2026-02-12T01:59:26,652 Created temporary directory: /tmp/pip-ephem-wheel-cache-7lk030x5 2026-02-12T01:59:26,654 Created temporary directory: /tmp/pip-build-tracker-igp6oopg 2026-02-12T01:59:26,655 Initialized build tracking at /tmp/pip-build-tracker-igp6oopg 2026-02-12T01:59:26,655 Created build tracker: /tmp/pip-build-tracker-igp6oopg 2026-02-12T01:59:26,656 Entered build tracker: /tmp/pip-build-tracker-igp6oopg 2026-02-12T01:59:26,657 Created temporary directory: /tmp/pip-wheel-w8689nlj 2026-02-12T01:59:26,659 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-12T01:59:26,662 Created temporary directory: /tmp/pip-ephem-wheel-cache-dhgb82mq 2026-02-12T01:59:26,686 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-12T01:59:26,690 2 location(s) to search for versions of kssdtree: 2026-02-12T01:59:26,690 * https://pypi.org/simple/kssdtree/ 2026-02-12T01:59:26,690 * https://www.piwheels.org/simple/kssdtree/ 2026-02-12T01:59:26,691 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2026-02-12T01:59:26,692 Getting page https://pypi.org/simple/kssdtree/ 2026-02-12T01:59:26,693 Found index url https://pypi.org/simple 2026-02-12T01:59:26,907 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2026-02-12T01:59:26,911 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 2026-02-12T01:59:26,912 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 2026-02-12T01:59:26,913 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 2026-02-12T01:59:26,914 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 2026-02-12T01:59:26,914 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 2026-02-12T01:59:26,915 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 2026-02-12T01:59:26,916 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 2026-02-12T01:59:26,916 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 2026-02-12T01:59:26,917 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 2026-02-12T01:59:26,918 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 2026-02-12T01:59:26,918 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 2026-02-12T01:59:26,919 Found link https://files.pythonhosted.org/packages/c0/0f/effc10c8e76dbe3b9a35a4b4d9e65a0a889ee805e10334541c3ca7ae3b94/kssdtree-2.0.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.3 2026-02-12T01:59:26,920 Found link https://files.pythonhosted.org/packages/fc/8d/d3790baa2f2f0a01c913005b94a82dc13ef601e7015e662ccff94bb1b458/kssdtree-2.0.4.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.4 2026-02-12T01:59:26,920 Found link https://files.pythonhosted.org/packages/b5/f8/19480a4c57704944f973ebf534f9582054949cca20170a33c6f874974440/kssdtree-2.0.5.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.5 2026-02-12T01:59:26,921 Found link https://files.pythonhosted.org/packages/46/ef/2d920d5d2fceded48c7add363e04f49ae85414bcd4360e1295d6fddc4a24/kssdtree-2.0.6.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.6 2026-02-12T01:59:26,921 Found link https://files.pythonhosted.org/packages/9c/1c/c6b3f05465d145856ac992328bd59e776286a59b120254620c1dbffcf67f/kssdtree-2.0.7.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.7 2026-02-12T01:59:26,922 Found link https://files.pythonhosted.org/packages/82/9b/dac2af6572f0c4421e5ba8341dcfddac466de30c62acfa019d9ef70b2670/kssdtree-2.0.8.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.8 2026-02-12T01:59:26,922 Found link https://files.pythonhosted.org/packages/41/14/6350a913694cb9af7e5d542e566286c28d7a96c0b257bf7e19e8cc0400d0/kssdtree-2.0.9.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.9 2026-02-12T01:59:26,923 Found link https://files.pythonhosted.org/packages/2d/27/624f3bdd2bb038c3095130be4908ff39cae2e05bdb693b709b1c87a463ec/kssdtree-2.1.0.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.1.0 2026-02-12T01:59:26,923 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2026-02-12T01:59:26,924 Getting page https://www.piwheels.org/simple/kssdtree/ 2026-02-12T01:59:26,925 Found index url https://www.piwheels.org/simple 2026-02-12T01:59:27,079 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2026-02-12T01:59:27,099 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-2.0.8-cp311-cp311-linux_armv6l.whl#sha256=af8a0b06198bfd1ce24b078cdad070d5c587b126973ade98efa6ab13b9c2fc32 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,100 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-2.0.8-cp311-cp311-linux_armv7l.whl#sha256=af8a0b06198bfd1ce24b078cdad070d5c587b126973ade98efa6ab13b9c2fc32 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,100 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-2.0.8-cp39-cp39-linux_armv6l.whl#sha256=fb6f717dcadeee1974e114645ccfca55bc46eb4f46872cea71acc544102be042 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,101 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-2.0.8-cp39-cp39-linux_armv7l.whl#sha256=fb6f717dcadeee1974e114645ccfca55bc46eb4f46872cea71acc544102be042 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,102 Skipping link: No binaries permitted for kssdtree: 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https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp311-cp311-linux_armv6l.whl#sha256=d4c397f5fcb0af48dbb11b9fb7d7b399cc180d65355b794a8fcc7327e9a7dde1 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,120 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp311-cp311-linux_armv7l.whl#sha256=d4c397f5fcb0af48dbb11b9fb7d7b399cc180d65355b794a8fcc7327e9a7dde1 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,121 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp39-cp39-linux_armv6l.whl#sha256=ab11dc15aca2923fe0d60bf11deb134bed4df89280b4ce40ca8e9bf3ca46b168 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,122 Skipping link: No binaries permitted for kssdtree: 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https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp311-cp311-linux_armv6l.whl#sha256=0901b6cf3efb240d5d32b1e88a8863f28e2986a2c0749886421c643b98a4aec2 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,127 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp311-cp311-linux_armv7l.whl#sha256=0901b6cf3efb240d5d32b1e88a8863f28e2986a2c0749886421c643b98a4aec2 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,128 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp39-cp39-linux_armv6l.whl#sha256=9defb70b5162efc2c0eb6e415a7e37c604aa9b248a006af86af8f59a3bce5d2b (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,128 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp39-cp39-linux_armv7l.whl#sha256=9defb70b5162efc2c0eb6e415a7e37c604aa9b248a006af86af8f59a3bce5d2b (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,129 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp37-cp37m-linux_armv6l.whl#sha256=ffef4ae0f634dd977cc2ec6798b9f36f73d788aca27bb7199f552d5513c34413 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,130 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp37-cp37m-linux_armv7l.whl#sha256=ffef4ae0f634dd977cc2ec6798b9f36f73d788aca27bb7199f552d5513c34413 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,130 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp311-cp311-linux_armv6l.whl#sha256=64b685362c3f9027bfeafdffb6a5d58c349a76fd551eeb7b98de146827463e75 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,130 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp311-cp311-linux_armv7l.whl#sha256=64b685362c3f9027bfeafdffb6a5d58c349a76fd551eeb7b98de146827463e75 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,131 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp39-cp39-linux_armv6l.whl#sha256=34527068d84569095aefee41a353c5dfc0dfa55b68097890da9a1eca2ee9b726 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,131 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp39-cp39-linux_armv7l.whl#sha256=34527068d84569095aefee41a353c5dfc0dfa55b68097890da9a1eca2ee9b726 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,132 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp311-cp311-linux_armv6l.whl#sha256=6b76f3b3f532934ad49a829e7bf8176af580f4687f1491c49c3f571bf081f961 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,132 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp311-cp311-linux_armv7l.whl#sha256=6b76f3b3f532934ad49a829e7bf8176af580f4687f1491c49c3f571bf081f961 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,133 Skipping link: No binaries permitted for kssdtree: 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https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp39-cp39-linux_armv7l.whl#sha256=6df2298fa80eefa823153fa0b9db67e35da72da7f88c5949f4f637872ff22c3b (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,135 