631 | | 2024-11-19T05:00:17,631 | unsigned int 2024-11-19T05:00:17,631 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:17,632 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-11-19T05:00:17,632 | ^ 2024-11-19T05:00:17,635 command_dist.c: In function ‘mco_co_dist_core’: 2024-11-19T05:00:17,635 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T05:00:17,635 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-11-19T05:00:17,636 | ^ 2024-11-19T05:00:17,641 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-11-19T05:00:17,642 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:17,642 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T05:00:17,642 | ^ 2024-11-19T05:00:17,643 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:17,644 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-19T05:00:17,644 | ^ 2024-11-19T05:00:17,649 command_dist.c: In function ‘dist_print_nobin’: 2024-11-19T05:00:17,649 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:17,649 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-11-19T05:00:17,650 | ^ 2024-11-19T05:00:17,651 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:17,652 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-19T05:00:17,652 | ^ 2024-11-19T05:00:17,653 command_dist.c:1380:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:17,653 1380 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T05:00:17,653 | ^ 2024-11-19T05:00:17,654 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:17,654 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T05:00:17,654 | ^ 2024-11-19T05:00:17,905 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-11-19T05:00:17,905 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-11-19T05:00:17,905 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-11-19T05:00:17,905 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:17,905 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-11-19T05:00:17,905 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-11-19T05:00:17,906 | ^~~~~~~~~~~~ 2024-11-19T05:00:18,631 command_dist.c: In function ‘get_dim_shuffle’: 2024-11-19T05:00:18,631 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-11-19T05:00:18,631 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-19T05:00:18,632 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:18,632 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-11-19T05:00:18,632 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-19T05:00:18,632 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,416 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-19T05:00:19,417 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:19,417 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:19,417 | ^~ ~~~~~~~~~ 2024-11-19T05:00:19,417 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T05:00:19,418 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:19,418 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,418 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:19,418 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:19,418 | ^~~~~~~~~~~~~~~ 2024-11-19T05:00:19,418 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T05:00:19,419 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:19,419 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,420 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:19,420 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:19,420 | ^~~~~~~~~~~ 2024-11-19T05:00:19,420 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-19T05:00:19,420 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:19,421 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,421 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:19,421 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:19,421 | ^~~~~ 2024-11-19T05:00:19,421 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:19,421 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:19,421 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,627 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-19T05:00:19,627 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:19,627 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:19,628 | ^~ ~~~~~~~~~ 2024-11-19T05:00:19,628 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T05:00:19,628 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:19,628 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,629 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:19,629 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:19,629 | ^~~~~~~~~~~~~~~ 2024-11-19T05:00:19,629 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T05:00:19,629 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:19,629 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,630 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:19,630 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:19,630 | ^~~~~~~~~~~~~ 2024-11-19T05:00:19,630 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T05:00:19,631 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:19,631 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,632 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:19,632 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T05:00:19,632 | ^ 2024-11-19T05:00:19,632 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-11-19T05:00:19,632 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T05:00:19,632 | ^~~~~~~~~~ 2024-11-19T05:00:19,633 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-19T05:00:19,633 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T05:00:19,633 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,633 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:19,634 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T05:00:19,634 | ^ 2024-11-19T05:00:19,634 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-11-19T05:00:19,634 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T05:00:19,634 | ^~~~~~~~~~ 