2024-09-24T21:15:31,226 Created temporary directory: /tmp/pip-build-tracker-t2badl9c 2024-09-24T21:15:31,227 Initialized build tracking at /tmp/pip-build-tracker-t2badl9c 2024-09-24T21:15:31,227 Created build tracker: /tmp/pip-build-tracker-t2badl9c 2024-09-24T21:15:31,228 Entered build tracker: /tmp/pip-build-tracker-t2badl9c 2024-09-24T21:15:31,229 Created temporary directory: /tmp/pip-wheel-bo89bqom 2024-09-24T21:15:31,233 Created temporary directory: /tmp/pip-ephem-wheel-cache-khgjgwto 2024-09-24T21:15:31,275 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-09-24T21:15:31,278 2 location(s) to search for versions of kssdtree: 2024-09-24T21:15:31,278 * https://pypi.org/simple/kssdtree/ 2024-09-24T21:15:31,278 * https://www.piwheels.org/simple/kssdtree/ 2024-09-24T21:15:31,279 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-09-24T21:15:31,280 Getting page https://pypi.org/simple/kssdtree/ 2024-09-24T21:15:31,282 Found index url https://pypi.org/simple/ 2024-09-24T21:15:31,501 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-09-24T21:15:31,504 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 2024-09-24T21:15:31,505 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 2024-09-24T21:15:31,505 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 2024-09-24T21:15:31,506 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 2024-09-24T21:15:31,507 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 2024-09-24T21:15:31,507 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 2024-09-24T21:15:31,508 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 2024-09-24T21:15:31,509 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 2024-09-24T21:15:31,510 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 2024-09-24T21:15:31,510 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 2024-09-24T21:15:31,511 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 2024-09-24T21:15:31,512 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-09-24T21:15:31,513 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-09-24T21:15:31,514 Found index url https://www.piwheels.org/simple/ 2024-09-24T21:15:31,677 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-09-24T21:15:31,690 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/) 2024-09-24T21:15:31,690 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/) 2024-09-24T21:15:31,691 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/) 2024-09-24T21:15:31,692 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,694 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.0-cp39-cp39-linux_armv7l.whl#sha256=131de046d905a575216e4344f66d988df06c39a828f970e791ab2dd8ce7c204c (from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,694 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp311-cp311-linux_armv6l.whl#sha256=d4c397f5fcb0af48dbb11b9fb7d7b399cc180d65355b794a8fcc7327e9a7dde1 (from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,695 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/) 2024-09-24T21:15:31,696 Skipping link: No binaries permitted for kssdtree: 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https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,698 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.8-cp311-cp311-linux_armv6l.whl#sha256=717afc6606ad3045caac8f3f1cd01a37edd2f01f1cc38bc1bc6c3320882bd392 (from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,699 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.8-cp311-cp311-linux_armv7l.whl#sha256=717afc6606ad3045caac8f3f1cd01a37edd2f01f1cc38bc1bc6c3320882bd392 (from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,699 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/) 2024-09-24T21:15:31,700 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,702 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp311-cp311-linux_armv7l.whl#sha256=0901b6cf3efb240d5d32b1e88a8863f28e2986a2c0749886421c643b98a4aec2 (from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,702 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp39-cp39-linux_armv6l.whl#sha256=9defb70b5162efc2c0eb6e415a7e37c604aa9b248a006af86af8f59a3bce5d2b (from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,703 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/) 2024-09-24T21:15:31,703 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,706 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp39-cp39-linux_armv6l.whl#sha256=34527068d84569095aefee41a353c5dfc0dfa55b68097890da9a1eca2ee9b726 (from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,706 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp39-cp39-linux_armv7l.whl#sha256=34527068d84569095aefee41a353c5dfc0dfa55b68097890da9a1eca2ee9b726 (from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,707 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/) 2024-09-24T21:15:31,707 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-09-24T21:15:31,709 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/) 2024-09-24T21:15:31,710 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/) 2024-09-24T21:15:31,710 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/) 2024-09-24T21:15:31,711 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/) 2024-09-24T21:15:31,711 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/) 2024-09-24T21:15:31,712 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/) 2024-09-24T21:15:31,712 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/) 2024-09-24T21:15:31,713 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/) 2024-09-24T21:15:31,713 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/) 2024-09-24T21:15:31,714 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/) 2024-09-24T21:15:31,715 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/) 2024-09-24T21:15:31,716 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/) 2024-09-24T21:15:31,716 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/) 2024-09-24T21:15:31,717 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-09-24T21:15:31,717 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-09-24T21:15:31,735 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-09-24T21:15:31,737 Collecting kssdtree==2.0.1 2024-09-24T21:15:31,739 Created temporary directory: /tmp/pip-unpack-8hvh3327 2024-09-24T21:15:31,878 Downloading kssdtree-2.0.1.tar.gz (112 kB) 2024-09-24T21:15:32,097 Added kssdtree==2.0.1 from https://files.pythonhosted.org/packages/ba/39/d443cac955912a0371c93b797311cb9ec3a8d6ee0a5d7673376d826aa6b2/kssdtree-2.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-t2badl9c' 2024-09-24T21:15:32,099 Running setup.py (path:/tmp/pip-wheel-bo89bqom/kssdtree_d28fd5ff82584a3cb2eb973701146dab/setup.py) egg_info for package kssdtree 2024-09-24T21:15:32,100 Created temporary directory: /tmp/pip-pip-egg-info-54_8kc49 2024-09-24T21:15:32,100 Preparing metadata (setup.py): started 2024-09-24T21:15:32,102 Running command python setup.py egg_info 2024-09-24T21:15:33,183 running egg_info 2024-09-24T21:15:33,185 creating /tmp/pip-pip-egg-info-54_8kc49/kssdtree.egg-info 2024-09-24T21:15:33,213 writing /tmp/pip-pip-egg-info-54_8kc49/kssdtree.egg-info/PKG-INFO 2024-09-24T21:15:33,216 writing dependency_links to /tmp/pip-pip-egg-info-54_8kc49/kssdtree.egg-info/dependency_links.txt 2024-09-24T21:15:33,218 writing requirements to /tmp/pip-pip-egg-info-54_8kc49/kssdtree.egg-info/requires.txt 2024-09-24T21:15:33,219 writing top-level names to /tmp/pip-pip-egg-info-54_8kc49/kssdtree.egg-info/top_level.txt 2024-09-24T21:15:33,221 writing manifest file '/tmp/pip-pip-egg-info-54_8kc49/kssdtree.egg-info/SOURCES.txt' 2024-09-24T21:15:33,330 reading manifest file '/tmp/pip-pip-egg-info-54_8kc49/kssdtree.egg-info/SOURCES.txt' 2024-09-24T21:15:33,331 reading manifest template 'MANIFEST.in' 2024-09-24T21:15:33,349 writing manifest file '/tmp/pip-pip-egg-info-54_8kc49/kssdtree.egg-info/SOURCES.txt' 2024-09-24T21:15:33,459 Preparing metadata (setup.py): finished with status 'done' 2024-09-24T21:15:33,462 Source in /tmp/pip-wheel-bo89bqom/kssdtree_d28fd5ff82584a3cb2eb973701146dab has version 2.0.1, which satisfies requirement kssdtree==2.0.1 from https://files.pythonhosted.org/packages/ba/39/d443cac955912a0371c93b797311cb9ec3a8d6ee0a5d7673376d826aa6b2/kssdtree-2.0.1.tar.gz 2024-09-24T21:15:33,463 Removed kssdtree==2.0.1 from https://files.pythonhosted.org/packages/ba/39/d443cac955912a0371c93b797311cb9ec3a8d6ee0a5d7673376d826aa6b2/kssdtree-2.