2024-07-17T05:30:02,956 Created temporary directory: /tmp/pip-build-tracker-eotfeqtf 2024-07-17T05:30:02,957 Initialized build tracking at /tmp/pip-build-tracker-eotfeqtf 2024-07-17T05:30:02,958 Created build tracker: /tmp/pip-build-tracker-eotfeqtf 2024-07-17T05:30:02,958 Entered build tracker: /tmp/pip-build-tracker-eotfeqtf 2024-07-17T05:30:02,958 Created temporary directory: /tmp/pip-wheel-up6krtwo 2024-07-17T05:30:02,962 Created temporary directory: /tmp/pip-ephem-wheel-cache-k8dtr1q8 2024-07-17T05:30:02,986 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-17T05:30:02,990 2 location(s) to search for versions of kssdtree: 2024-07-17T05:30:02,990 * https://pypi.org/simple/kssdtree/ 2024-07-17T05:30:02,990 * https://www.piwheels.org/simple/kssdtree/ 2024-07-17T05:30:02,990 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-07-17T05:30:02,991 Getting page https://pypi.org/simple/kssdtree/ 2024-07-17T05:30:02,992 Found index url https://pypi.org/simple/ 2024-07-17T05:30:03,043 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-07-17T05:30:03,046 Found link https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.1 2024-07-17T05:30:03,046 Found link https://files.pythonhosted.org/packages/9a/4c/6516f734f5860e4b30f9091aaac5811663bfae72c4de4ae6566c89192767/kssdtree-1.1.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.2 2024-07-17T05:30:03,047 Found link https://files.pythonhosted.org/packages/a4/cd/f2954686c636e853cc3fda197c459195377b78288874cf7d68218a8bdbf4/kssdtree-1.1.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.3 2024-07-17T05:30:03,047 Found link https://files.pythonhosted.org/packages/20/ea/b0301924e3f7d367cbb7b8da66837dba9af2a332bf56ed35e03a33faee76/kssdtree-1.1.4.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.4 2024-07-17T05:30:03,047 Found link https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.6 2024-07-17T05:30:03,047 Found link https://files.pythonhosted.org/packages/cd/4b/d886cbcc573ff0969da7d9c756049925b86141e60ee6708dfbbe0644d008/kssdtree-1.1.7.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.7 2024-07-17T05:30:03,048 Found link https://files.pythonhosted.org/packages/7e/8a/a62c8adc92df69ab8cb242827ee64a3e2b6d5c89b83425785dd00605af17/kssdtree-1.1.8.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.8 2024-07-17T05:30:03,048 Found link https://files.pythonhosted.org/packages/da/db/e458cca6427752c05428d2378ccdee631d32f760174fdaba65f73125e71b/kssdtree-1.1.9.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.9 2024-07-17T05:30:03,048 Found link https://files.pythonhosted.org/packages/9d/47/017180a30e73e421372377cbe6d01c5e51a5108ea2177f20ccd7d283f8d1/kssdtree-2.0.0.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.0 2024-07-17T05:30:03,049 Found link https://files.pythonhosted.org/packages/ba/39/d443cac955912a0371c93b797311cb9ec3a8d6ee0a5d7673376d826aa6b2/kssdtree-2.0.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.1 2024-07-17T05:30:03,049 Found link https://files.pythonhosted.org/packages/2e/32/e53c0e3735cbc913b2c96b4e0e1c1005fe816a4d71b38b80cdcfb5c67fa8/kssdtree-2.0.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.2 2024-07-17T05:30:03,049 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-07-17T05:30:03,049 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-07-17T05:30:03,051 Found index url https://www.piwheels.org/simple/ 2024-07-17T05:30:03,116 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-07-17T05:30:03,128 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.2-cp311-cp311-linux_armv6l.whl#sha256=ae7417e30efd12d8c6800d4167141c94a93f1ce51afd5ae9196cdfb6057ca7d2 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,129 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.2-cp311-cp311-linux_armv7l.whl#sha256=ae7417e30efd12d8c6800d4167141c94a93f1ce51afd5ae9196cdfb6057ca7d2 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,129 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.0-cp311-cp311-linux_armv6l.whl#sha256=16a2e46376ed2874435371fd57a97405d4b631b35c014b9e395a4528a1e655b8 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,129 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,130 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp311-cp311-linux_armv7l.whl#sha256=d4c397f5fcb0af48dbb11b9fb7d7b399cc180d65355b794a8fcc7327e9a7dde1 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,130 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp39-cp39-linux_armv6l.whl#sha256=ab11dc15aca2923fe0d60bf11deb134bed4df89280b4ce40ca8e9bf3ca46b168 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,130 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp39-cp39-linux_armv7l.whl#sha256=ab11dc15aca2923fe0d60bf11deb134bed4df89280b4ce40ca8e9bf3ca46b168 