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv6l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,136 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv7l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,136 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv6l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,137 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv7l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,138 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp39-cp39-linux_armv6l.whl#sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,138 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp39-cp39-linux_armv7l.whl#sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,138 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv6l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,139 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv7l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,139 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv6l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,140 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv7l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,140 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv6l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,141 Skipping link: No binaries permitted for kssdtree: https://archive1.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv7l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2026-02-12T01:59:27,142 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2026-02-12T01:59:27,142 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2026-02-12T01:59:27,163 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2026-02-12T01:59:27,181 Collecting kssdtree==2.1.0 2026-02-12T01:59:27,184 Created temporary directory: /tmp/pip-unpack-m5djtm6d 2026-02-12T01:59:27,317 Downloading kssdtree-2.1.0.tar.gz (114 kB) 2026-02-12T01:59:27,536 Added kssdtree==2.1.0 from https://files.pythonhosted.org/packages/2d/27/624f3bdd2bb038c3095130be4908ff39cae2e05bdb693b709b1c87a463ec/kssdtree-2.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-igp6oopg' 2026-02-12T01:59:27,537 Running setup.py (path:/tmp/pip-wheel-w8689nlj/kssdtree_ffd1d2d4963b4baf95112d04c059454f/setup.py) egg_info for package kssdtree 2026-02-12T01:59:27,538 Created temporary directory: /tmp/pip-pip-egg-info-wfoldmik 2026-02-12T01:59:27,539 Preparing metadata (setup.py): started 2026-02-12T01:59:27,540 Running command python setup.py egg_info 2026-02-12T01:59:28,454 running egg_info 2026-02-12T01:59:28,481 creating /tmp/pip-pip-egg-info-wfoldmik/kssdtree.egg-info 2026-02-12T01:59:28,482 writing /tmp/pip-pip-egg-info-wfoldmik/kssdtree.egg-info/PKG-INFO 2026-02-12T01:59:28,485 writing dependency_links to /tmp/pip-pip-egg-info-wfoldmik/kssdtree.egg-info/dependency_links.txt 2026-02-12T01:59:28,487 writing requirements to /tmp/pip-pip-egg-info-wfoldmik/kssdtree.egg-info/requires.txt 2026-02-12T01:59:28,488 writing top-level names to /tmp/pip-pip-egg-info-wfoldmik/kssdtree.egg-info/top_level.txt 2026-02-12T01:59:28,489 writing manifest file '/tmp/pip-pip-egg-info-wfoldmik/kssdtree.egg-info/SOURCES.txt' 2026-02-12T01:59:28,574 reading manifest file '/tmp/pip-pip-egg-info-wfoldmik/kssdtree.egg-info/SOURCES.txt' 2026-02-12T01:59:28,576 reading manifest template 'MANIFEST.in' 2026-02-12T01:59:28,593 writing manifest file '/tmp/pip-pip-egg-info-wfoldmik/kssdtree.egg-info/SOURCES.txt' 2026-02-12T01:59:28,700 Preparing metadata (setup.py): finished with status 'done' 2026-02-12T01:59:28,705 Source in /tmp/pip-wheel-w8689nlj/kssdtree_ffd1d2d4963b4baf95112d04c059454f has version 2.1.0, which satisfies requirement kssdtree==2.1.0 from https://files.pythonhosted.org/packages/2d/27/624f3bdd2bb038c3095130be4908ff39cae2e05bdb693b709b1c87a463ec/kssdtree-2.1.0.tar.gz 2026-02-12T01:59:28,706 Removed kssdtree==2.1.0 from https://files.pythonhosted.org/packages/2d/27/624f3bdd2bb038c3095130be4908ff39cae2e05bdb693b709b1c87a463ec/kssdtree-2.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-igp6oopg' 2026-02-12T01:59:28,710 Created temporary directory: /tmp/pip-unpack-gccs_342 2026-02-12T01:59:28,710 Building wheels for collected packages: kssdtree 2026-02-12T01:59:28,714 Created temporary directory: /tmp/pip-wheel-otx87r0k 2026-02-12T01:59:28,715 Building wheel for kssdtree (setup.py): started 2026-02-12T01:59:28,716 Destination directory: /tmp/pip-wheel-otx87r0k 2026-02-12T01:59:28,717 Running command python setup.py bdist_wheel 2026-02-12T01:59:29,542 running bdist_wheel 2026-02-12T01:59:29,645 running build 2026-02-12T01:59:29,646 running build_py 2026-02-12T01:59:29,676 creating build/lib.linux-armv7l-cpython-311 2026-02-12T01:59:29,678 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2026-02-12T01:59:29,681 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2026-02-12T01:59:29,683 running egg_info 2026-02-12T01:59:29,926 writing kssdtree.egg-info/PKG-INFO 2026-02-12T01:59:29,929 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2026-02-12T01:59:29,930 writing requirements to kssdtree.egg-info/requires.txt 2026-02-12T01:59:29,932 writing top-level names to kssdtree.egg-info/top_level.txt 2026-02-12T01:59:29,961 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2026-02-12T01:59:29,966 reading manifest template 'MANIFEST.in' 2026-02-12T01:59:29,983 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2026-02-12T01:59:29,986 running build_ext 2026-02-12T01:59:30,444 building 'kssd' extension 2026-02-12T01:59:30,445 creating build/temp.linux-armv7l-cpython-311 2026-02-12T01:59:30,447 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 2026-02-12T01:59:30,623 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2026-02-12T01:59:30,624 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-02-12T01:59:30,625 109 | for (unsigned int i = 0; i < comp_num; i++) { 2026-02-12T01:59:30,625 | ^ 2026-02-12T01:59:30,628 co2mco.c: In function ‘co2unitllmco’: 2026-02-12T01:59:30,629 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-02-12T01:59:30,630 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2026-02-12T01:59:30,630 | ^ 2026-02-12T01:59:31,365 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 2026-02-12T01:59:31,740 command_composite.c: In function ‘get_species_abundance’: 2026-02-12T01:59:31,741 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2026-02-12T01:59:31,741 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2026-02-12T01:59:31,741 | ^~ 2026-02-12T01:59:31,742 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2026-02-12T01:59:31,742 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2026-02-12T01:59:31,743 | ^~ 2026-02-12T01:59:31,743 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:31,744 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-02-12T01:59:31,744 | ^ 2026-02-12T01:59:31,745 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:31,745 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-02-12T01:59:31,746 | ^~~~~~~~~~ 2026-02-12T01:59:31,746 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-02-12T01:59:31,747 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-02-12T01:59:31,747 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:31,748 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:31,749 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-02-12T01:59:31,749 | ^ 2026-02-12T01:59:31,750 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:31,751 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-02-12T01:59:31,751 | ^~~~~~~~~~ 2026-02-12T01:59:31,752 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-02-12T01:59:31,753 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-02-12T01:59:31,753 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:31,754 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:31,755 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-02-12T01:59:31,755 | ^ 2026-02-12T01:59:31,756 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:31,757 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-02-12T01:59:31,757 | ^~~~~~~~~~ 2026-02-12T01:59:31,758 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-02-12T01:59:31,759 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-02-12T01:59:31,759 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:31,760 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:31,761 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-02-12T01:59:31,761 | ^ 2026-02-12T01:59:31,762 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:31,762 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-02-12T01:59:31,763 | ^~~~~~~~~~ 2026-02-12T01:59:31,763 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-02-12T01:59:31,764 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-02-12T01:59:31,764 