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-t2badl9c' 2024-09-24T21:15:33,468 Created temporary directory: /tmp/pip-unpack-ujxt8d8u 2024-09-24T21:15:33,469 Created temporary directory: /tmp/pip-unpack-msg_hfyu 2024-09-24T21:15:33,470 Building wheels for collected packages: kssdtree 2024-09-24T21:15:33,474 Created temporary directory: /tmp/pip-wheel-kbbeklw0 2024-09-24T21:15:33,474 Building wheel for kssdtree (setup.py): started 2024-09-24T21:15:33,475 Destination directory: /tmp/pip-wheel-kbbeklw0 2024-09-24T21:15:33,476 Running command python setup.py bdist_wheel 2024-09-24T21:15:34,493 running bdist_wheel 2024-09-24T21:15:34,623 running build 2024-09-24T21:15:34,624 running build_py 2024-09-24T21:15:34,653 creating build/lib.linux-armv7l-cpython-311 2024-09-24T21:15:34,654 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2024-09-24T21:15:34,657 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2024-09-24T21:15:34,659 running egg_info 2024-09-24T21:15:34,690 writing kssdtree.egg-info/PKG-INFO 2024-09-24T21:15:34,692 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-09-24T21:15:34,694 writing requirements to kssdtree.egg-info/requires.txt 2024-09-24T21:15:34,695 writing top-level names to kssdtree.egg-info/top_level.txt 2024-09-24T21:15:34,724 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-09-24T21:15:34,732 reading manifest template 'MANIFEST.in' 2024-09-24T21:15:34,749 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-09-24T21:15:34,751 running build_ext 2024-09-24T21:15:35,198 building 'kssd' extension 2024-09-24T21:15:35,199 creating build/temp.linux-armv7l-cpython-311 2024-09-24T21:15:35,200 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c co2mco.c -o build/temp.linux-armv7l-cpython-311/co2mco.o -fopenmp 2024-09-24T21:15:35,381 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-09-24T21:15:35,382 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-09-24T21:15:35,382 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-09-24T21:15:35,383 | ^ 2024-09-24T21:15:35,386 co2mco.c: In function ‘co2unitllmco’: 2024-09-24T21:15:35,386 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-09-24T21:15:35,387 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-09-24T21:15:35,388 | ^ 2024-09-24T21:15:36,096 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_composite.c -o build/temp.linux-armv7l-cpython-311/command_composite.o -fopenmp 2024-09-24T21:15:36,474 command_composite.c: In function ‘get_species_abundance’: 2024-09-24T21:15:36,475 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-09-24T21:15:36,476 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-09-24T21:15:36,476 | ^~ 2024-09-24T21:15:36,477 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-09-24T21:15:36,478 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-09-24T21:15:36,479 | ^~ 2024-09-24T21:15:36,479 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:36,480 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-09-24T21:15:36,481 | ^ 2024-09-24T21:15:36,482 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:36,483 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-09-24T21:15:36,483 | ^~~~~~~~~~ 2024-09-24T21:15:36,484 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-09-24T21:15:36,486 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-09-24T21:15:36,486 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:36,487 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:36,487 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-09-24T21:15:36,488 | ^ 2024-09-24T21:15:36,489 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:36,489 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-09-24T21:15:36,490 | ^~~~~~~~~~ 2024-09-24T21:15:36,491 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-09-24T21:15:36,491 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-09-24T21:15:36,492 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:36,492 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:36,493 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-09-24T21:15:36,494 | ^ 2024-09-24T21:15:36,494 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:36,495 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-09-24T21:15:36,496 | ^~~~~~~~~~ 2024-09-24T21:15:36,497 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-09-24T21:15:36,498 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-09-24T21:15:36,499 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:36,499 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:36,500 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-09-24T21:15:36,501 | ^ 2024-09-24T21:15:36,502 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:36,503 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-09-24T21:15:36,504 | ^~~~~~~~~~ 2024-09-24T21:15:36,504 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-09-24T21:15:36,505 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-09-24T21:15:36,506 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:36,507 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:36,507 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-09-24T21:15:36,508 | ^ 2024-09-24T21:15:36,509 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:36,510 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-09-24T21:15:36,511 | ^~~~~~~~~~~~ 2024-09-24T21:15:36,512 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2024-09-24T21:15:36,513 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-09-24T21:15:36,513 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:36,758 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist.c -o build/temp.linux-armv7l-cpython-311/command_dist.o -fopenmp 2024-09-24T21:15:36,993 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-09-24T21:15:36,995 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=] 2024-09-24T21:15:36,996 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-09-24T21:15:36,996 | ~~^ 2024-09-24T21:15:36,997 | | 2024-09-24T21:15:36,997 | long unsigned int 2024-09-24T21:15:36,998 | %u 2024-09-24T21:15:36,998 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-09-24T21:15:36,999 | ~~~~~~~ 2024-09-24T21:15:36,999 | | 2024-09-24T21:15:37,000 | size_t {aka unsigned int} 2024-09-24T21:15:37,000 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=] 2024-09-24T21:15:37,001 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-09-24T21:15:37,001 | ~~^ 2024-09-24T21:15:37,002 | | 2024-09-24T21:15:37,002 | long unsigned int 2024-09-24T21:15:37,003 | %u 2024-09-24T21:15:37,003 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-09-24T21:15:37,004 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-09-24T21:15:37,005 | ~~~~~~~~~ 2024-09-24T21:15:37,005 | | 2024-09-24T21:15:37,006 | size_t {aka unsigned int} 2024-09-24T21:15:37,006 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-09-24T21:15:37,007 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-09-24T21:15:37,007 | ~~^ 2024-09-24T21:15:37,008 | | 2024-09-24T21:15:37,009 | long unsigned int 2024-09-24T21:15:37,009 | %u 2024-09-24T21:15:37,010 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-09-24T21:15:37,010 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-09-24T21:15:37,011 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:37,012 | | 2024-09-24T21:15:37,013 | unsigned int 2024-09-24T21:15:37,014 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-09-24T21:15:37,014 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-09-24T21:15:37,015 | ^ 2024-09-24T21:15:37,022 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-09-24T21:15:37,023 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=] 2024-09-24T21:15:37,024 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-09-24T21:15:37,024 | ~~^ ~~~~~~~ 2024-09-24T21:15:37,025 | | | 2024-09-24T21:15:37,025 | long unsigned int size_t {aka unsigned int} 2024-09-24T21:15:37,026 | %u 2024-09-24T21:15:37,026 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=] 2024-09-24T21:15:37,027 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-09-24T21:15:37,027 | ~~^ 2024-09-24T21:15:37,028 | | 2024-09-24T21:15:37,029 | long unsigned int 2024-09-24T21:15:37,029 | %u 2024-09-24T21:15:37,030 