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,131 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,131 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.7-cp311-cp311-linux_armv6l.whl#sha256=388a8dabd657ea83e6d22b52300337c74e9d84e506806cfd4d2a76eb98777e17 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,132 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.7-cp311-cp311-linux_armv7l.whl#sha256=388a8dabd657ea83e6d22b52300337c74e9d84e506806cfd4d2a76eb98777e17 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,132 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.7-cp39-cp39-linux_armv6l.whl#sha256=e1df896451d30c12e01aceb3eb91f0f7dfe0ee6f16fd66864fdefbc21cc54856 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,132 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,133 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp39-cp39-linux_armv7l.whl#sha256=9defb70b5162efc2c0eb6e415a7e37c604aa9b248a006af86af8f59a3bce5d2b (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,133 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp37-cp37m-linux_armv6l.whl#sha256=ffef4ae0f634dd977cc2ec6798b9f36f73d788aca27bb7199f552d5513c34413 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,133 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp37-cp37m-linux_armv7l.whl#sha256=ffef4ae0f634dd977cc2ec6798b9f36f73d788aca27bb7199f552d5513c34413 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,133 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp311-cp311-linux_armv6l.whl#sha256=64b685362c3f9027bfeafdffb6a5d58c349a76fd551eeb7b98de146827463e75 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,134 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp311-cp311-linux_armv7l.whl#sha256=64b685362c3f9027bfeafdffb6a5d58c349a76fd551eeb7b98de146827463e75 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,134 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp39-cp39-linux_armv6l.whl#sha256=34527068d84569095aefee41a353c5dfc0dfa55b68097890da9a1eca2ee9b726 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,134 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp39-cp39-linux_armv7l.whl#sha256=34527068d84569095aefee41a353c5dfc0dfa55b68097890da9a1eca2ee9b726 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,134 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp311-cp311-linux_armv6l.whl#sha256=6b76f3b3f532934ad49a829e7bf8176af580f4687f1491c49c3f571bf081f961 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,134 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp311-cp311-linux_armv7l.whl#sha256=6b76f3b3f532934ad49a829e7bf8176af580f4687f1491c49c3f571bf081f961 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,135 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp37-cp37m-linux_armv6l.whl#sha256=d179f6c6c0ad4e0f06950e1609118b065b3476c47446325f6614bdbef5ede0d0 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,135 Skipping link: No binaries permitted for kssdtree: 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https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,136 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv7l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,136 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv6l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,136 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv7l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,136 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp39-cp39-linux_armv6l.whl#sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,136 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp39-cp39-linux_armv7l.whl#sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,137 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv6l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,137 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv7l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,137 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv6l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,137 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv7l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,137 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv6l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,137 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv7l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-17T05:30:03,138 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-07-17T05:30:03,138 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-07-17T05:30:03,157 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-07-17T05:30:03,174 Collecting kssdtree==2.0.2 2024-07-17T05:30:03,176 Created temporary directory: /tmp/pip-unpack-2c8f3o67 