2024-11-19T05:00:34,070 Disabling truststore because Python version isn't 3.10+ 2024-11-19T05:00:34,571 Created temporary directory: /tmp/pip-build-tracker-iqladn81 2024-11-19T05:00:34,572 Initialized build tracking at /tmp/pip-build-tracker-iqladn81 2024-11-19T05:00:34,572 Created build tracker: /tmp/pip-build-tracker-iqladn81 2024-11-19T05:00:34,572 Entered build tracker: /tmp/pip-build-tracker-iqladn81 2024-11-19T05:00:34,573 Created temporary directory: /tmp/pip-wheel-7hcmcv9h 2024-11-19T05:00:34,578 Created temporary directory: /tmp/pip-ephem-wheel-cache-5fctp05b 2024-11-19T05:00:34,641 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-11-19T05:00:34,645 2 location(s) to search for versions of kssdtree: 2024-11-19T05:00:34,645 * https://pypi.org/simple/kssdtree/ 2024-11-19T05:00:34,645 * https://www.piwheels.org/simple/kssdtree/ 2024-11-19T05:00:34,646 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-11-19T05:00:34,647 Getting page https://pypi.org/simple/kssdtree/ 2024-11-19T05:00:34,649 Found index url https://pypi.org/simple/ 2024-11-19T05:00:34,675 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-11-19T05:00:34,679 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 2024-11-19T05:00:34,680 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 2024-11-19T05:00:34,680 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 2024-11-19T05:00:34,681 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 2024-11-19T05:00:34,681 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 2024-11-19T05:00:34,681 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 2024-11-19T05:00:34,682 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 2024-11-19T05:00:34,682 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 2024-11-19T05:00:34,683 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 2024-11-19T05:00:34,683 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 2024-11-19T05:00:34,684 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 2024-11-19T05:00:34,684 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 2024-11-19T05:00:34,684 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 2024-11-19T05:00:34,685 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-11-19T05:00:34,685 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-11-19T05:00:34,686 Found index url https://www.piwheels.org/simple/ 2024-11-19T05:00:34,730 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-11-19T05:00:34,745 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/) 2024-11-19T05:00:34,745 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/) 2024-11-19T05:00:34,746 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/) 2024-11-19T05:00:34,746 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/) 2024-11-19T05:00:34,746 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/) 2024-11-19T05:00:34,746 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/) 2024-11-19T05:00:34,746 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/) 2024-11-19T05:00:34,747 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/) 2024-11-19T05:00:34,747 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/) 2024-11-19T05:00:34,747 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/) 2024-11-19T05:00:34,747 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/) 2024-11-19T05:00:34,747 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T05:00:34,748 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/) 2024-11-19T05:00:34,748 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/) 2024-11-19T05:00:34,749 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/) 2024-11-19T05:00:34,749 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T05:00:34,750 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/) 2024-11-19T05:00:34,750 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/) 2024-11-19T05:00:34,750 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/) 2024-11-19T05:00:34,750 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T05:00:34,751 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/) 2024-11-19T05:00:34,751 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/) 2024-11-19T05:00:34,751 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/) 2024-11-19T05:00:34,751 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-11-19T05:00:34,752 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/) 2024-11-19T05:00:34,753 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/) 2024-11-19T05:00:34,753 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/) 2024-11-19T05:00:34,753 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/) 2024-11-19T05:00:34,753 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/) 2024-11-19T05:00:34,753 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/) 2024-11-19T05:00:34,753 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/) 2024-11-19T05:00:34,754 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/) 2024-11-19T05:00:34,754 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/) 2024-11-19T05:00:34,754 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/) 2024-11-19T05:00:34,754 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/) 2024-11-19T05:00:34,754 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/) 2024-11-19T05:00:34,755 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/) 2024-11-19T05:00:34,755 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/) 2024-11-19T05:00:34,755 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/) 2024-11-19T05:00:34,755 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/) 2024-11-19T05:00:34,755 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/) 2024-11-19T05:00:34,756 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/) 2024-11-19T05:00:34,756 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-11-19T05:00:34,756 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-11-19T05:00:34,774 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-11-19T05:00:34,776 Collecting kssdtree==2.0.4 2024-11-19T05:00:34,778 Created temporary directory: /tmp/pip-unpack-oafmvsa0 2024-11-19T05:00:34,794 Downloading kssdtree-2.0.4.tar.gz (112 kB) 2024-11-19T05:00:34,995 Added kssdtree==2.0.4 from https://files.pythonhosted.org/packages/fc/8d/d3790baa2f2f0a01c913005b94a82dc13ef601e7015e662ccff94bb1b458/kssdtree-2.0.4.tar.gz to build tracker '/tmp/pip-build-tracker-iqladn81' 2024-11-19T05:00:34,997 Running setup.py (path:/tmp/pip-wheel-7hcmcv9h/kssdtree_53f8c4ca3bf547c3b0a3480852ee5518/setup.py) egg_info for package kssdtree 2024-11-19T05:00:34,998 Created temporary directory: /tmp/pip-pip-egg-info-lkcm_17b 2024-11-19T05:00:34,998 Preparing metadata (setup.py): started 2024-11-19T05:00:34,999 Running command python setup.py egg_info 2024-11-19T05:00:36,193 running egg_info 2024-11-19T05:00:36,225 creating /tmp/pip-pip-egg-info-lkcm_17b/kssdtree.egg-info 2024-11-19T05:00:36,226 writing /tmp/pip-pip-egg-info-lkcm_17b/kssdtree.egg-info/PKG-INFO 2024-11-19T05:00:36,231 writing dependency_links to /tmp/pip-pip-egg-info-lkcm_17b/kssdtree.egg-info/dependency_links.txt 