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-09-24T21:15:37,030 | ~~~~~~~~~ 2024-09-24T21:15:37,031 | | 2024-09-24T21:15:37,032 | size_t {aka unsigned int} 2024-09-24T21:15:37,032 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-09-24T21:15:37,033 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-09-24T21:15:37,033 | ~~^ 2024-09-24T21:15:37,034 | | 2024-09-24T21:15:37,034 | long unsigned int 2024-09-24T21:15:37,035 | %u 2024-09-24T21:15:37,036 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-09-24T21:15:37,036 865 | (size_t) b * unitsz_distf_mapped); 2024-09-24T21:15:37,037 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:37,038 | | 2024-09-24T21:15:37,039 | unsigned int 2024-09-24T21:15:37,039 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-09-24T21:15:37,040 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-09-24T21:15:37,040 | ^~~~~~~ 2024-09-24T21:15:37,041 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-09-24T21:15:37,041 809 | struct stat cbd_fcode_stat; 2024-09-24T21:15:37,042 | ^~~~~~~~~~~~~~ 2024-09-24T21:15:37,042 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-09-24T21:15:37,043 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-09-24T21:15:37,043 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:37,044 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-09-24T21:15:37,044 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-09-24T21:15:37,045 | ^~~~~~~~~~~~~~~~~ 2024-09-24T21:15:37,045 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-09-24T21:15:37,046 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=] 2024-09-24T21:15:37,046 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-09-24T21:15:37,047 | ~~^ 2024-09-24T21:15:37,047 | | 2024-09-24T21:15:37,048 | long unsigned int 2024-09-24T21:15:37,048 | %u 2024-09-24T21:15:37,049 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-09-24T21:15:37,050 | ~~~~~~~ 2024-09-24T21:15:37,050 | | 2024-09-24T21:15:37,051 | size_t {aka unsigned int} 2024-09-24T21:15:37,051 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=] 2024-09-24T21:15:37,052 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-09-24T21:15:37,052 | ~~^ 2024-09-24T21:15:37,053 | | 2024-09-24T21:15:37,054 | long unsigned int 2024-09-24T21:15:37,054 | %u 2024-09-24T21:15:37,055 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-09-24T21:15:37,056 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-09-24T21:15:37,056 | ~~~~~~~~~ 2024-09-24T21:15:37,057 | | 2024-09-24T21:15:37,058 | size_t {aka unsigned int} 2024-09-24T21:15:37,058 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-09-24T21:15:37,059 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-09-24T21:15:37,060 | ~~^ 2024-09-24T21:15:37,060 | | 2024-09-24T21:15:37,062 | long unsigned int 2024-09-24T21:15:37,062 | %u 2024-09-24T21:15:37,063 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-09-24T21:15:37,063 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-09-24T21:15:37,064 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:37,064 | | 2024-09-24T21:15:37,065 | unsigned int 2024-09-24T21:15:37,065 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-09-24T21:15:37,066 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-09-24T21:15:37,066 | ^ 2024-09-24T21:15:37,067 command_dist.c: In function ‘mco_co_dist_core’: 2024-09-24T21:15:37,068 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-09-24T21:15:37,068 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-09-24T21:15:37,069 | ^ 2024-09-24T21:15:37,069 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-09-24T21:15:37,070 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-09-24T21:15:37,071 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-09-24T21:15:37,071 | ^ 2024-09-24T21:15:37,072 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-09-24T21:15:37,073 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-09-24T21:15:37,073 | ^ 2024-09-24T21:15:37,078 command_dist.c: In function ‘dist_print_nobin’: 2024-09-24T21:15:37,079 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-09-24T21:15:37,080 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-09-24T21:15:37,080 | ^ 2024-09-24T21:15:37,082 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-09-24T21:15:37,083 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-09-24T21:15:37,083 | ^ 2024-09-24T21:15:37,085 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-09-24T21:15:37,085 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-09-24T21:15:37,086 | ^ 2024-09-24T21:15:37,446 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-09-24T21:15:37,447 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2024-09-24T21:15:37,448 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-09-24T21:15:37,448 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:37,449 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-09-24T21:15:37,450 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-09-24T21:15:37,451 | ^~~~~~~~~~~~ 2024-09-24T21:15:38,283 command_dist.c: In function ‘get_dim_shuffle’: 2024-09-24T21:15:38,283 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-09-24T21:15:38,284 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-09-24T21:15:38,285 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:38,285 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-09-24T21:15:38,286 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-09-24T21:15:38,286 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,185 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-09-24T21:15:39,186 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:39,186 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-09-24T21:15:39,187 | ^~ ~~~~~~~~~ 2024-09-24T21:15:39,188 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-09-24T21:15:39,188 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-09-24T21:15:39,189 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,190 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-09-24T21:15:39,190 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-09-24T21:15:39,191 | ^~~~~~~~~~~~~~~ 2024-09-24T21:15:39,191 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-09-24T21:15:39,192 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-09-24T21:15:39,192 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,193 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-09-24T21:15:39,194 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-09-24T21:15:39,194 | ^~~~~~~~~~~ 2024-09-24T21:15:39,195 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:39,196 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-09-24T21:15:39,196 | ^~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,197 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-09-24T21:15:39,198 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-09-24T21:15:39,198 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,199 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-09-24T21:15:39,200 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-09-24T21:15:39,201 | ^~~~~ 2024-09-24T21:15:39,201 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:39,202 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-09-24T21:15:39,203 | ^~~~~~~~~~~ 2024-09-24T21:15:39,203 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-09-24T21:15:39,204 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-09-24T21:15:39,205 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,436 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-09-24T21:15:39,437 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:39,438 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-09-24T21:15:39,438 | ^~ ~~~~~~~~~ 2024-09-24T21:15:39,439 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-09-24T21:15:39,439 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-09-24T21:15:39,440 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,440 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-09-24T21:15:39,441 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-09-24T21:15:39,441 | ^~~~~~~~~~~~~~~ 2024-09-24T21:15:39,442 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-09-24T21:15:39,442 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-09-24T21:15:39,443 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,443 