2024-07-17T05:30:03,218 Downloading kssdtree-2.0.2.tar.gz (112 kB) 2024-07-17T05:30:03,411 Added kssdtree==2.0.2 from https://files.pythonhosted.org/packages/2e/32/e53c0e3735cbc913b2c96b4e0e1c1005fe816a4d71b38b80cdcfb5c67fa8/kssdtree-2.0.2.tar.gz to build tracker '/tmp/pip-build-tracker-eotfeqtf' 2024-07-17T05:30:03,413 Running setup.py (path:/tmp/pip-wheel-up6krtwo/kssdtree_168fb8b0b4bc4642a5b3064cc5b85fd9/setup.py) egg_info for package kssdtree 2024-07-17T05:30:03,413 Created temporary directory: /tmp/pip-pip-egg-info-ky842107 2024-07-17T05:30:03,414 Preparing metadata (setup.py): started 2024-07-17T05:30:03,415 Running command python setup.py egg_info 2024-07-17T05:30:04,478 running egg_info 2024-07-17T05:30:04,480 creating /tmp/pip-pip-egg-info-ky842107/kssdtree.egg-info 2024-07-17T05:30:04,503 writing /tmp/pip-pip-egg-info-ky842107/kssdtree.egg-info/PKG-INFO 2024-07-17T05:30:04,506 writing dependency_links to /tmp/pip-pip-egg-info-ky842107/kssdtree.egg-info/dependency_links.txt 2024-07-17T05:30:04,508 writing requirements to /tmp/pip-pip-egg-info-ky842107/kssdtree.egg-info/requires.txt 2024-07-17T05:30:04,509 writing top-level names to /tmp/pip-pip-egg-info-ky842107/kssdtree.egg-info/top_level.txt 2024-07-17T05:30:04,511 writing manifest file '/tmp/pip-pip-egg-info-ky842107/kssdtree.egg-info/SOURCES.txt' 2024-07-17T05:30:04,609 reading manifest file '/tmp/pip-pip-egg-info-ky842107/kssdtree.egg-info/SOURCES.txt' 2024-07-17T05:30:04,611 reading manifest template 'MANIFEST.in' 2024-07-17T05:30:04,629 writing manifest file '/tmp/pip-pip-egg-info-ky842107/kssdtree.egg-info/SOURCES.txt' 2024-07-17T05:30:04,724 Preparing metadata (setup.py): finished with status 'done' 2024-07-17T05:30:04,729 Source in /tmp/pip-wheel-up6krtwo/kssdtree_168fb8b0b4bc4642a5b3064cc5b85fd9 has version 2.0.2, which satisfies requirement kssdtree==2.0.2 from https://files.pythonhosted.org/packages/2e/32/e53c0e3735cbc913b2c96b4e0e1c1005fe816a4d71b38b80cdcfb5c67fa8/kssdtree-2.0.2.tar.gz 2024-07-17T05:30:04,729 Removed kssdtree==2.0.2 from https://files.pythonhosted.org/packages/2e/32/e53c0e3735cbc913b2c96b4e0e1c1005fe816a4d71b38b80cdcfb5c67fa8/kssdtree-2.0.2.tar.gz from build tracker '/tmp/pip-build-tracker-eotfeqtf' 2024-07-17T05:30:04,737 Created temporary directory: /tmp/pip-unpack-f4mctzbb 2024-07-17T05:30:04,738 Created temporary directory: /tmp/pip-unpack-fkpwkzhu 2024-07-17T05:30:04,744 Building wheels for collected packages: kssdtree 2024-07-17T05:30:04,749 Created temporary directory: /tmp/pip-wheel-myg2ix8q 2024-07-17T05:30:04,749 Building wheel for kssdtree (setup.py): started 2024-07-17T05:30:04,750 Destination directory: /tmp/pip-wheel-myg2ix8q 2024-07-17T05:30:04,751 Running command python setup.py bdist_wheel 2024-07-17T05:30:05,823 running bdist_wheel 2024-07-17T05:30:05,915 running build 2024-07-17T05:30:05,915 running build_py 2024-07-17T05:30:05,941 creating build 2024-07-17T05:30:05,941 creating build/lib.linux-armv7l-cpython-39 2024-07-17T05:30:05,942 copying kssdtree.py -> build/lib.linux-armv7l-cpython-39 2024-07-17T05:30:05,944 copying toolutils.py -> build/lib.linux-armv7l-cpython-39 2024-07-17T05:30:05,947 running egg_info 2024-07-17T05:30:06,003 writing kssdtree.egg-info/PKG-INFO 2024-07-17T05:30:06,006 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-07-17T05:30:06,008 writing requirements to kssdtree.egg-info/requires.txt 2024-07-17T05:30:06,009 writing top-level names to kssdtree.egg-info/top_level.txt 2024-07-17T05:30:06,035 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-17T05:30:06,039 reading manifest template 'MANIFEST.in' 2024-07-17T05:30:06,056 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-17T05:30:06,058 running build_ext 2024-07-17T05:30:06,561 building 'kssd' extension 2024-07-17T05:30:06,562 creating build/temp.linux-armv7l-cpython-39 2024-07-17T05:30:06,563 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c co2mco.c -o build/temp.linux-armv7l-cpython-39/co2mco.o -fopenmp 2024-07-17T05:30:06,729 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-07-17T05:30:06,729 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-17T05:30:06,729 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-07-17T05:30:06,730 | ^ 2024-07-17T05:30:06,732 co2mco.c: In function ‘co2unitllmco’: 2024-07-17T05:30:06,732 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-17T05:30:06,732 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-07-17T05:30:06,733 | ^ 2024-07-17T05:30:07,347 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_composite.c -o build/temp.linux-armv7l-cpython-39/command_composite.o -fopenmp 2024-07-17T05:30:07,650 command_composite.c: In function ‘get_species_abundance’: 2024-07-17T05:30:07,651 