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:31,765 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:31,765 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-02-12T01:59:31,766 | ^ 2026-02-12T01:59:31,766 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:31,767 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-02-12T01:59:31,767 | ^~~~~~~~~~~~ 2026-02-12T01:59:31,768 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2026-02-12T01:59:31,769 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-02-12T01:59:31,769 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:32,047 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 2026-02-12T01:59:32,270 command_dist.c: In function ‘mco_cbd_co_dist’: 2026-02-12T01:59:32,271 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=] 2026-02-12T01:59:32,272 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-02-12T01:59:32,273 | ~~^ 2026-02-12T01:59:32,273 | | 2026-02-12T01:59:32,273 | long unsigned int 2026-02-12T01:59:32,274 | %u 2026-02-12T01:59:32,274 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-02-12T01:59:32,275 | ~~~~~~~ 2026-02-12T01:59:32,276 | | 2026-02-12T01:59:32,276 | size_t {aka unsigned int} 2026-02-12T01:59:32,277 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=] 2026-02-12T01:59:32,277 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-02-12T01:59:32,278 | ~~^ 2026-02-12T01:59:32,278 | | 2026-02-12T01:59:32,279 | long unsigned int 2026-02-12T01:59:32,280 | %u 2026-02-12T01:59:32,281 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-02-12T01:59:32,281 679 | maplength, (size_t) b * unitsz_distf_mapped); 2026-02-12T01:59:32,282 | ~~~~~~~~~ 2026-02-12T01:59:32,282 | | 2026-02-12T01:59:32,283 | size_t {aka unsigned int} 2026-02-12T01:59:32,283 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-02-12T01:59:32,284 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-02-12T01:59:32,284 | ~~^ 2026-02-12T01:59:32,284 | | 2026-02-12T01:59:32,285 | long unsigned int 2026-02-12T01:59:32,285 | %u 2026-02-12T01:59:32,286 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-02-12T01:59:32,286 679 | maplength, (size_t) b * unitsz_distf_mapped); 2026-02-12T01:59:32,287 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:32,287 | | 2026-02-12T01:59:32,288 | unsigned int 2026-02-12T01:59:32,289 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-02-12T01:59:32,289 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2026-02-12T01:59:32,290 | ^ 2026-02-12T01:59:32,296 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2026-02-12T01:59:32,298 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=] 2026-02-12T01:59:32,299 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-02-12T01:59:32,299 | ~~^ ~~~~~~~ 2026-02-12T01:59:32,300 | | | 2026-02-12T01:59:32,300 | long unsigned int size_t {aka unsigned int} 2026-02-12T01:59:32,301 | %u 2026-02-12T01:59:32,302 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=] 2026-02-12T01:59:32,302 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-02-12T01:59:32,303 | ~~^ 2026-02-12T01:59:32,303 | | 2026-02-12T01:59:32,304 | long unsigned int 2026-02-12T01:59:32,304 | %u 2026-02-12T01:59:32,305 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2026-02-12T01:59:32,306 | ~~~~~~~~~ 2026-02-12T01:59:32,306 | | 2026-02-12T01:59:32,307 | size_t {aka unsigned int} 2026-02-12T01:59:32,307 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-02-12T01:59:32,308 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-02-12T01:59:32,308 | ~~^ 2026-02-12T01:59:32,309 | | 2026-02-12T01:59:32,310 | long unsigned int 2026-02-12T01:59:32,310 | %u 2026-02-12T01:59:32,311 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2026-02-12T01:59:32,311 865 | (size_t) b * unitsz_distf_mapped); 2026-02-12T01:59:32,311 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:32,312 | | 2026-02-12T01:59:32,313 | unsigned int 2026-02-12T01:59:32,313 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2026-02-12T01:59:32,314 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2026-02-12T01:59:32,314 | ^~~~~~~ 2026-02-12T01:59:32,315 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2026-02-12T01:59:32,316 809 | struct stat cbd_fcode_stat; 2026-02-12T01:59:32,317 | ^~~~~~~~~~~~~~ 2026-02-12T01:59:32,317 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2026-02-12T01:59:32,318 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2026-02-12T01:59:32,319 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:32,319 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2026-02-12T01:59:32,320 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2026-02-12T01:59:32,320 | ^~~~~~~~~~~~~~~~~ 2026-02-12T01:59:32,326 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2026-02-12T01:59:32,328 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=] 2026-02-12T01:59:32,329 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-02-12T01:59:32,329 | ~~^ 2026-02-12T01:59:32,330 | | 2026-02-12T01:59:32,331 | long unsigned int 2026-02-12T01:59:32,331 | %u 2026-02-12T01:59:32,332 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-02-12T01:59:32,332 | ~~~~~~~ 2026-02-12T01:59:32,333 | | 2026-02-12T01:59:32,334 | size_t {aka unsigned int} 2026-02-12T01:59:32,335 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=] 2026-02-12T01:59:32,335 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-02-12T01:59:32,336 | ~~^ 2026-02-12T01:59:32,336 | | 2026-02-12T01:59:32,337 | long unsigned int 2026-02-12T01:59:32,337 | %u 2026-02-12T01:59:32,338 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-02-12T01:59:32,338 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2026-02-12T01:59:32,339 | ~~~~~~~~~ 2026-02-12T01:59:32,339 | | 2026-02-12T01:59:32,340 | size_t {aka unsigned int} 2026-02-12T01:59:32,340 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-02-12T01:59:32,341 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-02-12T01:59:32,341 | ~~^ 2026-02-12T01:59:32,342 | | 2026-02-12T01:59:32,342 | long unsigned int 2026-02-12T01:59:32,343 | %u 2026-02-12T01:59:32,344 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-02-12T01:59:32,344 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2026-02-12T01:59:32,345 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:32,346 | | 2026-02-12T01:59:32,347 | unsigned int 2026-02-12T01:59:32,347 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2026-02-12T01:59:32,348 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2026-02-12T01:59:32,349 | ^ 2026-02-12T01:59:32,349 command_dist.c: In function ‘mco_co_dist_core’: 2026-02-12T01:59:32,350 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-02-12T01:59:32,351 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2026-02-12T01:59:32,351 | ^ 2026-02-12T01:59:32,353 command_dist.c: In function ‘koc_dist_print_nobin’: 2026-02-12T01:59:32,354 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-02-12T01:59:32,355 1239 | for (int rid = 0; rid < ref_num; rid++) 2026-02-12T01:59:32,355 | ^ 2026-02-12T01:59:32,356 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-02-12T01:59:32,357 1245 | for (int rid = 0; rid < ref_num; rid++) { 2026-02-12T01:59:32,358 | ^ 2026-02-12T01:59:32,363 command_dist.c: In function ‘dist_print_nobin’: 2026-02-12T01:59:32,365 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-02-12T01:59:32,365 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2026-02-12T01:59:32,366 | ^ 2026-02-12T01:59:32,368 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-02-12T01:59:32,369 1356 | for (int rid = 0; rid < ref_num; rid++) { 2026-02-12T01:59:32,369 | ^ 2026-02-12T01:59:32,371 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-02-12T01:59:32,372 1382 | for (int rid = 0; rid < ref_num; rid++) 2026-02-12T01:59:32,372 | ^ 2026-02-12T01:59:32,731 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2026-02-12T01:59:32,732 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2026-02-12T01:59:32,733 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2026-02-12T01:59:32,733 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:32,734 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2026-02-12T01:59:32,735 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2026-02-12T01:59:32,735 | ^~~~~~~~~~~~ 2026-02-12T01:59:33,566 command_dist.c: In function ‘get_dim_shuffle’: 2026-02-12T01:59:33,567 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2026-02-12T01:59:33,568 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2026-02-12T01:59:33,569 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:33,569 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2026-02-12T01:59:33,570 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2026-02-12T01:59:33,570 