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-09-24T21:15:39,444 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-09-24T21:15:39,444 | ^~~~~~~~~~~~~ 2024-09-24T21:15:39,445 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-09-24T21:15:39,446 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-09-24T21:15:39,446 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,447 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:39,447 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-09-24T21:15:39,448 | ^ 2024-09-24T21:15:39,449 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-09-24T21:15:39,449 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-09-24T21:15:39,450 | ^~~~~~~~~~ 2024-09-24T21:15:39,451 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-09-24T21:15:39,451 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-09-24T21:15:39,452 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,453 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:39,453 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-09-24T21:15:39,454 | ^ 2024-09-24T21:15:39,455 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-09-24T21:15:39,455 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-09-24T21:15:39,456 | ^~~~~~~~~~ 2024-09-24T21:15:39,457 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-09-24T21:15:39,458 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-09-24T21:15:39,458 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,717 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-09-24T21:15:39,719 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:39,719 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-09-24T21:15:39,720 | ^~ ~~~~~~~~~ 2024-09-24T21:15:39,720 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-09-24T21:15:39,721 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-09-24T21:15:39,721 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,722 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-09-24T21:15:39,722 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-09-24T21:15:39,723 | ^~~~~~~~~~~~~~~ 2024-09-24T21:15:39,723 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-09-24T21:15:39,724 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-09-24T21:15:39,724 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,724 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-09-24T21:15:39,725 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-09-24T21:15:39,726 | ^~~~~~~~~~~~~ 2024-09-24T21:15:39,726 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-09-24T21:15:39,727 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-09-24T21:15:39,727 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,728 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-09-24T21:15:39,729 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-09-24T21:15:39,729 | ^~~~~~~~~~~ 2024-09-24T21:15:39,730 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:39,730 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-09-24T21:15:39,731 | ^~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,732 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-09-24T21:15:39,732 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-09-24T21:15:39,733 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:39,733 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-09-24T21:15:39,734 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-09-24T21:15:39,735 | ^~~~~ 2024-09-24T21:15:39,736 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:39,737 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-09-24T21:15:39,737 | ^~~~~~~~~~~ 2024-09-24T21:15:39,738 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-09-24T21:15:39,739 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-09-24T21:15:39,740 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:40,007 command_dist.c: In function ‘combine_queries’: 2024-09-24T21:15:40,009 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-09-24T21:15:40,009 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-09-24T21:15:40,010 | ^ 2024-09-24T21:15:40,011 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-09-24T21:15:40,011 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-09-24T21:15:40,011 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:40,012 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-09-24T21:15:40,013 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-09-24T21:15:40,013 | ^ 2024-09-24T21:15:40,014 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-09-24T21:15:40,014 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-09-24T21:15:40,015 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:40,017 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:40,017 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-09-24T21:15:40,018 | ^~ ~~~~~~~~ 2024-09-24T21:15:40,019 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-09-24T21:15:40,019 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-09-24T21:15:40,020 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:40,508 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o -fopenmp 2024-09-24T21:15:40,679 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_set.c -o build/temp.linux-armv7l-cpython-311/command_set.o -fopenmp 2024-09-24T21:15:40,848 command_set.c: In function ‘sketch_operate’: 2024-09-24T21:15:40,848 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-09-24T21:15:40,849 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-09-24T21:15:40,850 | ^ 2024-09-24T21:15:40,863 command_set.c: In function ‘combin_subset_pans’: 2024-09-24T21:15:40,863 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-09-24T21:15:40,864 458 | free(co_dstat_fpath); 2024-09-24T21:15:40,865 | ^~~~~~~~~~~~~~ 2024-09-24T21:15:40,865 In file included from kssdheaders/global_basic.h:159, 2024-09-24T21:15:40,866 from command_set.c:15: 2024-09-24T21:15:40,866 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-09-24T21:15:40,867 568 | extern void free (void *__ptr) __THROW; 2024-09-24T21:15:40,868 | ~~~~~~^~~~~ 2024-09-24T21:15:40,873 command_set.c: In function ‘grouping_genomes’: 2024-09-24T21:15:40,874 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-09-24T21:15:40,875 563 | free(co_dstat_fpath); 2024-09-24T21:15:40,876 | ^~~~~~~~~~~~~~ 2024-09-24T21:15:40,876 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-09-24T21:15:40,877 568 | extern void free (void *__ptr) __THROW; 2024-09-24T21:15:40,877 | ~~~~~~^~~~~ 2024-09-24T21:15:41,044 command_set.c: In function ‘sketch_union’: 2024-09-24T21:15:41,045 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-09-24T21:15:41,045 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:41,046 | ^ 2024-09-24T21:15:41,046 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-09-24T21:15:41,047 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:41,047 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,047 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,048 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-09-24T21:15:41,049 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,049 command_set.c:83:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,050 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-09-24T21:15:41,050 | ^~~~~~~~~~ 2024-09-24T21:15:41,051 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-09-24T21:15:41,051 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-09-24T21:15:41,052 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,053 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,053 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-09-24T21:15:41,054 | ^~ ~~~~~~~~~~ 2024-09-24T21:15:41,054 command_set.c:93:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,055 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-09-24T21:15:41,056 | ^~~~~~~~~~ 2024-09-24T21:15:41,057 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-09-24T21:15:41,057 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-09-24T21:15:41,058 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,184 command_set.c: In function ‘sketch_operate’: 2024-09-24T21:15:41,185 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,185 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-09-24T21:15:41,186 | ^~ ~~~~~~~~~~ 2024-09-24T21:15:41,186 command_set.c:154:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,187 