2024-11-19T05:00:19,635 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-19T05:00:19,635 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T05:00:19,635 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,871 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-19T05:00:19,872 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:19,872 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:19,872 | ^~ ~~~~~~~~~ 2024-11-19T05:00:19,873 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T05:00:19,873 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:19,873 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,874 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:19,874 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:19,874 | ^~~~~~~~~~~~~~~ 2024-11-19T05:00:19,874 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T05:00:19,874 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:19,874 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,875 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:19,875 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:19,875 | ^~~~~~~~~~~~~ 2024-11-19T05:00:19,876 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T05:00:19,876 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:19,876 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,877 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:19,877 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:19,877 | ^~~~~~~~~~~ 2024-11-19T05:00:19,878 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-19T05:00:19,878 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:19,878 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:19,879 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:19,879 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:19,879 | ^~~~~ 2024-11-19T05:00:19,879 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:19,879 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:19,879 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:20,125 command_dist.c: In function ‘combine_queries’: 2024-11-19T05:00:20,126 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:20,126 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-19T05:00:20,127 | ^ 2024-11-19T05:00:20,127 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:20,128 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-19T05:00:20,128 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:20,128 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:20,129 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-19T05:00:20,129 | ^ 2024-11-19T05:00:20,129 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:20,130 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-19T05:00:20,130 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:20,132 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:20,132 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-19T05:00:20,132 | ^~ ~~~~~~~~ 2024-11-19T05:00:20,133 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T05:00:20,133 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-19T05:00:20,133 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:25,404 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o -fopenmp 2024-11-19T05:00:26,713 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_set.c -o build/temp.linux-armv7l-cpython-39/command_set.o -fopenmp 2024-11-19T05:00:28,709 command_set.c: In function ‘sketch_operate’: 2024-11-19T05:00:28,709 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T05:00:28,709 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-11-19T05:00:28,709 | ^ 2024-11-19T05:00:28,719 command_set.c: In function ‘combin_subset_pans’: 2024-11-19T05:00:28,719 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-19T05:00:28,720 457 | free(co_dstat_fpath); 2024-11-19T05:00:28,720 | ^~~~~~~~~~~~~~ 2024-11-19T05:00:28,720 In file included from kssdheaders/global_basic.h:159, 2024-11-19T05:00:28,720 from command_set.c:15: 2024-11-19T05:00:28,720 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-19T05:00:28,721 565 | extern void free (void *__ptr) __THROW; 2024-11-19T05:00:28,721 | ~~~~~~^~~~~ 2024-11-19T05:00:28,725 command_set.c: In function ‘grouping_genomes’: 2024-11-19T05:00:28,725 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-19T05:00:28,725 562 | free(co_dstat_fpath); 2024-11-19T05:00:28,725 | ^~~~~~~~~~~~~~ 2024-11-19T05:00:28,725 In file included from kssdheaders/global_basic.h:159, 2024-11-19T05:00:28,726 from command_set.c:15: 2024-11-19T05:00:28,726 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-19T05:00:28,726 565 | extern void free (void *__ptr) __THROW; 2024-11-19T05:00:28,726 | ~~~~~~^~~~~ 2024-11-19T05:00:28,843 command_set.c: In function ‘sketch_union’: 2024-11-19T05:00:28,843 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:28,844 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:28,844 | ^ 2024-11-19T05:00:28,844 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:28,844 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:28,844 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:28,844 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:28,844 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:28,845 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:28,845 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:28,845 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:28,845 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:28,845 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:28,845 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T05:00:28,845 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:28,846 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:28,846 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T05:00:28,846 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:28,957 command_set.c: In function ‘sketch_operate’: 2024-11-19T05:00:28,957 