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,465 command_dist.c: In function ‘mco_cbd_co_dist’: 2026-02-12T01:59:34,466 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:34,467 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-02-12T01:59:34,467 | ^~ ~~~~~~~~~ 2026-02-12T01:59:34,468 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-02-12T01:59:34,468 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-02-12T01:59:34,469 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,470 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-02-12T01:59:34,470 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-02-12T01:59:34,471 | ^~~~~~~~~~~~~~~ 2026-02-12T01:59:34,471 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-02-12T01:59:34,472 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-02-12T01:59:34,473 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,473 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-02-12T01:59:34,474 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-02-12T01:59:34,474 | ^~~~~~~~~~~ 2026-02-12T01:59:34,475 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:34,475 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-02-12T01:59:34,476 | ^~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,476 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2026-02-12T01:59:34,477 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-02-12T01:59:34,477 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,478 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-02-12T01:59:34,479 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-02-12T01:59:34,479 | ^~~~~ 2026-02-12T01:59:34,480 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:34,480 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-02-12T01:59:34,481 | ^~~~~~~~~~~ 2026-02-12T01:59:34,481 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-02-12T01:59:34,482 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-02-12T01:59:34,483 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,714 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2026-02-12T01:59:34,715 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:34,716 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-02-12T01:59:34,716 | ^~ ~~~~~~~~~ 2026-02-12T01:59:34,717 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-02-12T01:59:34,718 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-02-12T01:59:34,718 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,719 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-02-12T01:59:34,719 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-02-12T01:59:34,720 | ^~~~~~~~~~~~~~~ 2026-02-12T01:59:34,720 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-02-12T01:59:34,721 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-02-12T01:59:34,721 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,722 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-02-12T01:59:34,722 823 | sprintf(distf, "%s/distance.out", distout_dir); 2026-02-12T01:59:34,723 | ^~~~~~~~~~~~~ 2026-02-12T01:59:34,724 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-02-12T01:59:34,724 823 | sprintf(distf, "%s/distance.out", distout_dir); 2026-02-12T01:59:34,725 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,725 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:34,726 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-02-12T01:59:34,727 | ^ 2026-02-12T01:59:34,728 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2026-02-12T01:59:34,728 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-02-12T01:59:34,729 | ^~~~~~~~~~ 2026-02-12T01:59:34,729 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2026-02-12T01:59:34,730 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-02-12T01:59:34,730 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,731 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:34,731 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-02-12T01:59:34,732 | ^ 2026-02-12T01:59:34,732 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2026-02-12T01:59:34,733 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-02-12T01:59:34,733 | ^~~~~~~~~~ 2026-02-12T01:59:34,734 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2026-02-12T01:59:34,734 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-02-12T01:59:34,735 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:34,993 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2026-02-12T01:59:34,995 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:34,996 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-02-12T01:59:34,998 | ^~ ~~~~~~~~~ 2026-02-12T01:59:35,000 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-02-12T01:59:35,002 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-02-12T01:59:35,004 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:35,005 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-02-12T01:59:35,007 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-02-12T01:59:35,009 | ^~~~~~~~~~~~~~~ 2026-02-12T01:59:35,011 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-02-12T01:59:35,013 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-02-12T01:59:35,015 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:35,017 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-02-12T01:59:35,019 990 | sprintf(distf, "%s/distance.out", distout_dir); 2026-02-12T01:59:35,021 | ^~~~~~~~~~~~~ 2026-02-12T01:59:35,024 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-02-12T01:59:35,024 990 | sprintf(distf, "%s/distance.out", distout_dir); 2026-02-12T01:59:35,025 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:35,026 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-02-12T01:59:35,027 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-02-12T01:59:35,027 | ^~~~~~~~~~~ 2026-02-12T01:59:35,028 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:35,029 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-02-12T01:59:35,029 | ^~~~~~~~~~~~~~~~~ 2026-02-12T01:59:35,030 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2026-02-12T01:59:35,030 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-02-12T01:59:35,031 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:35,031 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-02-12T01:59:35,031 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-02-12T01:59:35,032 | ^~~~~ 2026-02-12T01:59:35,032 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:35,033 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-02-12T01:59:35,033 | ^~~~~~~~~~~ 2026-02-12T01:59:35,034 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-02-12T01:59:35,034 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-02-12T01:59:35,035 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:35,285 command_dist.c: In function ‘combine_queries’: 2026-02-12T01:59:35,287 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-12T01:59:35,290 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2026-02-12T01:59:35,292 | ^ 2026-02-12T01:59:35,293 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-02-12T01:59:35,294 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2026-02-12T01:59:35,295 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:35,295 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-12T01:59:35,296 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2026-02-12T01:59:35,296 | ^ 2026-02-12T01:59:35,297 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-02-12T01:59:35,298 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2026-02-12T01:59:35,298 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:35,299 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:35,299 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2026-02-12T01:59:35,300 | ^~ ~~~~~~~~ 2026-02-12T01:59:35,301 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-02-12T01:59:35,301 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2026-02-12T01:59:35,302 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:35,785 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 2026-02-12T01:59:35,957 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 2026-02-12T01:59:36,124 command_set.c: In function ‘sketch_operate’: 2026-02-12T01:59:36,124 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-02-12T01:59:36,125 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2026-02-12T01:59:36,125 | ^ 2026-02-12T01:59:36,137 command_set.c: In function ‘combin_subset_pans’: 2026-02-12T01:59:36,138 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-12T01:59:36,138 457 | free(co_dstat_fpath); 2026-02-12T01:59:36,139 | ^~~~~~~~~~~~~~ 2026-02-12T01:59:36,139 In file included from kssdheaders/global_basic.h:159, 