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-09-24T21:15:41,188 | ^~~~~~~~~~ 2024-09-24T21:15:41,188 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-09-24T21:15:41,189 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-09-24T21:15:41,189 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,190 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,191 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-09-24T21:15:41,191 | ^~ ~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,192 command_set.c:156:29: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,192 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-09-24T21:15:41,192 | ^~~~~~~~~~ 2024-09-24T21:15:41,193 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-09-24T21:15:41,193 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-09-24T21:15:41,194 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,194 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,195 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-09-24T21:15:41,195 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,195 command_set.c:166:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,196 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-09-24T21:15:41,196 | ^~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,197 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-09-24T21:15:41,198 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-09-24T21:15:41,198 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,199 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,200 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-09-24T21:15:41,200 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,201 command_set.c:170:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,202 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-09-24T21:15:41,202 | ^~~~~~~~~~ 2024-09-24T21:15:41,203 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-09-24T21:15:41,204 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-09-24T21:15:41,204 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,205 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,205 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-09-24T21:15:41,206 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,206 command_set.c:175:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,207 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-09-24T21:15:41,208 | ^~~~~~~~~~ 2024-09-24T21:15:41,208 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-09-24T21:15:41,209 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-09-24T21:15:41,210 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,210 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,211 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-09-24T21:15:41,212 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,212 command_set.c:188:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,212 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-09-24T21:15:41,213 | ^~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,213 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-09-24T21:15:41,214 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-09-24T21:15:41,215 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,215 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-09-24T21:15:41,216 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:41,216 | ^ 2024-09-24T21:15:41,217 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-09-24T21:15:41,217 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:41,218 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,372 command_set.c: In function ‘uniq_sketch_union’: 2024-09-24T21:15:41,372 command_set.c:220:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-09-24T21:15:41,373 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-09-24T21:15:41,373 | ^ 2024-09-24T21:15:41,374 command_set.c:220:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2024-09-24T21:15:41,374 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-09-24T21:15:41,375 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,376 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-09-24T21:15:41,377 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:41,377 | ^ 2024-09-24T21:15:41,378 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-09-24T21:15:41,379 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:41,379 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,380 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,381 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-09-24T21:15:41,381 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,382 command_set.c:248:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,382 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-09-24T21:15:41,383 | ^~~~~~~~~~ 2024-09-24T21:15:41,384 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-09-24T21:15:41,385 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-09-24T21:15:41,385 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,386 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,387 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-09-24T21:15:41,387 | ^~ ~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,388 command_set.c:260:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,389 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-09-24T21:15:41,389 | ^~~~~~~~~~ 2024-09-24T21:15:41,390 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-09-24T21:15:41,390 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-09-24T21:15:41,391 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,517 command_set.c: In function ‘combin_pans’: 2024-09-24T21:15:41,517 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,518 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-09-24T21:15:41,518 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,519 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-09-24T21:15:41,519 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-09-24T21:15:41,520 | ^~~~~~~~~~ 2024-09-24T21:15:41,520 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-09-24T21:15:41,521 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-09-24T21:15:41,521 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,522 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,523 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-09-24T21:15:41,523 | ^~ ~~~~~~~~~~ 2024-09-24T21:15:41,524 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-09-24T21:15:41,525 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-09-24T21:15:41,525 | ^~~~~~~~~~ 2024-09-24T21:15:41,526 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-09-24T21:15:41,527 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-09-24T21:15:41,527 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,528 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-09-24T21:15:41,529 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:41,529 | ^ 2024-09-24T21:15:41,530 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-09-24T21:15:41,530 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:41,531 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,734 command_set.c: In function ‘combin_subset_pans’: 2024-09-24T21:15:41,735 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,736 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-09-24T21:15:41,736 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,737 command_set.c:470:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,737 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-09-24T21:15:41,738 | ^~~~~~~~~~ 2024-09-24T21:15:41,739 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-09-24T21:15:41,739 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-09-24T21:15:41,740 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,740 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,741 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-09-24T21:15:41,741 | ^~ ~~~~~~~~~~ 2024-09-24T21:15:41,742 command_set.c:476:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,742 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-09-24T21:15:41,742 | ^~~~~~~~~~ 2024-09-24T21:15:41,743 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-09-24T21:15:41,743 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-09-24T21:15:41,744 