2024-11-19T05:00:36,233 writing requirements to /tmp/pip-pip-egg-info-lkcm_17b/kssdtree.egg-info/requires.txt 2024-11-19T05:00:36,234 writing top-level names to /tmp/pip-pip-egg-info-lkcm_17b/kssdtree.egg-info/top_level.txt 2024-11-19T05:00:36,236 writing manifest file '/tmp/pip-pip-egg-info-lkcm_17b/kssdtree.egg-info/SOURCES.txt' 2024-11-19T05:00:36,363 reading manifest file '/tmp/pip-pip-egg-info-lkcm_17b/kssdtree.egg-info/SOURCES.txt' 2024-11-19T05:00:36,364 reading manifest template 'MANIFEST.in' 2024-11-19T05:00:36,387 writing manifest file '/tmp/pip-pip-egg-info-lkcm_17b/kssdtree.egg-info/SOURCES.txt' 2024-11-19T05:00:36,475 Preparing metadata (setup.py): finished with status 'done' 2024-11-19T05:00:36,480 Source in /tmp/pip-wheel-7hcmcv9h/kssdtree_53f8c4ca3bf547c3b0a3480852ee5518 has version 2.0.4, which satisfies requirement kssdtree==2.0.4 from https://files.pythonhosted.org/packages/fc/8d/d3790baa2f2f0a01c913005b94a82dc13ef601e7015e662ccff94bb1b458/kssdtree-2.0.4.tar.gz 2024-11-19T05:00:36,481 Removed kssdtree==2.0.4 from https://files.pythonhosted.org/packages/fc/8d/d3790baa2f2f0a01c913005b94a82dc13ef601e7015e662ccff94bb1b458/kssdtree-2.0.4.tar.gz from build tracker '/tmp/pip-build-tracker-iqladn81' 2024-11-19T05:00:36,488 Created temporary directory: /tmp/pip-unpack-q1fgda_9 2024-11-19T05:00:36,489 Created temporary directory: /tmp/pip-unpack-qn8odwv5 2024-11-19T05:00:36,489 Building wheels for collected packages: kssdtree 2024-11-19T05:00:36,494 Created temporary directory: /tmp/pip-wheel-6__zqsmz 2024-11-19T05:00:36,495 Building wheel for kssdtree (setup.py): started 2024-11-19T05:00:36,496 Destination directory: /tmp/pip-wheel-6__zqsmz 2024-11-19T05:00:36,496 Running command python setup.py bdist_wheel 2024-11-19T05:00:38,473 running bdist_wheel 2024-11-19T05:00:38,626 running build 2024-11-19T05:00:38,627 running build_py 2024-11-19T05:00:38,658 creating build/lib.linux-armv7l-cpython-39 2024-11-19T05:00:38,661 copying kssdtree.py -> build/lib.linux-armv7l-cpython-39 2024-11-19T05:00:38,664 copying toolutils.py -> build/lib.linux-armv7l-cpython-39 2024-11-19T05:00:38,666 running egg_info 2024-11-19T05:00:38,697 writing kssdtree.egg-info/PKG-INFO 2024-11-19T05:00:38,701 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-11-19T05:00:38,703 writing requirements to kssdtree.egg-info/requires.txt 2024-11-19T05:00:38,704 writing top-level names to kssdtree.egg-info/top_level.txt 2024-11-19T05:00:38,736 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-11-19T05:00:38,742 reading manifest template 'MANIFEST.in' 2024-11-19T05:00:38,765 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-11-19T05:00:38,767 running build_ext 2024-11-19T05:00:38,775 building 'kssd' extension 2024-11-19T05:00:38,776 creating build/temp.linux-armv7l-cpython-39 2024-11-19T05:00:38,778 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 2024-11-19T05:00:39,032 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-11-19T05:00:39,032 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:39,033 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-11-19T05:00:39,033 | ^ 2024-11-19T05:00:39,035 co2mco.c: In function ‘co2unitllmco’: 2024-11-19T05:00:39,035 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:39,036 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-11-19T05:00:39,036 | ^ 2024-11-19T05:00:43,697 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 2024-11-19T05:00:44,059 command_composite.c: In function ‘get_species_abundance’: 2024-11-19T05:00:44,059 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-19T05:00:44,059 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-11-19T05:00:44,059 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:44,059 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-19T05:00:44,060 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-11-19T05:00:44,060 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:44,060 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:44,060 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T05:00:44,060 | ^ 2024-11-19T05:00:44,060 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:44,060 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T05:00:44,061 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:44,061 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:44,061 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T05:00:44,061 | ^ 2024-11-19T05:00:44,061 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:44,061 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T05:00:44,061 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:44,062 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:44,062 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:44,062 | ^ 2024-11-19T05:00:44,062 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:44,062 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:44,062 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:44,062 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:44,063 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T05:00:44,063 | ^ 2024-11-19T05:00:44,063 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:44,063 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T05:00:44,063 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:44,063 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:44,063 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:44,064 | ^ 2024-11-19T05:00:44,064 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-11-19T05:00:44,064 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:44,064 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:44,300 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 2024-11-19T05:00:46,518 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-19T05:00:46,519 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=] 2024-11-19T05:00:46,519 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:46,519 | ~~^ 2024-11-19T05:00:46,519 | | 2024-11-19T05:00:46,519 | long unsigned int 2024-11-19T05:00:46,520 | %u 2024-11-19T05:00:46,520 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:46,520 | ~~~~~~~ 2024-11-19T05:00:46,520 | | 2024-11-19T05:00:46,520 | size_t {aka unsigned int} 2024-11-19T05:00:46,520 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=] 2024-11-19T05:00:46,520 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:46,520 | ~~^ 2024-11-19T05:00:46,520 | | 2024-11-19T05:00:46,521 | long unsigned int 2024-11-19T05:00:46,521 | %u 2024-11-19T05:00:46,521 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:46,521 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:46,521 | ~~~~~~~~~ 2024-11-19T05:00:46,521 | | 2024-11-19T05:00:46,521 | size_t {aka unsigned int} 2024-11-19T05:00:46,522 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T05:00:46,522 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:46,522 | ~~^ 2024-11-19T05:00:46,522 | | 2024-11-19T05:00:46,522 | long unsigned int 2024-11-19T05:00:46,522 | %u 2024-11-19T05:00:46,522 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:46,523 