2026-02-12T01:59:36,140 from command_set.c:15: 2026-02-12T01:59:36,141 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2026-02-12T01:59:36,141 568 | extern void free (void *__ptr) __THROW; 2026-02-12T01:59:36,142 | ~~~~~~^~~~~ 2026-02-12T01:59:36,146 command_set.c: In function ‘grouping_genomes’: 2026-02-12T01:59:36,146 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-02-12T01:59:36,147 562 | free(co_dstat_fpath); 2026-02-12T01:59:36,148 | ^~~~~~~~~~~~~~ 2026-02-12T01:59:36,148 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2026-02-12T01:59:36,149 568 | extern void free (void *__ptr) __THROW; 2026-02-12T01:59:36,149 | ~~~~~~^~~~~ 2026-02-12T01:59:36,315 command_set.c: In function ‘sketch_union’: 2026-02-12T01:59:36,315 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-12T01:59:36,316 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:36,317 | ^ 2026-02-12T01:59:36,317 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-02-12T01:59:36,318 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:36,318 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,319 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,320 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-02-12T01:59:36,320 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:36,321 command_set.c:82:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,322 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-02-12T01:59:36,322 | ^~~~~~~~~~ 2026-02-12T01:59:36,323 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-02-12T01:59:36,323 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-02-12T01:59:36,324 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,325 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,325 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-02-12T01:59:36,326 | ^~ ~~~~~~~~~~ 2026-02-12T01:59:36,327 command_set.c:92:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,327 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-02-12T01:59:36,328 | ^~~~~~~~~~ 2026-02-12T01:59:36,328 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-02-12T01:59:36,329 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-02-12T01:59:36,330 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,449 command_set.c: In function ‘sketch_operate’: 2026-02-12T01:59:36,449 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,450 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-02-12T01:59:36,450 | ^~ ~~~~~~~~~~ 2026-02-12T01:59:36,451 command_set.c:153:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,451 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-02-12T01:59:36,452 | ^~~~~~~~~~ 2026-02-12T01:59:36,452 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-02-12T01:59:36,453 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-02-12T01:59:36,453 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,454 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,455 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-02-12T01:59:36,455 | ^~ ~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,456 command_set.c:155:29: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,457 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-02-12T01:59:36,458 | ^~~~~~~~~~ 2026-02-12T01:59:36,458 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2026-02-12T01:59:36,459 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-02-12T01:59:36,460 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,461 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,461 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-02-12T01:59:36,462 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:36,463 command_set.c:165:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,463 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-02-12T01:59:36,464 | ^~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,464 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-02-12T01:59:36,465 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-02-12T01:59:36,466 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,467 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,467 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-02-12T01:59:36,468 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:36,469 command_set.c:169:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,469 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-02-12T01:59:36,470 | ^~~~~~~~~~ 2026-02-12T01:59:36,470 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-02-12T01:59:36,470 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-02-12T01:59:36,471 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,471 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,472 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-02-12T01:59:36,472 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:36,473 command_set.c:174:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,473 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-02-12T01:59:36,474 | ^~~~~~~~~~ 2026-02-12T01:59:36,474 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-02-12T01:59:36,475 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-02-12T01:59:36,475 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,476 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,476 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-02-12T01:59:36,477 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:36,478 command_set.c:187:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,478 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-02-12T01:59:36,479 | ^~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,479 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-02-12T01:59:36,480 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-02-12T01:59:36,481 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,481 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-12T01:59:36,482 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:36,483 | ^ 2026-02-12T01:59:36,483 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-02-12T01:59:36,484 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:36,485 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,627 command_set.c: In function ‘uniq_sketch_union’: 2026-02-12T01:59:36,628 command_set.c:219:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-12T01:59:36,628 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2026-02-12T01:59:36,629 | ^ 2026-02-12T01:59:36,629 command_set.c:219:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2026-02-12T01:59:36,630 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2026-02-12T01:59:36,631 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,631 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-12T01:59:36,632 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:36,633 | ^ 2026-02-12T01:59:36,634 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-02-12T01:59:36,634 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:36,635 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,635 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,636 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-02-12T01:59:36,636 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:36,637 command_set.c:247:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,637 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-02-12T01:59:36,638 | ^~~~~~~~~~ 2026-02-12T01:59:36,638 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-02-12T01:59:36,639 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-02-12T01:59:36,639 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,640 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,640 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-02-12T01:59:36,641 | ^~ ~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,642 command_set.c:259:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,643 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-02-12T01:59:36,643 | ^~~~~~~~~~ 2026-02-12T01:59:36,644 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2026-02-12T01:59:36,645 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-02-12T01:59:36,645 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,777 command_set.c: In function ‘combin_pans’: 2026-02-12T01:59:36,778 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,778 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-02-12T01:59:36,779 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:36,780 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2026-02-12T01:59:36,780 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-02-12T01:59:36,781 | ^~~~~~~~~~ 2026-02-12T01:59:36,781 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2026-02-12T01:59:36,782 