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,744 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,745 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-09-24T21:15:41,745 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,746 command_set.c:482:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,747 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-09-24T21:15:41,747 | ^~~~~~~~~~ 2024-09-24T21:15:41,748 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-09-24T21:15:41,749 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-09-24T21:15:41,750 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,750 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,751 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-09-24T21:15:41,752 | ^~ ~~~~~~~~~~ 2024-09-24T21:15:41,752 command_set.c:513:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,753 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-09-24T21:15:41,754 | ^~~~~~~~~~ 2024-09-24T21:15:41,754 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-09-24T21:15:41,755 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-09-24T21:15:41,755 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,756 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-09-24T21:15:41,757 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:41,757 | ^ 2024-09-24T21:15:41,758 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-09-24T21:15:41,759 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:41,759 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,980 command_set.c: In function ‘grouping_genomes’: 2024-09-24T21:15:41,981 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,981 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-09-24T21:15:41,982 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,983 command_set.c:575:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,983 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-09-24T21:15:41,983 | ^~~~~~~~~~ 2024-09-24T21:15:41,984 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-09-24T21:15:41,984 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-09-24T21:15:41,985 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,985 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,986 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-09-24T21:15:41,986 | ^~ ~~~~~~~~~~ 2024-09-24T21:15:41,986 command_set.c:581:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,987 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-09-24T21:15:41,987 | ^~~~~~~~~~ 2024-09-24T21:15:41,988 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-09-24T21:15:41,988 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-09-24T21:15:41,989 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,989 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,990 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-09-24T21:15:41,990 | ^~ ~~~~~~~~~~~ 2024-09-24T21:15:41,991 command_set.c:613:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,992 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-09-24T21:15:41,993 | ^~~~~~~~~~ 2024-09-24T21:15:41,993 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-09-24T21:15:41,994 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-09-24T21:15:41,995 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:41,995 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-09-24T21:15:41,996 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-09-24T21:15:41,997 | ^~ ~~~~~~~~~~ 2024-09-24T21:15:41,997 command_set.c:635:25: note: directive argument in the range [-2147483644, 2147483646] 2024-09-24T21:15:41,998 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-09-24T21:15:41,999 | ^~~~~~~~~~ 2024-09-24T21:15:41,999 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-09-24T21:15:42,000 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-09-24T21:15:42,001 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:42,001 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-09-24T21:15:42,002 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:42,002 | ^ 2024-09-24T21:15:42,003 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-09-24T21:15:42,004 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-09-24T21:15:42,005 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:15:42,275 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-311/command_shuffle.o -fopenmp 2024-09-24T21:15:42,588 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c global_basic.c -o build/temp.linux-armv7l-cpython-311/global_basic.o -fopenmp 2024-09-24T21:15:42,757 global_basic.c: In function ‘organize_infile_list’: 2024-09-24T21:15:42,758 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-09-24T21:15:42,759 195 | while (isspace(*buf)) buf++; 2024-09-24T21:15:42,759 | ^~~~~~~ 2024-09-24T21:15:42,760 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2024-09-24T21:15:42,760 34 | #include 2024-09-24T21:15:42,761 +++ |+#include 2024-09-24T21:15:42,761 35 | 2024-09-24T21:15:42,762 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=] 2024-09-24T21:15:42,763 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-09-24T21:15:42,763 | ~~^ 2024-09-24T21:15:42,764 | | 2024-09-24T21:15:42,765 | long unsigned int 2024-09-24T21:15:42,765 | %u 2024-09-24T21:15:42,766 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-09-24T21:15:42,766 | ~~~~~~~~~~~ 2024-09-24T21:15:42,767 | | 2024-09-24T21:15:42,767 | size_t {aka unsigned int} 2024-09-24T21:15:42,768 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=] 2024-09-24T21:15:42,769 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-09-24T21:15:42,770 | ~~^ 2024-09-24T21:15:42,771 | | 2024-09-24T21:15:42,771 | long unsigned int 2024-09-24T21:15:42,772 | %u 2024-09-24T21:15:42,772 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-09-24T21:15:42,773 | ~~~~~~~~~~~ 2024-09-24T21:15:42,774 | | 2024-09-24T21:15:42,774 | size_t {aka unsigned int} 2024-09-24T21:15:43,549 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-311/iseq2comem.o -fopenmp 2024-09-24T21:15:43,724 iseq2comem.c: In function ‘reads2mco’: 2024-09-24T21:15:43,725 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,725 156 | if (base > TL) { 2024-09-24T21:15:43,726 | ^ 2024-09-24T21:15:43,726 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,727 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-09-24T21:15:43,727 | ^~ 2024-09-24T21:15:43,728 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,728 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-09-24T21:15:43,729 | ^ 2024-09-24T21:15:43,730 iseq2comem.c: In function ‘fasta2co’: 2024-09-24T21:15:43,730 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,731 239 | if (base > TL) { 2024-09-24T21:15:43,731 | ^ 2024-09-24T21:15:43,732 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,732 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-09-24T21:15:43,733 | ^~ 2024-09-24T21:15:43,734 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,734 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-09-24T21:15:43,735 | ^ 2024-09-24T21:15:43,736 iseq2comem.c: In function ‘fastq2co’: 2024-09-24T21:15:43,737 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-09-24T21:15:43,737 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-09-24T21:15:43,738 | ^~ 2024-09-24T21:15:43,739 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,739 318 | if (base > TL) { 2024-09-24T21:15:43,740 | ^ 2024-09-24T21:15:43,741 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,741 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-09-24T21:15:43,742 | ^~ 2024-09-24T21:15:43,742 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,743 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-09-24T21:15:43,744 | ^ 2024-09-24T21:15:43,745 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,745 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-09-24T21:15:43,746 | ^ 2024-09-24T21:15:43,747 iseq2comem.c: In function ‘fastq2koc’: 2024-09-24T21:15:43,748 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,748 402 | if (base > TL) { 2024-09-24T21:15:43,749 | ^ 2024-09-24T21:15:43,749 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,750 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-09-24T21:15:43,751 | ^~ 2024-09-24T21:15:43,752 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,753 