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:28,957 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T05:00:28,957 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:28,957 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:28,957 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T05:00:28,958 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:28,958 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:28,958 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T05:00:28,958 | ^~ ~~~~~~~~~~~~~~~ 2024-11-19T05:00:28,958 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-19T05:00:28,958 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T05:00:28,958 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:28,958 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:28,959 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:28,959 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:28,959 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:28,959 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:28,959 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:28,959 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:28,959 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:28,959 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:28,960 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:28,960 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:28,960 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:28,960 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:28,960 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:28,960 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:28,960 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:28,961 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:28,961 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:28,961 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:28,961 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:28,961 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:28,961 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:28,961 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:28,961 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:28,962 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:28,962 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:28,962 | ^ 2024-11-19T05:00:28,962 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:28,962 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:28,962 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,110 command_set.c: In function ‘uniq_sketch_union’: 2024-11-19T05:00:29,111 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:29,111 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:29,111 | ^ 2024-11-19T05:00:29,111 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:29,111 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:29,111 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,111 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,111 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:29,112 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:29,112 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:29,112 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:29,112 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,112 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,112 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T05:00:29,112 | ^~ ~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,113 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-19T05:00:29,113 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T05:00:29,113 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,237 command_set.c: In function ‘combin_pans’: 2024-11-19T05:00:29,238 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,238 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:29,238 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:29,238 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2024-11-19T05:00:29,238 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:29,238 | ^~~~~~~~~~ 2024-11-19T05:00:29,238 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-11-19T05:00:29,239 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:29,239 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,239 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,239 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:29,239 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:29,239 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2024-11-19T05:00:29,239 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:29,239 | ^~~~~~~~~~ 2024-11-19T05:00:29,240 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-11-19T05:00:29,240 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:29,240 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,240 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:29,240 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:29,240 | ^ 2024-11-19T05:00:29,241 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:29,241 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:29,241 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,423 command_set.c: In function ‘combin_subset_pans’: 2024-11-19T05:00:29,423 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,423 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:29,424 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:29,424 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:29,424 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:29,424 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,424 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,424 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:29,424 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:29,425 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:29,425 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:29,425 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,425 