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-02-12T01:59:36,783 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,783 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,784 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-02-12T01:59:36,785 | ^~ ~~~~~~~~~~ 2026-02-12T01:59:36,785 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2026-02-12T01:59:36,786 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-02-12T01:59:36,787 | ^~~~~~~~~~ 2026-02-12T01:59:36,788 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2026-02-12T01:59:36,788 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-02-12T01:59:36,789 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,789 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-12T01:59:36,790 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:36,790 | ^ 2026-02-12T01:59:36,791 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-02-12T01:59:36,791 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:36,792 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,994 command_set.c: In function ‘combin_subset_pans’: 2026-02-12T01:59:36,994 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:36,995 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-02-12T01:59:36,995 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:36,996 command_set.c:469:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:36,996 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-02-12T01:59:36,997 | ^~~~~~~~~~ 2026-02-12T01:59:36,997 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-02-12T01:59:36,998 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-02-12T01:59:36,999 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:36,999 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:37,000 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-02-12T01:59:37,000 | ^~ ~~~~~~~~~~ 2026-02-12T01:59:37,001 command_set.c:475:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:37,002 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-02-12T01:59:37,002 | ^~~~~~~~~~ 2026-02-12T01:59:37,003 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-02-12T01:59:37,004 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-02-12T01:59:37,004 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:37,005 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:37,006 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-02-12T01:59:37,006 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:37,007 command_set.c:481:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:37,008 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-02-12T01:59:37,008 | ^~~~~~~~~~ 2026-02-12T01:59:37,009 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-02-12T01:59:37,010 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-02-12T01:59:37,010 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:37,011 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:37,012 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-02-12T01:59:37,013 | ^~ ~~~~~~~~~~ 2026-02-12T01:59:37,013 command_set.c:512:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:37,014 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-02-12T01:59:37,014 | ^~~~~~~~~~ 2026-02-12T01:59:37,015 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-02-12T01:59:37,015 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-02-12T01:59:37,016 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:37,016 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-12T01:59:37,017 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:37,017 | ^ 2026-02-12T01:59:37,018 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-02-12T01:59:37,018 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:37,019 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:37,239 command_set.c: In function ‘grouping_genomes’: 2026-02-12T01:59:37,240 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:37,240 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-02-12T01:59:37,241 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:37,241 command_set.c:574:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:37,242 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-02-12T01:59:37,243 | ^~~~~~~~~~ 2026-02-12T01:59:37,243 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-02-12T01:59:37,244 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-02-12T01:59:37,244 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:37,245 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:37,246 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-02-12T01:59:37,246 | ^~ ~~~~~~~~~~ 2026-02-12T01:59:37,247 command_set.c:580:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:37,247 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-02-12T01:59:37,248 | ^~~~~~~~~~ 2026-02-12T01:59:37,248 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-02-12T01:59:37,249 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-02-12T01:59:37,250 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:37,250 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:37,251 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-02-12T01:59:37,251 | ^~ ~~~~~~~~~~~ 2026-02-12T01:59:37,252 command_set.c:612:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:37,253 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-02-12T01:59:37,254 | ^~~~~~~~~~ 2026-02-12T01:59:37,255 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-02-12T01:59:37,255 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-02-12T01:59:37,256 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:37,256 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-02-12T01:59:37,257 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-02-12T01:59:37,257 | ^~ ~~~~~~~~~~ 2026-02-12T01:59:37,258 command_set.c:634:25: note: directive argument in the range [-2147483644, 2147483646] 2026-02-12T01:59:37,258 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-02-12T01:59:37,259 | ^~~~~~~~~~ 2026-02-12T01:59:37,259 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-02-12T01:59:37,260 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-02-12T01:59:37,260 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:37,261 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-02-12T01:59:37,261 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:37,262 | ^ 2026-02-12T01:59:37,262 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-02-12T01:59:37,263 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-02-12T01:59:37,263 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:37,536 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 2026-02-12T01:59:37,848 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 2026-02-12T01:59:38,013 global_basic.c: In function ‘organize_infile_list’: 2026-02-12T01:59:38,014 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2026-02-12T01:59:38,015 195 | while (isspace(*buf)) buf++; 2026-02-12T01:59:38,015 | ^~~~~~~ 2026-02-12T01:59:38,016 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2026-02-12T01:59:38,016 34 | #include 2026-02-12T01:59:38,017 +++ |+#include 2026-02-12T01:59:38,018 35 | 2026-02-12T01:59:38,018 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=] 2026-02-12T01:59:38,019 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2026-02-12T01:59:38,019 | ~~^ 2026-02-12T01:59:38,020 | | 2026-02-12T01:59:38,021 | long unsigned int 2026-02-12T01:59:38,022 | %u 2026-02-12T01:59:38,022 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2026-02-12T01:59:38,023 | ~~~~~~~~~~~ 2026-02-12T01:59:38,024 | | 2026-02-12T01:59:38,024 | size_t {aka unsigned int} 2026-02-12T01:59:38,025 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=] 2026-02-12T01:59:38,025 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2026-02-12T01:59:38,026 | ~~^ 2026-02-12T01:59:38,026 | | 2026-02-12T01:59:38,027 | long unsigned int 2026-02-12T01:59:38,027 | %u 2026-02-12T01:59:38,028 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2026-02-12T01:59:38,028 | ~~~~~~~~~~~ 2026-02-12T01:59:38,029 | | 2026-02-12T01:59:38,029 | size_t {aka unsigned int} 2026-02-12T01:59:38,783 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 2026-02-12T01:59:38,960 iseq2comem.c: In function ‘reads2mco’: 2026-02-12T01:59:38,961 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,962 156 | if (base > TL) { 2026-02-12T01:59:38,962 | ^ 2026-02-12T01:59:38,963 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,964 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-02-12T01:59:38,965 | ^~ 2026-02-12T01:59:38,965 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,966 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-02-12T01:59:38,967 | ^ 2026-02-12T01:59:38,968 