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-09-24T21:15:43,753 | ^ 2024-09-24T21:15:43,754 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-09-24T21:15:43,754 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,755 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-09-24T21:15:43,755 | ^~ 2024-09-24T21:15:43,756 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:43,756 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-09-24T21:15:43,757 | ^ 2024-09-24T21:15:45,088 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2024-09-24T21:15:45,142 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mytime.c -o build/temp.linux-armv7l-cpython-311/mytime.o -fopenmp 2024-09-24T21:15:45,268 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c pykssd.c -o build/temp.linux-armv7l-cpython-311/pykssd.o -fopenmp 2024-09-24T21:15:45,652 pykssd.c: In function ‘py_dist_dispatch’: 2024-09-24T21:15:45,653 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-09-24T21:15:45,654 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-09-24T21:15:45,654 | ^~~~~~ 2024-09-24T21:15:45,655 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-09-24T21:15:45,656 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-09-24T21:15:45,656 | ^~~~~~ 2024-09-24T21:15:45,657 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-09-24T21:15:45,658 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-09-24T21:15:45,658 | ^~~~~~ 2024-09-24T21:15:46,218 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/co2mco.o build/temp.linux-armv7l-cpython-311/command_composite.o build/temp.linux-armv7l-cpython-311/command_dist.o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o build/temp.linux-armv7l-cpython-311/command_set.o build/temp.linux-armv7l-cpython-311/command_shuffle.o build/temp.linux-armv7l-cpython-311/global_basic.o build/temp.linux-armv7l-cpython-311/iseq2comem.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/mytime.o build/temp.linux-armv7l-cpython-311/pykssd.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -fopenmp 2024-09-24T21:15:46,366 building 'nj' extension 2024-09-24T21:15:46,367 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c align.c -o build/temp.linux-armv7l-cpython-311/align.o 2024-09-24T21:15:46,857 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c buildtree.c -o build/temp.linux-armv7l-cpython-311/buildtree.o 2024-09-24T21:15:47,006 buildtree.c: In function ‘UPGMA_buildtree’: 2024-09-24T21:15:47,006 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-09-24T21:15:47,007 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-09-24T21:15:47,007 | ^~ 2024-09-24T21:15:47,008 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-09-24T21:15:47,009 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-09-24T21:15:47,010 | ^~ 2024-09-24T21:15:47,667 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c cluster.c -o build/temp.linux-armv7l-cpython-311/cluster.o 2024-09-24T21:15:48,255 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c distancemat.c -o build/temp.linux-armv7l-cpython-311/distancemat.o 2024-09-24T21:15:48,390 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-09-24T21:15:48,391 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-09-24T21:15:48,391 226 | for( i=0; i < dest->size; i++) { 2024-09-24T21:15:48,392 | ^ 2024-09-24T21:15:48,393 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-09-24T21:15:48,393 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-09-24T21:15:48,394 260 | for( i=0; i < mat->size; i++) { 2024-09-24T21:15:48,394 | ^ 2024-09-24T21:15:48,395 distancemat.c: In function ‘print_DistanceMatrix’: 2024-09-24T21:15:48,396 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-09-24T21:15:48,397 349 | for(row=0; row < mat->size; row++) { 2024-09-24T21:15:48,398 | ^ 2024-09-24T21:15:48,398 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-09-24T21:15:48,399 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-09-24T21:15:48,400 410 | while(c = fgetc(handle)) { 2024-09-24T21:15:48,400 | ^ 2024-09-24T21:15:48,781 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c pynj.c -o build/temp.linux-armv7l-cpython-311/pynj.o 2024-09-24T21:15:49,215 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c sequence.c -o build/temp.linux-armv7l-cpython-311/sequence.o 2024-09-24T21:15:49,430 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c tree.c -o build/temp.linux-armv7l-cpython-311/tree.o 2024-09-24T21:15:50,271 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c util.c -o build/temp.linux-armv7l-cpython-311/util.o 2024-09-24T21:15:50,444 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/align.o build/temp.linux-armv7l-cpython-311/buildtree.o build/temp.linux-armv7l-cpython-311/cluster.o build/temp.linux-armv7l-cpython-311/distancemat.o build/temp.linux-armv7l-cpython-311/pynj.o build/temp.linux-armv7l-cpython-311/sequence.o build/temp.linux-armv7l-cpython-311/tree.o build/temp.linux-armv7l-cpython-311/util.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so 2024-09-24T21:15:50,556 building 'dnj' extension 2024-09-24T21:15:50,556 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c bytescale.c -o build/temp.linux-armv7l-cpython-311/bytescale.o -fopenmp 2024-09-24T21:15:50,613 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c dnj.c -o build/temp.linux-armv7l-cpython-311/dnj.o -fopenmp 2024-09-24T21:15:50,752 dnj.c: In function ‘minQpair’: 2024-09-24T21:15:50,752 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,753 70 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,754 | ^~~ 2024-09-24T21:15:50,755 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,755 126 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,756 | ^~~ 2024-09-24T21:15:50,757 dnj.c: In function ‘maxQpair’: 2024-09-24T21:15:50,758 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,758 157 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,759 | ^~~ 2024-09-24T21:15:50,760 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,761 213 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,762 | ^~~ 2024-09-24T21:15:50,762 dnj.c: In function ‘UPGMApair’: 2024-09-24T21:15:50,763 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,763 237 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,764 | ^~~ 2024-09-24T21:15:50,765 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,766 284 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,766 | ^~~ 2024-09-24T21:15:50,767 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,768 291 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,768 | ^~~ 2024-09-24T21:15:50,769 dnj.c: In function ‘minQrow’: 2024-09-24T21:15:50,770 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,770 374 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,771 | ^~~ 2024-09-24T21:15:50,772 dnj.c: In function ‘maxQrow’: 2024-09-24T21:15:50,773 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,774 435 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,774 | ^~~ 2024-09-24T21:15:50,775 dnj.c: In function ‘UPGMArow’: 2024-09-24T21:15:50,775 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,776 488 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,776 | ^~~ 2024-09-24T21:15:50,777 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,777 494 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,778 | ^~~ 2024-09-24T21:15:50,778 dnj.c: In function ‘minQ_thread’: 2024-09-24T21:15:50,779 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:50,779 553 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:50,780 | ^~~ 2024-09-24T21:15:52,121 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c filebuff.c -o build/temp.linux-armv7l-cpython-311/filebuff.o -fopenmp 2024-09-24T21:15:52,240 filebuff.c: In function ‘BuffgzFileBuff’: 2024-09-24T21:15:52,241 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:52,241 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-09-24T21:15:52,242 | ^~ 2024-09-24T21:15:52,568 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c hclust.c -o build/temp.linux-armv7l-cpython-311/hclust.o -fopenmp 2024-09-24T21:15:52,703 hclust.c: In function ‘minQ’: 2024-09-24T21:15:52,704 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-09-24T21:15:52,705 364 | while(++i < Q->n) { 2024-09-24T21:15:52,705 | ^ 2024-09-24T21:15:52,706 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:52,707 