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,425 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:29,425 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:29,425 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:29,426 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:29,426 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,427 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,427 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:29,427 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:29,427 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:29,428 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:29,428 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,428 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:29,428 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:29,428 | ^ 2024-11-19T05:00:29,428 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:29,428 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:29,428 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,629 command_set.c: In function ‘grouping_genomes’: 2024-11-19T05:00:29,630 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,630 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:29,630 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:29,630 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:29,630 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:29,630 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,631 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,631 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:29,631 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:29,631 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:29,631 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:29,631 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,633 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,633 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:29,633 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:29,633 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:29,634 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:29,634 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,634 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:29,635 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:29,635 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:29,635 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:29,635 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:29,635 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:29,635 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:29,636 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:29,636 | ^ 2024-11-19T05:00:29,636 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:29,636 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:29,636 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:30,120 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-39/command_shuffle.o -fopenmp 2024-11-19T05:00:30,435 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c global_basic.c -o build/temp.linux-armv7l-cpython-39/global_basic.o -fopenmp 2024-11-19T05:00:30,617 global_basic.c: In function ‘organize_infile_list’: 2024-11-19T05:00:30,617 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-11-19T05:00:30,617 195 | while (isspace(*buf)) buf++; 2024-11-19T05:00:30,618 | ^~~~~~~ 2024-11-19T05:00:30,618 global_basic.c:201:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-11-19T05:00:30,618 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-19T05:00:30,618 | ~~^ 2024-11-19T05:00:30,618 | | 2024-11-19T05:00:30,618 | long unsigned int 2024-11-19T05:00:30,619 | %u 2024-11-19T05:00:30,619 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-19T05:00:30,619 | ~~~~~~~~~~~ 2024-11-19T05:00:30,619 | | 2024-11-19T05:00:30,619 | size_t {aka unsigned int} 2024-11-19T05:00:30,619 global_basic.c:233:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-11-19T05:00:30,619 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-19T05:00:30,620 | ~~^ 2024-11-19T05:00:30,620 | | 2024-11-19T05:00:30,620 | long unsigned int 2024-11-19T05:00:30,620 | %u 2024-11-19T05:00:30,620 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-19T05:00:30,620 | ~~~~~~~~~~~ 2024-11-19T05:00:30,620 | | 2024-11-19T05:00:30,621 | size_t {aka unsigned int} 2024-11-19T05:00:31,330 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-39/iseq2comem.o -fopenmp 2024-11-19T05:00:31,928 iseq2comem.c: In function ‘reads2mco’: 2024-11-19T05:00:31,928 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,928 156 | if (base > TL) { 2024-11-19T05:00:31,928 | ^ 2024-11-19T05:00:31,929 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,929 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:31,929 | ^~ 2024-11-19T05:00:31,929 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,929 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:31,929 | ^ 2024-11-19T05:00:31,930 iseq2comem.c: In function ‘fasta2co’: 2024-11-19T05:00:31,930 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,931 239 | if (base > TL) { 2024-11-19T05:00:31,931 | ^ 2024-11-19T05:00:31,931 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,931 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:31,931 | ^~ 2024-11-19T05:00:31,931 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,932 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:31,932 | ^ 2024-11-19T05:00:31,932 iseq2comem.c: In function ‘fastq2co’: 2024-11-19T05:00:31,932 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-11-19T05:00:31,932 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-11-19T05:00:31,932 | ^~ 2024-11-19T05:00:31,933 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,933 318 | if (base > TL) { 2024-11-19T05:00:31,934 | ^ 2024-11-19T05:00:31,934 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,934 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:31,934 | ^~ 2024-11-19T05:00:31,934 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,934 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:31,934 | ^ 2024-11-19T05:00:31,935 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,935 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-11-19T05:00:31,935 | ^ 2024-11-19T05:00:31,936 iseq2comem.c: In function ‘fastq2koc’: 2024-11-19T05:00:31,936 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,937 402 | if (base > TL) { 2024-11-19T05:00:31,937 | ^ 2024-11-19T05:00:31,937 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,937 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:31,937 | ^~ 2024-11-19T05:00:31,937 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,937 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:31,938 | ^ 2024-11-19T05:00:31,942 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-11-19T05:00:31,943 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,943 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:31,943 | ^~ 2024-11-19T05:00:31,943 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:31,943 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:31,943 | ^ 2024-11-19T05:00:33,120 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-11-19T05:00:33,229 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mytime.c -o build/temp.linux-armv7l-cpython-39/mytime.o -fopenmp 2024-11-19T05:00:33,794 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c pykssd.c -o build/temp.linux-armv7l-cpython-39/pykssd.o -fopenmp 2024-11-19T05:00:34,221 pykssd.c: In function ‘py_dist_dispatch’: 2024-11-19T05:00:34,222 pykssd.c:329:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-11-19T05:00:34,222 329 | int state1 = dist_dispatch(&dist_opt_val1); 2024-11-19T05:00:34,222 | ^~~~~~ 2024-11-19T05:00:34,222 pykssd.c:386:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-11-19T05:00:34,223 386 | int state2 = dist_dispatch(&dist_opt_val2); 2024-11-19T05:00:34,223 | ^~~~~~ 2024-11-19T05:00:34,224 pykssd.c:510:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-11-19T05:00:34,224 510 | int state4 = dist_dispatch(&dist_opt_val4); 2024-11-19T05:00:34,224 | ^~~~~~ 2024-11-19T05:00:34,367 pykssd.c: In function ‘rename_file’: 2024-11-19T05:00:34,368 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-11-19T05:00:34,368 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-11-19T05:00:34,368 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:34,368 pykssd.c:41:15: note: length computed here 2024-11-19T05:00:34,368 41 | int len = strlen(p1); 2024-11-19T05:00:34,368 | ^~~~~~~~~~ 2024-11-19T05:00:34,790 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/co2mco.o build/temp.linux-armv7l-cpython-39/command_composite.o build/temp.linux-armv7l-cpython-39/command_dist.o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o build/temp.linux-armv7l-cpython-39/command_set.o build/temp.linux-armv7l-cpython-39/command_shuffle.o build/temp.linux-armv7l-cpython-39/global_basic.o build/temp.linux-armv7l-cpython-39/iseq2comem.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/mytime.o build/temp.linux-armv7l-cpython-39/pykssd.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-11-19T05:00:35,392 building 'nj' extension 2024-11-19T05:00:35,396 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c align.c -o build/temp.linux-armv7l-cpython-39/align.o 2024-11-19T05:00:35,838 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c buildtree.c -o build/temp.linux-armv7l-cpython-39/buildtree.o 2024-11-19T05:00:35,978 buildtree.c: In function ‘UPGMA_buildtree’: 2024-11-19T05:00:35,978 buildtree.c:716:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:35,978 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-11-19T05:00:35,978 | ^~ 2024-11-19T05:00:35,978 buildtree.c:716:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:35,978 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-11-19T05:00:35,979 | ^~ 2024-11-19T05:00:36,542 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c cluster.c -o build/temp.linux-armv7l-cpython-39/cluster.o 2024-11-19T05:00:37,749 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c distancemat.c -o build/temp.linux-armv7l-cpython-39/distancemat.o 2024-11-19T05:00:37,905 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-11-19T05:00:37,905 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:37,906 226 | for( i=0; i < dest->size; i++) { 2024-11-19T05:00:37,906 | ^ 2024-11-19T05:00:37,906 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-11-19T05:00:37,906 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:37,906 260 | for( i=0; i < mat->size; i++) { 2024-11-19T05:00:37,906 | ^ 2024-11-19T05:00:37,906 distancemat.c: In function ‘print_DistanceMatrix’: 2024-11-19T05:00:37,907 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:37,907 349 | for(row=0; row < mat->size; row++) { 2024-11-19T05:00:37,907 | ^ 2024-11-19T05:00:37,907 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-11-19T05:00:37,907 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-11-19T05:00:37,908 410 | while(c = fgetc(handle)) { 2024-11-19T05:00:37,908 | ^ 2024-11-19T05:00:38,457 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c pynj.c -o build/temp.linux-armv7l-cpython-39/pynj.o 2024-11-19T05:00:43,655 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c sequence.c -o build/temp.linux-armv7l-cpython-39/sequence.o 2024-11-19T05:00:43,945 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c tree.c -o build/temp.linux-armv7l-cpython-39/tree.o 2024-11-19T05:00:46,422 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c util.c -o build/temp.linux-armv7l-cpython-39/util.o 2024-11-19T05:00:46,640 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/align.o build/temp.linux-armv7l-cpython-39/buildtree.o build/temp.linux-armv7l-cpython-39/cluster.o build/temp.linux-armv7l-cpython-39/distancemat.o build/temp.linux-armv7l-cpython-39/pynj.o