iseq2comem.c: In function ‘fasta2co’: 2026-02-12T01:59:38,968 iseq2comem.c:213:69: warning: too many arguments for format [-Wformat-extra-args] 2026-02-12T01:59:38,969 213 | if ((infp = popen(fas_fname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2026-02-12T01:59:38,969 | ^~~~~~~~~~~~~~~ 2026-02-12T01:59:38,970 iseq2comem.c:219:69: warning: too many arguments for format [-Wformat-extra-args] 2026-02-12T01:59:38,971 219 | if ((infp = popen(fas_fname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2026-02-12T01:59:38,971 | ^~~~~~~~~~~~~~~ 2026-02-12T01:59:38,972 iseq2comem.c:261:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,972 261 | if (base > TL) { 2026-02-12T01:59:38,973 | ^ 2026-02-12T01:59:38,974 iseq2comem.c:265:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,975 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-02-12T01:59:38,976 | ^~ 2026-02-12T01:59:38,976 iseq2comem.c:265:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,977 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-02-12T01:59:38,977 | ^ 2026-02-12T01:59:38,978 iseq2comem.c: In function ‘fastq2co’: 2026-02-12T01:59:38,978 iseq2comem.c:295:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2026-02-12T01:59:38,979 295 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2026-02-12T01:59:38,979 | ^~ 2026-02-12T01:59:38,980 iseq2comem.c:307:68: warning: too many arguments for format [-Wformat-extra-args] 2026-02-12T01:59:38,980 307 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2026-02-12T01:59:38,981 | ^~~~~~~~~~~~~~~ 2026-02-12T01:59:38,981 iseq2comem.c:313:68: warning: too many arguments for format [-Wformat-extra-args] 2026-02-12T01:59:38,982 313 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2026-02-12T01:59:38,982 | ^~~~~~~~~~~~~~~ 2026-02-12T01:59:38,983 iseq2comem.c:352:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,984 352 | if (base > TL) { 2026-02-12T01:59:38,984 | ^ 2026-02-12T01:59:38,985 iseq2comem.c:356:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,986 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-02-12T01:59:38,987 | ^~ 2026-02-12T01:59:38,987 iseq2comem.c:356:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,988 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-02-12T01:59:38,989 | ^ 2026-02-12T01:59:38,989 iseq2comem.c:375:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,991 375 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2026-02-12T01:59:38,992 | ^ 2026-02-12T01:59:38,992 iseq2comem.c: In function ‘fastq2koc’: 2026-02-12T01:59:38,993 iseq2comem.c:403:68: warning: too many arguments for format [-Wformat-extra-args] 2026-02-12T01:59:38,993 403 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2026-02-12T01:59:38,994 | ^~~~~~~~~~~~~~~~ 2026-02-12T01:59:38,995 iseq2comem.c:409:68: warning: too many arguments for format [-Wformat-extra-args] 2026-02-12T01:59:38,995 409 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2026-02-12T01:59:38,996 | ^~~~~~~~~~~~~~~~ 2026-02-12T01:59:38,997 iseq2comem.c:448:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:38,998 448 | if (base > TL) { 2026-02-12T01:59:38,999 | ^ 2026-02-12T01:59:38,999 iseq2comem.c:452:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:39,000 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-02-12T01:59:39,000 | ^~ 2026-02-12T01:59:39,000 iseq2comem.c:452:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:39,001 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-02-12T01:59:39,001 | ^ 2026-02-12T01:59:39,002 iseq2comem.c: In function ‘mt_shortreads2koc’: 2026-02-12T01:59:39,002 iseq2comem.c:628:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:39,003 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-02-12T01:59:39,003 | ^~ 2026-02-12T01:59:39,004 iseq2comem.c:628:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:39,004 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-02-12T01:59:39,005 | ^ 2026-02-12T01:59:40,386 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 2026-02-12T01:59:40,439 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 2026-02-12T01:59:40,560 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 2026-02-12T01:59:40,948 pykssd.c: In function ‘py_dist_dispatch’: 2026-02-12T01:59:40,949 pykssd.c:334:13: warning: unused variable ‘state1’ [-Wunused-variable] 2026-02-12T01:59:40,949 334 | int state1 = dist_dispatch(&dist_opt_val1); 2026-02-12T01:59:40,950 | ^~~~~~ 2026-02-12T01:59:40,951 pykssd.c:396:13: warning: unused variable ‘state2’ [-Wunused-variable] 2026-02-12T01:59:40,952 396 | int state2 = dist_dispatch(&dist_opt_val2); 2026-02-12T01:59:40,952 | ^~~~~~ 2026-02-12T01:59:40,955 pykssd.c:530:13: warning: unused variable ‘state4’ [-Wunused-variable] 2026-02-12T01:59:40,955 530 | int state4 = dist_dispatch(&dist_opt_val4); 2026-02-12T01:59:40,956 | ^~~~~~ 2026-02-12T01:59:41,607 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 2026-02-12T01:59:41,754 building 'nj' extension 2026-02-12T01:59:41,756 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 2026-02-12T01:59:42,215 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 buildtree.c -o build/temp.linux-armv7l-cpython-311/buildtree.o 2026-02-12T01:59:42,366 buildtree.c: In function ‘UPGMA_buildtree’: 2026-02-12T01:59:42,366 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-02-12T01:59:42,367 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2026-02-12T01:59:42,367 | ^~ 2026-02-12T01:59:42,368 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-02-12T01:59:42,369 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2026-02-12T01:59:42,370 | ^~ 2026-02-12T01:59:43,026 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 2026-02-12T01:59:43,405 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 2026-02-12T01:59:43,540 distancemat.c: In function ‘clone_DistanceMatrix’: 2026-02-12T01:59:43,541 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-02-12T01:59:43,542 226 | for( i=0; i < dest->size; i++) { 2026-02-12T01:59:43,543 | ^ 2026-02-12T01:59:43,543 distancemat.c: In function ‘empty_DistanceMatrix’: 2026-02-12T01:59:43,544 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-02-12T01:59:43,545 260 | for( i=0; i < mat->size; i++) { 2026-02-12T01:59:43,546 | ^ 2026-02-12T01:59:43,547 distancemat.c: In function ‘print_DistanceMatrix’: 2026-02-12T01:59:43,548 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-02-12T01:59:43,548 349 | for(row=0; row < mat->size; row++) { 2026-02-12T01:59:43,549 | ^ 2026-02-12T01:59:43,550 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2026-02-12T01:59:43,550 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2026-02-12T01:59:43,551 410 | while(c = fgetc(handle)) { 2026-02-12T01:59:43,552 | ^ 2026-02-12T01:59:43,938 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 2026-02-12T01:59:44,380 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 2026-02-12T01:59:44,596 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 2026-02-12T01:59:45,462 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 2026-02-12T01:59:45,638 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 2026-02-12T01:59:45,747 building 'dnj' extension 2026-02-12T01:59:45,749 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 2026-02-12T01:59:45,805 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 2026-02-12T01:59:45,939 dnj.c: In function ‘minQpair’: 2026-02-12T01:59:45,940 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,940 70 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,941 | ^~~ 2026-02-12T01:59:45,942 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,943 126 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,943 | ^~~ 2026-02-12T01:59:45,944 dnj.c: In function ‘maxQpair’: 2026-02-12T01:59:45,944 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,945 157 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,946 | ^~~ 2026-02-12T01:59:45,947 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,947 213 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,948 | ^~~ 2026-02-12T01:59:45,948 dnj.c: In function ‘UPGMApair’: 2026-02-12T01:59:45,949 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,950 237 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,950 | ^~~ 2026-02-12T01:59:45,951 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,952 284 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,953 | ^~~ 2026-02-12T01:59:45,953 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,954 291 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,954 | ^~~ 2026-02-12T01:59:45,956 dnj.c: In function ‘minQrow’: 2026-02-12T01:59:45,957 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,957 374 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,958 | ^~~ 2026-02-12T01:59:45,959 dnj.c: In function ‘maxQrow’: 2026-02-12T01:59:45,960 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,961 435 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,961 | ^~~ 2026-02-12T01:59:45,963 dnj.c: In function ‘UPGMArow’: 2026-02-12T01:59:45,963 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,964 488 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,964 | ^~~ 2026-02-12T01:59:45,965 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,965 494 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,966 | ^~~ 2026-02-12T01:59:45,968 dnj.c: In function ‘minQ_thread’: 2026-02-12T01:59:45,968 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:45,969 553 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:45,969 | ^~~ 2026-02-12T01:59:47,323 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 2026-02-12T01:59:47,440 filebuff.c: In function ‘BuffgzFileBuff’: 2026-02-12T01:59:47,440 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:47,441 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2026-02-12T01:59:47,441 | ^~ 2026-02-12T01:59:47,765 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 2026-02-12T01:59:47,899 hclust.c: In function ‘minQ’: 2026-02-12T01:59:47,900 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-02-12T01:59:47,900 364 | while(++i < Q->n) { 2026-02-12T01:59:47,901 | ^ 2026-02-12T01:59:47,902 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:47,902 377 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:47,903 | ^~~ 2026-02-12T01:59:47,904 hclust.c: In function ‘maxQ’: 2026-02-12T01:59:47,904 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-02-12T01:59:47,905 394 | while(++i < Q->n) { 2026-02-12T01:59:47,906 | ^ 2026-02-12T01:59:47,907 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:47,907 407 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:47,908 | ^~~ 2026-02-12T01:59:50,291 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 2026-02-12T01:59:50,421 matrix.c: In function ‘ltdMatrix_popArrange’: 2026-02-12T01:59:50,422 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-02-12T01:59:50,423 538 | if(pos != n) { 2026-02-12T01:59:50,423 | ^~ 2026-02-12T01:59:51,299 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 2026-02-12T01:59:51,353 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 2026-02-12T01:59:51,483 nj.c: In function ‘initQ’: 2026-02-12T01:59:51,484 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:51,484 243 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:51,485 | ^~~ 2026-02-12T01:59:51,486 nj.c: In function ‘initQ_MN’: 2026-02-12T01:59:51,487 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:51,487 358 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:51,488 | ^~~ 2026-02-12T01:59:51,491 nj.c: In function ‘minD’: 2026-02-12T01:59:51,492 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:51,492 559 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:51,493 | ^~~ 2026-02-12T01:59:51,493 nj.c: In function ‘maxD’: 2026-02-12T01:59:51,494 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:51,495 642 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:51,495 | ^~~ 2026-02-12T01:59:51,499 nj.c: In function ‘minPair’: 2026-02-12T01:59:51,499 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2026-02-12T01:59:51,500 826 | pos <<= sizeof(unsigned) * 8; 2026-02-12T01:59:51,500 | ^~~ 2026-02-12T01:59:53,874 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 2026-02-12T01:59:54,413 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 2026-02-12T01:59:54,506 pherror.c: In function ‘cfread’: 2026-02-12T01:59:54,506 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2026-02-12T01:59:54,507 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2026-02-12T01:59:54,508 | ^~ 2026-02-12T01:59:54,600 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 2026-02-12T01:59:55,668 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 2026-02-12T01:59:56,040 In file included from pydnj.c:11: 2026-02-12T01:59:56,041 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2026-02-12T01:59:56,042 20 | #define _XOPEN_SOURCE 600 2026-02-12T01:59:56,042 | 2026-02-12T01:59:56,043 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2026-02-12T01:59:56,043 from /usr/include/stdlib.h:26, 2026-02-12T01:59:56,044 from /usr/include/python3.11/Python.h:23, 2026-02-12T01:59:56,044 from pydnj.c:1: 2026-02-12T01:59:56,045 /usr/include/features.h:214: note: this is the location of the previous definition 2026-02-12T01:59:56,046 214 | # define _XOPEN_SOURCE 700 2026-02-12T01:59:56,047 | 2026-02-12T01:59:56,065 pydnj.c: In function ‘py_build’: 2026-02-12T01:59:56,066 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2026-02-12T01:59:56,068 165 | p = omp_get_num_procs(); 2026-02-12T01:59:56,069 | ^~~~~~~~~~~~~~~~~ 2026-02-12T01:59:56,186 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2026-02-12T01:59:56,186 169 | free(file); 2026-02-12T01:59:56,187 | ^~~~~~~~~~ 2026-02-12T01:59:56,187 pydnj.c:125:12: note: returned from ‘fopen’ 2026-02-12T01:59:56,188 125 | file = fopen(inputfilename, "r"); 2026-02-12T01:59:56,188 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-12T01:59:56,260 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 2026-02-12T01:59:56,468 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 2026-02-12T01:59:56,578 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 2026-02-12T01:59:56,774 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 2026-02-12T01:59:56,935 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 2026-02-12T01:59:57,101 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-02-12T01:59:57,101 !! 2026-02-12T01:59:57,103 ******************************************************************************** 2026-02-12T01:59:57,103 Please avoid running ``setup.py`` directly. 2026-02-12T01:59:57,104 Instead, use pypa/build, pypa/installer or other 2026-02-12T01:59:57,105 standards-based tools. 2026-02-12T01:59:57,106 This deprecation is overdue, please update your project and remove deprecated 2026-02-12T01:59:57,106 calls to avoid build errors in the future. 2026-02-12T01:59:57,107 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-02-12T01:59:57,108 ******************************************************************************** 2026-02-12T01:59:57,109 !! 2026-02-12T01:59:57,110 self.initialize_options() 2026-02-12T01:59:57,131 installing to build/bdist.linux-armv7l/wheel 2026-02-12T01:59:57,131 running install 2026-02-12T01:59:57,154 running install_lib 2026-02-12T01:59:57,181 creating build/bdist.linux-armv7l/wheel 2026-02-12T01:59:57,182 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2026-02-12T01:59:57,191 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2026-02-12T01:59:57,201 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2026-02-12T01:59:57,206 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel/. 2026-02-12T01:59:57,208 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel/. 2026-02-12T01:59:57,211 running install_egg_info 2026-02-12T01:59:57,244 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/./kssdtree-2.1.0-py3.11.egg-info 2026-02-12T01:59:57,258 running install_scripts 2026-02-12T01:59:57,330 creating build/bdist.linux-armv7l/wheel/kssdtree-2.1.0.dist-info/WHEEL 2026-02-12T01:59:57,334 creating '/tmp/pip-wheel-otx87r0k/kssdtree-2.1.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-02-12T01:59:57,409 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2026-02-12T01:59:57,493 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2026-02-12T01:59:57,498 adding 'kssdtree.py' 2026-02-12T01:59:57,521 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2026-02-12T01:59:57,524 adding 'toolutils.py' 2026-02-12T01:59:57,526 adding 'kssdtree-2.1.0.dist-info/METADATA' 2026-02-12T01:59:57,528 adding 'kssdtree-2.1.0.dist-info/WHEEL' 2026-02-12T01:59:57,531 adding 'kssdtree-2.1.0.dist-info/dependency_links.txt' 2026-02-12T01:59:57,532 adding 'kssdtree-2.1.0.dist-info/top_level.txt' 2026-02-12T01:59:57,533 adding 'kssdtree-2.1.0.dist-info/RECORD' 2026-02-12T01:59:57,542 removing build/bdist.linux-armv7l/wheel 2026-02-12T01:59:57,697 Building wheel for kssdtree (setup.py): finished with status 'done' 2026-02-12T01:59:57,704 Created wheel for kssdtree: filename=kssdtree-2.1.0-cp311-cp311-linux_armv7l.whl size=382219 sha256=169d23da665645c804665ee8db85ae8198a3f174255c0726286c29a0f454e68e 2026-02-12T01:59:57,705 Stored in directory: /tmp/pip-ephem-wheel-cache-dhgb82mq/wheels/0e/ce/8a/646cc861d8a9e8780f12fe49309282767b8c11d2394f4034e1 2026-02-12T01:59:57,714 Successfully built kssdtree 2026-02-12T01:59:57,731 Removed build tracker: '/tmp/pip-build-tracker-igp6oopg'