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:46,523 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:46,523 | | 2024-11-19T05:00:46,523 | unsigned int 2024-11-19T05:00:46,524 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T05:00:46,524 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-11-19T05:00:46,524 | ^ 2024-11-19T05:00:46,530 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-19T05:00:46,531 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=] 2024-11-19T05:00:46,531 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T05:00:46,531 | ~~^ ~~~~~~~ 2024-11-19T05:00:46,531 | | | 2024-11-19T05:00:46,532 | long unsigned int size_t {aka unsigned int} 2024-11-19T05:00:46,532 | %u 2024-11-19T05:00:46,533 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=] 2024-11-19T05:00:46,533 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T05:00:46,533 | ~~^ 2024-11-19T05:00:46,533 | | 2024-11-19T05:00:46,533 | long unsigned int 2024-11-19T05:00:46,533 | %u 2024-11-19T05:00:46,533 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-19T05:00:46,533 | ~~~~~~~~~ 2024-11-19T05:00:46,534 | | 2024-11-19T05:00:46,534 | size_t {aka unsigned int} 2024-11-19T05:00:46,534 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T05:00:46,534 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T05:00:46,534 | ~~^ 2024-11-19T05:00:46,534 | | 2024-11-19T05:00:46,535 | long unsigned int 2024-11-19T05:00:46,535 | %u 2024-11-19T05:00:46,535 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-19T05:00:46,535 865 | (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:46,535 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:46,535 | | 2024-11-19T05:00:46,535 | unsigned int 2024-11-19T05:00:46,536 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-11-19T05:00:46,536 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-11-19T05:00:46,536 | ^~~~~~~ 2024-11-19T05:00:46,537 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-11-19T05:00:46,537 809 | struct stat cbd_fcode_stat; 2024-11-19T05:00:46,537 | ^~~~~~~~~~~~~~ 2024-11-19T05:00:46,537 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-11-19T05:00:46,537 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-19T05:00:46,537 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:46,538 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-11-19T05:00:46,538 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-19T05:00:46,538 | ^~~~~~~~~~~~~~~~~ 2024-11-19T05:00:46,543 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-19T05:00:46,545 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=] 2024-11-19T05:00:46,545 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:46,545 | ~~^ 2024-11-19T05:00:46,545 | | 2024-11-19T05:00:46,545 | long unsigned int 2024-11-19T05:00:46,545 | %u 2024-11-19T05:00:46,545 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:46,545 | ~~~~~~~ 2024-11-19T05:00:46,546 | | 2024-11-19T05:00:46,546 | size_t {aka unsigned int} 2024-11-19T05:00:46,546 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=] 2024-11-19T05:00:46,547 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:46,547 | ~~^ 2024-11-19T05:00:46,547 | | 2024-11-19T05:00:46,547 | long unsigned int 2024-11-19T05:00:46,547 | %u 2024-11-19T05:00:46,547 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:46,547 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:46,547 | ~~~~~~~~~ 2024-11-19T05:00:46,547 | | 2024-11-19T05:00:46,548 | size_t {aka unsigned int} 2024-11-19T05:00:46,548 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T05:00:46,548 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:46,548 | ~~^ 2024-11-19T05:00:46,549 | | 2024-11-19T05:00:46,549 | long unsigned int 2024-11-19T05:00:46,549 | %u 2024-11-19T05:00:46,549 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:46,549 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:46,549 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:46,549 | | 2024-11-19T05:00:46,549 | unsigned int 2024-11-19T05:00:46,550 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:46,550 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-11-19T05:00:46,550 | ^ 2024-11-19T05:00:46,553 command_dist.c: In function ‘mco_co_dist_core’: 2024-11-19T05:00:46,554 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T05:00:46,554 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-11-19T05:00:46,554 | ^ 2024-11-19T05:00:46,559 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-11-19T05:00:46,560 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:46,560 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T05:00:46,560 | ^ 2024-11-19T05:00:46,562 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:46,562 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-19T05:00:46,562 | ^ 2024-11-19T05:00:46,567 command_dist.c: In function ‘dist_print_nobin’: 2024-11-19T05:00:46,568 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:46,568 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-11-19T05:00:46,568 | ^ 2024-11-19T05:00:46,570 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:46,570 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-19T05:00:46,570 | ^ 2024-11-19T05:00:46,571 command_dist.c:1380:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:46,572 1380 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T05:00:46,572 | ^ 2024-11-19T05:00:46,572 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:46,572 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T05:00:46,573 | ^ 2024-11-19T05:00:46,823 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-11-19T05:00:46,823 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-11-19T05:00:46,823 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-11-19T05:00:46,823 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:46,823 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-11-19T05:00:46,824 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-11-19T05:00:46,824 | ^~~~~~~~~~~~ 2024-11-19T05:00:47,545 command_dist.c: In function ‘get_dim_shuffle’: 2024-11-19T05:00:47,545 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-11-19T05:00:47,545 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-19T05:00:47,545 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:47,546 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-11-19T05:00:47,546 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-19T05:00:47,546 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,326 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-19T05:00:48,327 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:48,327 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:48,327 | ^~ ~~~~~~~~~ 2024-11-19T05:00:48,327 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T05:00:48,327 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:48,327 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,328 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:48,328 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:48,328 | ^~~~~~~~~~~~~~~ 