build/temp.linux-armv7l-cpython-39/sequence.o build/temp.linux-armv7l-cpython-39/tree.o build/temp.linux-armv7l-cpython-39/util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so 2024-11-19T05:00:47,235 building 'dnj' extension 2024-11-19T05:00:47,240 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c bytescale.c -o build/temp.linux-armv7l-cpython-39/bytescale.o -fopenmp 2024-11-19T05:00:47,529 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c dnj.c -o build/temp.linux-armv7l-cpython-39/dnj.o -fopenmp 2024-11-19T05:00:47,672 dnj.c: In function ‘minQpair’: 2024-11-19T05:00:47,673 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,673 70 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,673 | ^~~ 2024-11-19T05:00:47,674 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,674 126 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,674 | ^~~ 2024-11-19T05:00:47,674 dnj.c: In function ‘maxQpair’: 2024-11-19T05:00:47,674 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,674 157 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,675 | ^~~ 2024-11-19T05:00:47,675 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,675 213 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,675 | ^~~ 2024-11-19T05:00:47,675 dnj.c: In function ‘UPGMApair’: 2024-11-19T05:00:47,676 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,676 237 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,676 | ^~~ 2024-11-19T05:00:47,676 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,676 284 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,677 | ^~~ 2024-11-19T05:00:47,677 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,677 291 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,677 | ^~~ 2024-11-19T05:00:47,678 dnj.c: In function ‘minQrow’: 2024-11-19T05:00:47,678 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,678 374 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,678 | ^~~ 2024-11-19T05:00:47,679 dnj.c: In function ‘maxQrow’: 2024-11-19T05:00:47,679 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,680 435 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,680 | ^~~ 2024-11-19T05:00:47,680 dnj.c: In function ‘UPGMArow’: 2024-11-19T05:00:47,680 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,681 488 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,681 | ^~~ 2024-11-19T05:00:47,681 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,681 494 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,681 | ^~~ 2024-11-19T05:00:47,682 dnj.c: In function ‘minQ_thread’: 2024-11-19T05:00:47,682 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:47,682 553 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:47,682 | ^~~ 2024-11-19T05:00:48,854 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c filebuff.c -o build/temp.linux-armv7l-cpython-39/filebuff.o -fopenmp 2024-11-19T05:00:49,203 filebuff.c: In function ‘BuffgzFileBuff’: 2024-11-19T05:00:49,203 filebuff.c:99:47: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:49,203 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-11-19T05:00:49,204 | ^~ 2024-11-19T05:00:49,528 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c hclust.c -o build/temp.linux-armv7l-cpython-39/hclust.o -fopenmp 2024-11-19T05:00:49,669 hclust.c: In function ‘minQ’: 2024-11-19T05:00:49,669 hclust.c:364:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:49,669 364 | while(++i < Q->n) { 2024-11-19T05:00:49,670 | ^ 2024-11-19T05:00:49,670 hclust.c:377:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:49,670 377 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:49,670 | ^~~ 2024-11-19T05:00:49,670 hclust.c: In function ‘maxQ’: 2024-11-19T05:00:49,670 hclust.c:394:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:49,670 394 | while(++i < Q->n) { 2024-11-19T05:00:49,671 | ^ 2024-11-19T05:00:49,671 hclust.c:407:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:49,671 407 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:49,671 | ^~~ 2024-11-19T05:00:51,843 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c matrix.c -o build/temp.linux-armv7l-cpython-39/matrix.o -fopenmp 2024-11-19T05:00:52,266 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-11-19T05:00:52,266 matrix.c:538:9: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:52,266 538 | if(pos != n) { 2024-11-19T05:00:52,267 | ^~ 2024-11-19T05:00:53,147 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-11-19T05:00:53,249 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c nj.c -o build/temp.linux-armv7l-cpython-39/nj.o -fopenmp 2024-11-19T05:00:53,427 nj.c: In function ‘initQ’: 2024-11-19T05:00:53,428 nj.c:243:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:53,428 243 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:53,428 | ^~~ 2024-11-19T05:00:53,429 nj.c: In function ‘initQ_MN’: 2024-11-19T05:00:53,430 nj.c:358:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:53,430 358 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:53,430 | ^~~ 2024-11-19T05:00:53,433 nj.c: In function ‘minD’: 2024-11-19T05:00:53,433 nj.c:559:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:53,433 559 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:53,433 | ^~~ 2024-11-19T05:00:53,435 nj.c: In function ‘maxD’: 2024-11-19T05:00:53,435 nj.c:642:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:53,435 642 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:53,435 | ^~~ 2024-11-19T05:00:53,438 nj.c: In function ‘minPair’: 2024-11-19T05:00:53,438 nj.c:826:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:00:53,438 826 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:00:53,439 | ^~~ 2024-11-19T05:00:55,463 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c nwck.c -o build/temp.linux-armv7l-cpython-39/nwck.o -fopenmp 2024-11-19T05:00:58,344 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pherror.c -o build/temp.linux-armv7l-cpython-39/pherror.o -fopenmp 2024-11-19T05:00:58,442 pherror.c: In function ‘cfread’: 2024-11-19T05:00:58,442 pherror.c:58:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:58,442 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-11-19T05:00:58,442 | ^~ 2024-11-19T05:00:58,534 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c phy.c -o build/temp.linux-armv7l-cpython-39/phy.o -fopenmp 2024-11-19T05:01:04,000 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pydnj.c -o build/temp.linux-armv7l-cpython-39/pydnj.o -fopenmp 2024-11-19T05:01:04,556 In file included from pydnj.c:11: 2024-11-19T05:01:04,556 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-11-19T05:01:04,556 20 | #define _XOPEN_SOURCE 600 2024-11-19T05:01:04,556 | 2024-11-19T05:01:04,556 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-11-19T05:01:04,556 from /usr/include/limits.h:26, 2024-11-19T05:01:04,557 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:195, 2024-11-19T05:01:04,557 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/syslimits.h:7, 2024-11-19T05:01:04,557 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:34, 2024-11-19T05:01:04,557 from /usr/include/python3.9/Python.h:11, 2024-11-19T05:01:04,557 from pydnj.c:1: 2024-11-19T05:01:04,557 /usr/include/features.h:207: note: this is the location of the previous definition 2024-11-19T05:01:04,557 207 | # define _XOPEN_SOURCE 700 2024-11-19T05:01:04,558 | 2024-11-19T05:01:04,571 pydnj.c: In function ‘py_build’: 2024-11-19T05:01:04,571 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-11-19T05:01:04,571 165 | p = omp_get_num_procs(); 2024-11-19T05:01:04,572 | ^~~~~~~~~~~~~~~~~ 2024-11-19T05:01:04,761 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c qseqs.c -o build/temp.linux-armv7l-cpython-39/qseqs.o -fopenmp 2024-11-19T05:01:04,952 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c str.c -o build/temp.linux-armv7l-cpython-39/str.o -fopenmp 2024-11-19T05:01:05,062 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c tmp.c -o build/temp.linux-armv7l-cpython-39/tmp.o -fopenmp 2024-11-19T05:01:05,264 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c vector.c -o build/temp.linux-armv7l-cpython-39/vector.o -fopenmp 2024-11-19T05:01:06,882 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/bytescale.o build/temp.linux-armv7l-cpython-39/dnj.o build/temp.linux-armv7l-cpython-39/filebuff.o build/temp.linux-armv7l-cpython-39/hclust.o build/temp.linux-armv7l-cpython-39/matrix.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/nj.o build/temp.linux-armv7l-cpython-39/nwck.o build/temp.linux-armv7l-cpython-39/pherror.o build/temp.linux-armv7l-cpython-39/phy.o build/temp.linux-armv7l-cpython-39/pydnj.o build/temp.linux-armv7l-cpython-39/qseqs.o build/temp.linux-armv7l-cpython-39/str.o build/temp.linux-armv7l-cpython-39/tmp.o build/temp.linux-armv7l-cpython-39/vector.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-11-19T05:01:07,740 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-11-19T05:01:07,741 !! 2024-11-19T05:01:07,741 ******************************************************************************** 2024-11-19T05:01:07,741 Please avoid running ``setup.py`` directly. 2024-11-19T05:01:07,741 Instead, use pypa/build, pypa/installer or other 2024-11-19T05:01:07,742 standards-based tools. 2024-11-19T05:01:07,742 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-11-19T05:01:07,742 ******************************************************************************** 2024-11-19T05:01:07,742 !! 2024-11-19T05:01:07,742 self.initialize_options() 2024-11-19T05:01:07,770 installing to build/bdist.linux-armv7l/wheel 2024-11-19T05:01:07,771 running install 2024-11-19T05:01:07,797 running install_lib 2024-11-19T05:01:07,827 creating build/bdist.linux-armv7l/wheel 2024-11-19T05:01:07,830 copying build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:01:07,837 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:01:11,366 copying build/lib.linux-armv7l-cpython-39/kssdtree.py -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:01:11,372 copying build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:01:11,397 copying build/lib.linux-armv7l-cpython-39/toolutils.py -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:01:11,401 running install_egg_info 2024-11-19T05:01:11,464 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/./kssdtree-2.0.3-py3.9.egg-info 2024-11-19T05:01:11,484 running install_scripts 2024-11-19T05:01:11,539 creating build/bdist.linux-armv7l/wheel/kssdtree-2.0.3.dist-info/WHEEL 2024-11-19T05:01:11,543 creating '/tmp/pip-wheel-gw8zceqg/kssdtree-2.0.3-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-11-19T05:01:11,623 adding 'dnj.cpython-39-arm-linux-gnueabihf.so' 2024-11-19T05:01:11,718 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2024-11-19T05:01:11,724 adding 'kssdtree.py' 2024-11-19T05:01:11,747 adding 'nj.cpython-39-arm-linux-gnueabihf.so' 2024-11-19T05:01:11,750 adding 'toolutils.py' 2024-11-19T05:01:11,753 adding 'kssdtree-2.0.3.dist-info/METADATA' 2024-11-19T05:01:11,755 adding 'kssdtree-2.0.3.dist-info/WHEEL' 2024-11-19T05:01:11,756 adding 'kssdtree-2.0.3.dist-info/dependency_links.txt' 2024-11-19T05:01:11,757 adding 'kssdtree-2.0.3.dist-info/top_level.txt' 2024-11-19T05:01:11,758 adding 'kssdtree-2.0.3.dist-info/RECORD' 2024-11-19T05:01:11,770 removing build/bdist.linux-armv7l/wheel 2024-11-19T05:01:11,903 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-11-19T05:01:11,911 Created wheel for kssdtree: filename=kssdtree-2.0.3-cp39-cp39-linux_armv7l.whl size=376808 sha256=f629766f3426bb8a83c6f4adca8b02b03cb85452c129c9694cef65efd715fabd 2024-11-19T05:01:11,912 Stored in directory: /tmp/pip-ephem-wheel-cache-5pl464pn/wheels/1b/d1/86/61a758b2f2666f2f0018da0f80ee10a943d68e5fc0feaa5259 2024-11-19T05:01:11,923 Successfully built kssdtree 2024-11-19T05:01:11,952 Removed build tracker: '/tmp/pip-build-tracker-quh_ir_h'