377 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:52,707 | ^~~ 2024-09-24T21:15:52,708 hclust.c: In function ‘maxQ’: 2024-09-24T21:15:52,709 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-09-24T21:15:52,710 394 | while(++i < Q->n) { 2024-09-24T21:15:52,710 | ^ 2024-09-24T21:15:52,711 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:52,711 407 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:52,712 | ^~~ 2024-09-24T21:15:55,080 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c matrix.c -o build/temp.linux-armv7l-cpython-311/matrix.o -fopenmp 2024-09-24T21:15:55,227 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-09-24T21:15:55,228 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-09-24T21:15:55,228 538 | if(pos != n) { 2024-09-24T21:15:55,229 | ^~ 2024-09-24T21:15:56,136 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2024-09-24T21:15:56,191 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nj.c -o build/temp.linux-armv7l-cpython-311/nj.o -fopenmp 2024-09-24T21:15:56,321 nj.c: In function ‘initQ’: 2024-09-24T21:15:56,321 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:56,322 243 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:56,322 | ^~~ 2024-09-24T21:15:56,323 nj.c: In function ‘initQ_MN’: 2024-09-24T21:15:56,324 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:56,324 358 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:56,325 | ^~~ 2024-09-24T21:15:56,329 nj.c: In function ‘minD’: 2024-09-24T21:15:56,329 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:56,330 559 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:56,330 | ^~~ 2024-09-24T21:15:56,331 nj.c: In function ‘maxD’: 2024-09-24T21:15:56,331 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:56,332 642 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:56,333 | ^~~ 2024-09-24T21:15:56,336 nj.c: In function ‘minPair’: 2024-09-24T21:15:56,336 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-09-24T21:15:56,337 826 | pos <<= sizeof(unsigned) * 8; 2024-09-24T21:15:56,338 | ^~~ 2024-09-24T21:15:58,692 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nwck.c -o build/temp.linux-armv7l-cpython-311/nwck.o -fopenmp 2024-09-24T21:15:59,261 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pherror.c -o build/temp.linux-armv7l-cpython-311/pherror.o -fopenmp 2024-09-24T21:15:59,353 pherror.c: In function ‘cfread’: 2024-09-24T21:15:59,354 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-09-24T21:15:59,355 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-09-24T21:15:59,356 | ^~ 2024-09-24T21:15:59,447 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c phy.c -o build/temp.linux-armv7l-cpython-311/phy.o -fopenmp 2024-09-24T21:16:00,507 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pydnj.c -o build/temp.linux-armv7l-cpython-311/pydnj.o -fopenmp 2024-09-24T21:16:00,878 In file included from pydnj.c:11: 2024-09-24T21:16:00,878 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-09-24T21:16:00,879 20 | #define _XOPEN_SOURCE 600 2024-09-24T21:16:00,879 | 2024-09-24T21:16:00,880 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-09-24T21:16:00,881 from /usr/include/stdlib.h:26, 2024-09-24T21:16:00,881 from /usr/include/python3.11/Python.h:23, 2024-09-24T21:16:00,882 from pydnj.c:1: 2024-09-24T21:16:00,883 /usr/include/features.h:214: note: this is the location of the previous definition 2024-09-24T21:16:00,883 214 | # define _XOPEN_SOURCE 700 2024-09-24T21:16:00,884 | 2024-09-24T21:16:00,903 pydnj.c: In function ‘py_build’: 2024-09-24T21:16:00,904 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-09-24T21:16:00,905 165 | p = omp_get_num_procs(); 2024-09-24T21:16:00,907 | ^~~~~~~~~~~~~~~~~ 2024-09-24T21:16:01,023 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2024-09-24T21:16:01,024 169 | free(file); 2024-09-24T21:16:01,025 | ^~~~~~~~~~ 2024-09-24T21:16:01,025 pydnj.c:125:12: note: returned from ‘fopen’ 2024-09-24T21:16:01,026 125 | file = fopen(inputfilename, "r"); 2024-09-24T21:16:01,026 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-09-24T21:16:01,097 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c qseqs.c -o build/temp.linux-armv7l-cpython-311/qseqs.o -fopenmp 2024-09-24T21:16:01,304 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c str.c -o build/temp.linux-armv7l-cpython-311/str.o -fopenmp 2024-09-24T21:16:01,415 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c tmp.c -o build/temp.linux-armv7l-cpython-311/tmp.o -fopenmp 2024-09-24T21:16:01,610 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c vector.c -o build/temp.linux-armv7l-cpython-311/vector.o -fopenmp 2024-09-24T21:16:01,773 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/bytescale.o build/temp.linux-armv7l-cpython-311/dnj.o build/temp.linux-armv7l-cpython-311/filebuff.o build/temp.linux-armv7l-cpython-311/hclust.o build/temp.linux-armv7l-cpython-311/matrix.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/nj.o build/temp.linux-armv7l-cpython-311/nwck.o build/temp.linux-armv7l-cpython-311/pherror.o build/temp.linux-armv7l-cpython-311/phy.o build/temp.linux-armv7l-cpython-311/pydnj.o build/temp.linux-armv7l-cpython-311/qseqs.o build/temp.linux-armv7l-cpython-311/str.o build/temp.linux-armv7l-cpython-311/tmp.o build/temp.linux-armv7l-cpython-311/vector.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -fopenmp 2024-09-24T21:16:01,962 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-09-24T21:16:01,963 !! 2024-09-24T21:16:01,964 ******************************************************************************** 2024-09-24T21:16:01,965 Please avoid running ``setup.py`` directly. 2024-09-24T21:16:01,966 Instead, use pypa/build, pypa/installer or other 2024-09-24T21:16:01,967 standards-based tools. 2024-09-24T21:16:01,968 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-09-24T21:16:01,969 ******************************************************************************** 2024-09-24T21:16:01,970 !! 2024-09-24T21:16:01,971 self.initialize_options() 2024-09-24T21:16:02,011 installing to build/bdist.linux-armv7l/wheel 2024-09-24T21:16:02,012 running install 2024-09-24T21:16:02,040 running install_lib 2024-09-24T21:16:02,071 creating build/bdist.linux-armv7l/wheel 2024-09-24T21:16:02,074 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-09-24T21:16:02,084 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-09-24T21:16:02,094 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel/. 2024-09-24T21:16:02,098 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel/. 2024-09-24T21:16:02,101 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-09-24T21:16:02,106 running install_egg_info 2024-09-24T21:16:02,143 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/./kssdtree-2.0.1-py3.11.egg-info 2024-09-24T21:16:02,156 running install_scripts 2024-09-24T21:16:02,213 creating build/bdist.linux-armv7l/wheel/kssdtree-2.0.1.dist-info/WHEEL 2024-09-24T21:16:02,217 creating '/tmp/pip-wheel-kbbeklw0/kssdtree-2.0.1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-09-24T21:16:02,283 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2024-09-24T21:16:02,368 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2024-09-24T21:16:02,373 adding 'kssdtree.py' 2024-09-24T21:16:02,394 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2024-09-24T21:16:02,397 adding 'toolutils.py' 2024-09-24T21:16:02,400 adding 'kssdtree-2.0.1.dist-info/METADATA' 2024-09-24T21:16:02,401 adding 'kssdtree-2.0.1.dist-info/WHEEL' 2024-09-24T21:16:02,403 adding 'kssdtree-2.0.1.dist-info/dependency_links.txt' 2024-09-24T21:16:02,404 adding 'kssdtree-2.0.1.dist-info/top_level.txt' 2024-09-24T21:16:02,405 adding 'kssdtree-2.0.1.dist-info/RECORD' 2024-09-24T21:16:02,412 removing build/bdist.linux-armv7l/wheel 2024-09-24T21:16:02,560 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-09-24T21:16:02,567 Created wheel for kssdtree: filename=kssdtree-2.0.1-cp311-cp311-linux_armv7l.whl size=379987 sha256=8b8c3190a5a4a010758772e9d53c3c12436541437bc9c503bec9a8f6a007cdcc 2024-09-24T21:16:02,568 Stored in directory: /tmp/pip-ephem-wheel-cache-khgjgwto/wheels/a4/5e/47/3fcb5df67d6fb35de270c5f22707bee06ff18ea91045d8c86f 2024-09-24T21:16:02,577 Successfully built kssdtree 2024-09-24T21:16:02,593 Removed build tracker: '/tmp/pip-build-tracker-t2badl9c'