2024-11-19T05:00:48,328 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T05:00:48,328 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:48,329 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,330 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:48,330 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:48,330 | ^~~~~~~~~~~ 2024-11-19T05:00:48,330 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-19T05:00:48,330 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:48,330 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,330 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:48,331 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:48,331 | ^~~~~ 2024-11-19T05:00:48,331 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:48,331 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:48,331 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,537 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-19T05:00:48,538 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:48,538 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:48,538 | ^~ ~~~~~~~~~ 2024-11-19T05:00:48,538 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T05:00:48,538 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:48,538 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,539 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:48,539 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:48,539 | ^~~~~~~~~~~~~~~ 2024-11-19T05:00:48,539 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T05:00:48,539 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:48,540 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,540 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:48,540 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:48,540 | ^~~~~~~~~~~~~ 2024-11-19T05:00:48,541 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T05:00:48,541 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:48,541 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,542 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:48,542 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T05:00:48,542 | ^ 2024-11-19T05:00:48,542 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-11-19T05:00:48,542 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T05:00:48,543 | ^~~~~~~~~~ 2024-11-19T05:00:48,543 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-19T05:00:48,543 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T05:00:48,543 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,544 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:48,544 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T05:00:48,544 | ^ 2024-11-19T05:00:48,544 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-11-19T05:00:48,544 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T05:00:48,544 | ^~~~~~~~~~ 2024-11-19T05:00:48,545 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-19T05:00:48,545 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T05:00:48,545 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,780 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-19T05:00:48,781 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:48,781 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:48,781 | ^~ ~~~~~~~~~ 2024-11-19T05:00:48,782 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T05:00:48,782 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:48,782 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,783 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:48,783 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:48,783 | ^~~~~~~~~~~~~~~ 2024-11-19T05:00:48,783 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T05:00:48,784 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:48,784 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,784 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:48,784 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:48,785 | ^~~~~~~~~~~~~ 2024-11-19T05:00:48,785 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T05:00:48,785 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:48,785 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,786 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:48,787 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:48,787 | ^~~~~~~~~~~ 2024-11-19T05:00:48,787 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-19T05:00:48,787 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:48,787 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:48,788 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:48,788 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:48,788 | ^~~~~ 2024-11-19T05:00:48,788 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:48,789 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:48,789 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:49,035 command_dist.c: In function ‘combine_queries’: 2024-11-19T05:00:49,036 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:49,036 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-19T05:00:49,036 | ^ 2024-11-19T05:00:49,037 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:49,037 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-19T05:00:49,037 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:49,038 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:49,038 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-19T05:00:49,038 | ^ 2024-11-19T05:00:49,039 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:49,039 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-19T05:00:49,039 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:49,041 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:49,041 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-19T05:00:49,041 | ^~ ~~~~~~~~ 2024-11-19T05:00:49,042 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T05:00:49,042 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-19T05:00:49,042 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:49,515 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 2024-11-19T05:00:49,697 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 2024-11-19T05:00:50,110 command_set.c: In function ‘sketch_operate’: 2024-11-19T05:00:50,110 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T05:00:50,110 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-11-19T05:00:50,110 | ^ 2024-11-19T05:00:50,125 command_set.c: In function ‘combin_subset_pans’: 2024-11-19T05:00:50,126 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-19T05:00:50,126 457 | free(co_dstat_fpath); 2024-11-19T05:00:50,126 | ^~~~~~~~~~~~~~ 2024-11-19T05:00:50,127 In file included from kssdheaders/global_basic.h:159, 2024-11-19T05:00:50,127 from command_set.c:15: 2024-11-19T05:00:50,127 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-19T05:00:50,127 565 | extern void free (void *__ptr) __THROW; 2024-11-19T05:00:50,128 | ~~~~~~^~~~~ 2024-11-19T05:00:50,134 command_set.c: In function ‘grouping_genomes’: 2024-11-19T05:00:50,134 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-19T05:00:50,134 