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-17T05:30:07,651 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-07-17T05:30:07,651 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:07,651 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-17T05:30:07,651 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-07-17T05:30:07,651 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:07,652 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:07,652 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-17T05:30:07,652 | ^ 2024-07-17T05:30:07,652 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-17T05:30:07,652 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-17T05:30:07,652 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:07,652 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:07,652 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-17T05:30:07,653 | ^ 2024-07-17T05:30:07,653 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-17T05:30:07,653 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-17T05:30:07,653 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:07,653 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:07,653 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-17T05:30:07,653 | ^ 2024-07-17T05:30:07,654 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-17T05:30:07,654 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-17T05:30:07,654 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:07,654 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:07,654 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-17T05:30:07,654 | ^ 2024-07-17T05:30:07,654 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-17T05:30:07,655 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-17T05:30:07,655 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:07,655 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:07,655 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-17T05:30:07,655 | ^ 2024-07-17T05:30:07,655 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-07-17T05:30:07,655 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-17T05:30:07,656 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:07,922 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist.c -o build/temp.linux-armv7l-cpython-39/command_dist.o -fopenmp 2024-07-17T05:30:08,116 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-17T05:30:08,117 command_dist.c:677:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-17T05:30:08,117 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-17T05:30:08,117 | ~~^ 2024-07-17T05:30:08,117 | | 2024-07-17T05:30:08,117 | long unsigned int 2024-07-17T05:30:08,117 | %u 2024-07-17T05:30:08,117 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-17T05:30:08,118 | ~~~~~~~ 2024-07-17T05:30:08,118 | | 2024-07-17T05:30:08,118 | size_t {aka unsigned int} 2024-07-17T05:30:08,118 command_dist.c:677:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-17T05:30:08,118 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-17T05:30:08,118 | ~~^ 2024-07-17T05:30:08,118 | | 2024-07-17T05:30:08,118 | long unsigned int 2024-07-17T05:30:08,119 | %u 2024-07-17T05:30:08,119 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-17T05:30:08,119 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-17T05:30:08,119 | ~~~~~~~~~ 2024-07-17T05:30:08,119 | | 2024-07-17T05:30:08,119 | size_t {aka unsigned int} 2024-07-17T05:30:08,119 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-17T05:30:08,119 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-17T05:30:08,120 | ~~^ 2024-07-17T05:30:08,120 | | 2024-07-17T05:30:08,120 | long unsigned int 2024-07-17T05:30:08,120 | %u 2024-07-17T05:30:08,120 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-17T05:30:08,120 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-17T05:30:08,120 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:08,121 | | 2024-07-17T05:30:08,121 | unsigned int 2024-07-17T05:30:08,121 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-17T05:30:08,122 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-07-17T05:30:08,122 | ^ 2024-07-17T05:30:08,128 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-17T05:30:08,129 command_dist.c:863:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-17T05:30:08,129 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-17T05:30:08,129 | ~~^ ~~~~~~~ 2024-07-17T05:30:08,129 | | | 2024-07-17T05:30:08,129 | long unsigned int size_t {aka unsigned int} 2024-07-17T05:30:08,129 | %u 2024-07-17T05:30:08,130 command_dist.c:863:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-17T05:30:08,130 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-17T05:30:08,131 | ~~^ 