562 | free(co_dstat_fpath); 2024-11-19T05:00:50,135 | ^~~~~~~~~~~~~~ 2024-11-19T05:00:50,135 In file included from kssdheaders/global_basic.h:159, 2024-11-19T05:00:50,135 from command_set.c:15: 2024-11-19T05:00:50,135 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-19T05:00:50,136 565 | extern void free (void *__ptr) __THROW; 2024-11-19T05:00:50,136 | ~~~~~~^~~~~ 2024-11-19T05:00:50,272 command_set.c: In function ‘sketch_union’: 2024-11-19T05:00:50,272 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:50,273 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:50,273 | ^ 2024-11-19T05:00:50,273 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:50,273 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:50,273 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,273 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,273 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:50,274 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:50,274 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:50,274 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:50,274 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,274 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,274 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T05:00:50,275 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:50,275 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:50,275 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T05:00:50,275 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,386 command_set.c: In function ‘sketch_operate’: 2024-11-19T05:00:50,386 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,386 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T05:00:50,386 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:50,386 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:50,386 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T05:00:50,387 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,387 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,387 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T05:00:50,387 | ^~ ~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,387 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-19T05:00:50,387 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T05:00:50,387 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,387 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,388 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:50,388 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:50,388 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:50,388 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:50,388 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,388 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,388 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:50,389 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:50,389 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:50,389 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:50,389 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,389 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,389 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:50,389 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:50,389 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:50,390 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:50,390 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,390 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,390 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:50,390 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:50,390 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:50,390 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:50,391 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,391 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:50,391 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:50,391 | ^ 2024-11-19T05:00:50,391 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:50,391 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:50,391 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,539 command_set.c: In function ‘uniq_sketch_union’: 2024-11-19T05:00:50,539 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:50,539 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:50,539 | ^ 2024-11-19T05:00:50,540 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:50,540 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:50,540 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,540 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,540 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:50,540 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:50,540 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:50,541 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:50,541 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,541 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,541 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T05:00:50,541 | ^~ ~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,541 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-19T05:00:50,541 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T05:00:50,541 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,665 command_set.c: In function ‘combin_pans’: 2024-11-19T05:00:50,666 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,666 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:50,666 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:50,666 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2024-11-19T05:00:50,666 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:50,666 | ^~~~~~~~~~ 2024-11-19T05:00:50,666 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-11-19T05:00:50,667 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:50,667 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,667 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,667 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:50,667 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:50,667 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2024-11-19T05:00:50,667 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:50,668 | ^~~~~~~~~~ 2024-11-19T05:00:50,668 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-11-19T05:00:50,668 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:50,668 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,668 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:50,668 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:50,668 | ^ 2024-11-19T05:00:50,668 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:50,669 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:50,669 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,851 command_set.c: In function ‘combin_subset_pans’: 2024-11-19T05:00:50,851 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,851 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:50,851 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:50,852 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:50,852 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:50,852 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,852 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,852 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:50,852 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:50,852 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:50,853 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:50,853 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,853 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,853 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:50,853 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:50,853 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:50,853 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:50,854 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,855 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:50,855 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:50,855 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:50,855 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:50,855 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:50,856 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:50,856 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:50,856 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:50,856 | ^ 2024-11-19T05:00:50,856 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:50,856 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:50,856 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:51,057 command_set.c: In function ‘grouping_genomes’: 2024-11-19T05:00:51,058 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:51,058 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:51,058 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:51,058 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:51,058 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:51,059 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:51,059 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:51,059 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:51,059 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:51,059 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:51,059 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:51,060 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:51,061 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:51,061 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:51,061 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:51,062 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:51,062 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:51,062 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:51,063 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:51,063 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:51,063 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:51,063 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:51,063 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:51,063 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:51,064 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:51,064 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:51,064 | ^ 2024-11-19T05:00:51,064 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:51,064 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:51,064 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:51,783 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 2024-11-19T05:00:52,313 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 2024-11-19T05:00:53,102 global_basic.c: In function ‘organize_infile_list’: 2024-11-19T05:00:53,102 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-11-19T05:00:53,102 195 | while (isspace(*buf)) buf++; 2024-11-19T05:00:53,103 | ^~~~~~~ 2024-11-19T05:00:53,103 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=] 2024-11-19T05:00:53,104 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-19T05:00:53,104 | ~~^ 2024-11-19T05:00:53,104 | | 2024-11-19T05:00:53,104 | long unsigned int 2024-11-19T05:00:53,105 | %u 2024-11-19T05:00:53,105 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-19T05:00:53,105 | ~~~~~~~~~~~ 2024-11-19T05:00:53,105 | | 2024-11-19T05:00:53,106 | size_t {aka unsigned int} 2024-11-19T05:00:53,106 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=] 2024-11-19T05:00:53,106 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-19T05:00:53,107 | ~~^ 2024-11-19T05:00:53,107 | | 2024-11-19T05:00:53,107 | long unsigned int 2024-11-19T05:00:53,107 | %u 2024-11-19T05:00:53,108 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-19T05:00:53,108 | ~~~~~~~~~~~ 2024-11-19T05:00:53,108 | | 2024-11-19T05:00:53,109 | size_t {aka unsigned int} 2024-11-19T05:00:53,816 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 2024-11-19T05:00:54,003 iseq2comem.c: In function ‘reads2mco’: 2024-11-19T05:00:54,003 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,004 156 | if (base > TL) { 2024-11-19T05:00:54,004 | ^ 2024-11-19T05:00:54,004 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,004 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:54,004 | ^~ 2024-11-19T05:00:54,004 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,005 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:54,005 | ^ 2024-11-19T05:00:54,006 iseq2comem.c: In function ‘fasta2co’: 2024-11-19T05:00:54,006 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,006 239 | if (base > TL) { 2024-11-19T05:00:54,006 | ^ 2024-11-19T05:00:54,006 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,006 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:54,007 | ^~ 2024-11-19T05:00:54,007 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,007 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:54,007 | ^ 2024-11-19T05:00:54,007 iseq2comem.c: In function ‘fastq2co’: 2024-11-19T05:00:54,007 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-11-19T05:00:54,007 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-11-19T05:00:54,008 | ^~ 2024-11-19T05:00:54,008 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,008 318 | if (base > TL) { 2024-11-19T05:00:54,009 | ^ 2024-11-19T05:00:54,009 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,009 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:54,009 | ^~ 2024-11-19T05:00:54,009 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,009 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:54,009 | ^ 2024-11-19T05:00:54,010 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,010 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-11-19T05:00:54,010 | ^ 2024-11-19T05:00:54,011 iseq2comem.c: In function ‘fastq2koc’: 2024-11-19T05:00:54,011 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,012 402 | if (base > TL) { 2024-11-19T05:00:54,012 | ^ 2024-11-19T05:00:54,012 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,012 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:54,012 | ^~ 2024-11-19T05:00:54,012 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,012 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:54,013 | ^ 2024-11-19T05:00:54,017 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-11-19T05:00:54,018 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,018 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:54,018 | ^~ 2024-11-19T05:00:54,018 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:54,018 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:54,018 | ^ 2024-11-19T05:00:55,231 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 2024-11-19T05:00:55,323 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 2024-11-19T05:00:55,458 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 2024-11-19T05:00:58,434 pykssd.c: In function ‘py_dist_dispatch’: 2024-11-19T05:00:58,434 pykssd.c:329:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-11-19T05:00:58,434 329 | int state1 = dist_dispatch(&dist_opt_val1); 2024-11-19T05:00:58,435 | ^~~~~~ 2024-11-19T05:00:58,435 pykssd.c:386:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-11-19T05:00:58,435 386 | int state2 = dist_dispatch(&dist_opt_val2); 2024-11-19T05:00:58,435 | ^~~~~~ 2024-11-19T05:00:58,436 pykssd.c:510:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-11-19T05:00:58,437 510 | int state4 = dist_dispatch(&dist_opt_val4); 2024-11-19T05:00:58,437 | ^~~~~~ 2024-11-19T05:00:58,580 pykssd.c: In function ‘rename_file’: 2024-11-19T05:00:58,580 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-11-19T05:00:58,580 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-11-19T05:00:58,581 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:58,581 pykssd.c:41:15: note: length computed here 2024-11-19T05:00:58,581 41 | int len = strlen(p1); 2024-11-19T05:00:58,581 | ^~~~~~~~~~ 2024-11-19T05:01:00,789 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 2024-11-19T05:01:01,432 building 'nj' extension 2024-11-19T05:01:01,432 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 2024-11-19T05:01:01,862 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 2024-11-19T05:01:03,974 buildtree.c: In function ‘UPGMA_buildtree’: 2024-11-19T05:01:03,975 buildtree.c:716:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:01:03,975 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-11-19T05:01:03,975 | ^~ 2024-11-19T05:01:03,976 buildtree.c:716:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:01:03,977 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-11-19T05:01:03,977 | ^~ 2024-11-19T05:01:04,563 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 2024-11-19T05:01:04,890 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 2024-11-19T05:01:05,014 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-11-19T05:01:05,014 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:01:05,014 226 | for( i=0; i < dest->size; i++) { 2024-11-19T05:01:05,014 | ^ 2024-11-19T05:01:05,014 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-11-19T05:01:05,015 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:01:05,015 260 | for( i=0; i < mat->size; i++) { 2024-11-19T05:01:05,015 | ^ 2024-11-19T05:01:05,015 distancemat.c: In function ‘print_DistanceMatrix’: 2024-11-19T05:01:05,015 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:01:05,015 349 | for(row=0; row < mat->size; row++) { 2024-11-19T05:01:05,016 | ^ 2024-11-19T05:01:05,016 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-11-19T05:01:05,016 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-11-19T05:01:05,016 410 | while(c = fgetc(handle)) { 2024-11-19T05:01:05,016 | ^ 2024-11-19T05:01:05,354 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 -Injheaders -I/usr/include/python3.9 -c pynj.c -o build/temp.linux-armv7l-cpython-39/pynj.o 2024-11-19T05:01:11,527 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 2024-11-19T05:01:11,812 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 2024-11-19T05:01:12,569 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 2024-11-19T05:01:12,748 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 2024-11-19T05:01:12,868 building 'dnj' extension 2024-11-19T05:01:12,871 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 2024-11-19T05:01:12,940 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 2024-11-19T05:01:13,099 dnj.c: In function ‘minQpair’: 2024-11-19T05:01:13,099 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,100 70 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,100 | ^~~ 2024-11-19T05:01:13,100 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,101 126 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,101 | ^~~ 2024-11-19T05:01:13,101 dnj.c: In function ‘maxQpair’: 2024-11-19T05:01:13,101 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,101 157 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,101 | ^~~ 2024-11-19T05:01:13,102 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,102 213 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,102 | ^~~ 2024-11-19T05:01:13,102 dnj.c: In function ‘UPGMApair’: 2024-11-19T05:01:13,103 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,103 237 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,103 | ^~~ 2024-11-19T05:01:13,103 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,104 284 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,104 | ^~~ 2024-11-19T05:01:13,104 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,104 291 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,104 | ^~~ 2024-11-19T05:01:13,105 dnj.c: In function ‘minQrow’: 2024-11-19T05:01:13,105 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,105 374 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,105 | ^~~ 2024-11-19T05:01:13,106 dnj.c: In function ‘maxQrow’: 2024-11-19T05:01:13,106 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,107 435 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,107 | ^~~ 2024-11-19T05:01:13,107 dnj.c: In function ‘UPGMArow’: 2024-11-19T05:01:13,108 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,108 488 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,108 | ^~~ 2024-11-19T05:01:13,108 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,108 494 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,108 | ^~~ 2024-11-19T05:01:13,109 dnj.c: In function ‘minQ_thread’: 2024-11-19T05:01:13,109 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:13,109 553 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:13,110 | ^~~ 2024-11-19T05:01:16,279 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 2024-11-19T05:01:16,398 filebuff.c: In function ‘BuffgzFileBuff’: 2024-11-19T05:01:16,399 filebuff.c:99:47: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:01:16,399 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-11-19T05:01:16,399 | ^~ 2024-11-19T05:01:16,688 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 2024-11-19T05:01:16,809 hclust.c: In function ‘minQ’: 2024-11-19T05:01:16,809 hclust.c:364:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:01:16,810 364 | while(++i < Q->n) { 2024-11-19T05:01:16,810 | ^ 2024-11-19T05:01:16,810 hclust.c:377:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:16,810 377 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:16,810 | ^~~ 2024-11-19T05:01:16,810 hclust.c: In function ‘maxQ’: 2024-11-19T05:01:16,811 hclust.c:394:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:01:16,811 394 | while(++i < Q->n) { 2024-11-19T05:01:16,811 | ^ 2024-11-19T05:01:16,811 hclust.c:407:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:16,811 407 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:16,811 | ^~~ 2024-11-19T05:01:18,870 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 2024-11-19T05:01:18,997 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-11-19T05:01:18,997 matrix.c:538:9: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:01:18,997 538 | if(pos != n) { 2024-11-19T05:01:18,997 | ^~ 2024-11-19T05:01:19,756 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 2024-11-19T05:01:19,819 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 2024-11-19T05:01:19,937 nj.c: In function ‘initQ’: 2024-11-19T05:01:19,938 nj.c:243:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:19,938 243 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:19,938 | ^~~ 2024-11-19T05:01:19,939 nj.c: In function ‘initQ_MN’: 2024-11-19T05:01:19,939 nj.c:358:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:19,940 358 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:19,940 | ^~~ 2024-11-19T05:01:19,943 nj.c: In function ‘minD’: 2024-11-19T05:01:19,943 nj.c:559:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:19,943 559 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:19,943 | ^~~ 2024-11-19T05:01:19,945 nj.c: In function ‘maxD’: 2024-11-19T05:01:19,945 nj.c:642:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:19,945 642 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:19,945 | ^~~ 2024-11-19T05:01:19,948 nj.c: In function ‘minPair’: 2024-11-19T05:01:19,948 nj.c:826:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-11-19T05:01:19,949 826 | pos <<= sizeof(unsigned) * 8; 2024-11-19T05:01:19,949 | ^~~ 2024-11-19T05:01:23,102 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 2024-11-19T05:01:23,579 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 2024-11-19T05:01:23,666 pherror.c: In function ‘cfread’: 2024-11-19T05:01:23,666 pherror.c:58:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:01:23,667 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-11-19T05:01:23,667 | ^~ 2024-11-19T05:01:23,769 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 2024-11-19T05:01:24,690 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 2024-11-19T05:01:25,003 In file included from pydnj.c:11: 2024-11-19T05:01:25,003 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-11-19T05:01:25,003 20 | #define _XOPEN_SOURCE 600 2024-11-19T05:01:25,004 | 2024-11-19T05:01:25,004 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-11-19T05:01:25,004 from /usr/include/limits.h:26, 2024-11-19T05:01:25,004 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:195, 2024-11-19T05:01:25,004 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/syslimits.h:7, 2024-11-19T05:01:25,004 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:34, 2024-11-19T05:01:25,005 from /usr/include/python3.9/Python.h:11, 2024-11-19T05:01:25,005 from pydnj.c:1: 2024-11-19T05:01:25,005 /usr/include/features.h:207: note: this is the location of the previous definition 2024-11-19T05:01:25,005 207 | # define _XOPEN_SOURCE 700 2024-11-19T05:01:25,005 | 2024-11-19T05:01:25,018 pydnj.c: In function ‘py_build’: 2024-11-19T05:01:25,018 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-11-19T05:01:25,019 165 | p = omp_get_num_procs(); 2024-11-19T05:01:25,019 | ^~~~~~~~~~~~~~~~~ 2024-11-19T05:01:25,202 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 2024-11-19T05:01:25,401 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 2024-11-19T05:01:25,508 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 2024-11-19T05:01:25,700 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 2024-11-19T05:01:25,860 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 2024-11-19T05:01:26,075 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-11-19T05:01:26,075 !! 2024-11-19T05:01:26,075 ******************************************************************************** 2024-11-19T05:01:26,075 Please avoid running ``setup.py`` directly. 2024-11-19T05:01:26,075 Instead, use pypa/build, pypa/installer or other 2024-11-19T05:01:26,076 standards-based tools. 2024-11-19T05:01:26,076 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-11-19T05:01:26,076 ******************************************************************************** 2024-11-19T05:01:26,076 !! 2024-11-19T05:01:26,076 self.initialize_options() 2024-11-19T05:01:26,110 installing to build/bdist.linux-armv7l/wheel 2024-11-19T05:01:26,110 running install 2024-11-19T05:01:26,136 running install_lib 2024-11-19T05:01:26,165 creating build/bdist.linux-armv7l/wheel 2024-11-19T05:01:26,168 copying build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:01:26,174 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:01:26,184 copying build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:01:26,195 copying build/lib.linux-armv7l-cpython-39/kssdtree.py -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:01:26,198 copying build/lib.linux-armv7l-cpython-39/toolutils.py -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:01:26,200 running install_egg_info 2024-11-19T05:01:26,237 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/./kssdtree-2.0.4-py3.9.egg-info 2024-11-19T05:01:26,254 running install_scripts 2024-11-19T05:01:26,310 creating build/bdist.linux-armv7l/wheel/kssdtree-2.0.4.dist-info/WHEEL 2024-11-19T05:01:26,313 creating '/tmp/pip-wheel-6__zqsmz/kssdtree-2.0.4-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-11-19T05:01:26,391 adding 'dnj.cpython-39-arm-linux-gnueabihf.so' 2024-11-19T05:01:26,487 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2024-11-19T05:01:26,493 adding 'kssdtree.py' 2024-11-19T05:01:26,522 adding 'nj.cpython-39-arm-linux-gnueabihf.so' 2024-11-19T05:01:26,525 adding 'toolutils.py' 2024-11-19T05:01:26,528 adding 'kssdtree-2.0.4.dist-info/METADATA' 2024-11-19T05:01:26,529 adding 'kssdtree-2.0.4.dist-info/WHEEL' 2024-11-19T05:01:26,530 adding 'kssdtree-2.0.4.dist-info/dependency_links.txt' 2024-11-19T05:01:26,531 adding 'kssdtree-2.0.4.dist-info/top_level.txt' 2024-11-19T05:01:26,532 adding 'kssdtree-2.0.4.dist-info/RECORD' 2024-11-19T05:01:26,541 removing build/bdist.linux-armv7l/wheel 2024-11-19T05:01:26,642 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-11-19T05:01:26,650 Created wheel for kssdtree: filename=kssdtree-2.0.4-cp39-cp39-linux_armv7l.whl size=376797 sha256=00938a03bead64e58bc1928832b7952b04d844e79b41da12160490c7edbb9e9f 2024-11-19T05:01:26,651 Stored in directory: /tmp/pip-ephem-wheel-cache-5fctp05b/wheels/72/c5/e7/e2e42b78cc92811970a2dc6f00e546311a166b02823654d272 2024-11-19T05:01:26,661 Successfully built kssdtree 2024-11-19T05:01:26,678 Removed build tracker: '/tmp/pip-build-tracker-iqladn81'