2024-07-17T05:30:08,131 | | 2024-07-17T05:30:08,131 | long unsigned int 2024-07-17T05:30:08,131 | %u 2024-07-17T05:30:08,131 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-17T05:30:08,131 | ~~~~~~~~~ 2024-07-17T05:30:08,131 | | 2024-07-17T05:30:08,131 | size_t {aka unsigned int} 2024-07-17T05:30:08,132 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-17T05:30:08,132 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-17T05:30:08,132 | ~~^ 2024-07-17T05:30:08,132 | | 2024-07-17T05:30:08,132 | long unsigned int 2024-07-17T05:30:08,132 | %u 2024-07-17T05:30:08,133 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-17T05:30:08,133 865 | (size_t) b * unitsz_distf_mapped); 2024-07-17T05:30:08,133 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:08,133 | | 2024-07-17T05:30:08,133 | unsigned int 2024-07-17T05:30:08,134 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-07-17T05:30:08,134 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-07-17T05:30:08,134 | ^~~~~~~ 2024-07-17T05:30:08,134 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-07-17T05:30:08,134 809 | struct stat cbd_fcode_stat; 2024-07-17T05:30:08,135 | ^~~~~~~~~~~~~~ 2024-07-17T05:30:08,135 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-07-17T05:30:08,135 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-17T05:30:08,135 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:08,135 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-07-17T05:30:08,136 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-17T05:30:08,136 | ^~~~~~~~~~~~~~~~~ 2024-07-17T05:30:08,141 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-17T05:30:08,142 command_dist.c:1018:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-17T05:30:08,143 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-17T05:30:08,143 | ~~^ 2024-07-17T05:30:08,143 | | 2024-07-17T05:30:08,143 | long unsigned int 2024-07-17T05:30:08,143 | %u 2024-07-17T05:30:08,143 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-17T05:30:08,143 | ~~~~~~~ 2024-07-17T05:30:08,143 | | 2024-07-17T05:30:08,143 | size_t {aka unsigned int} 2024-07-17T05:30:08,144 command_dist.c:1018:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-17T05:30:08,144 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-17T05:30:08,144 | ~~^ 2024-07-17T05:30:08,144 | | 2024-07-17T05:30:08,145 | long unsigned int 2024-07-17T05:30:08,145 | %u 2024-07-17T05:30:08,145 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-17T05:30:08,145 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-17T05:30:08,145 | ~~~~~~~~~ 2024-07-17T05:30:08,145 | | 2024-07-17T05:30:08,145 | size_t {aka unsigned int} 2024-07-17T05:30:08,146 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-17T05:30:08,146 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-17T05:30:08,146 | ~~^ 2024-07-17T05:30:08,146 | | 2024-07-17T05:30:08,146 | long unsigned int 2024-07-17T05:30:08,147 | %u 2024-07-17T05:30:08,147 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-17T05:30:08,147 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-17T05:30:08,147 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:08,147 | | 2024-07-17T05:30:08,147 | unsigned int 2024-07-17T05:30:08,148 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:08,148 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-07-17T05:30:08,148 | ^ 2024-07-17T05:30:08,151 command_dist.c: In function ‘mco_co_dist_core’: 2024-07-17T05:30:08,151 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-17T05:30:08,152 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-07-17T05:30:08,152 | ^ 2024-07-17T05:30:08,157 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-07-17T05:30:08,158 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:08,158 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-07-17T05:30:08,158 | ^ 2024-07-17T05:30:08,160 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:08,160 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-17T05:30:08,160 | ^ 2024-07-17T05:30:08,165 command_dist.c: In function ‘dist_print_nobin’: 2024-07-17T05:30:08,166 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:08,166 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-07-17T05:30:08,166 | ^ 2024-07-17T05:30:08,168 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:08,168 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-17T05:30:08,168 | ^ 2024-07-17T05:30:08,169 command_dist.c:1380:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:08,170 1380 | for (int rid = 0; rid < ref_num; rid++) 2024-07-17T05:30:08,170 | ^ 2024-07-17T05:30:08,170 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:08,170 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-07-17T05:30:08,171 | ^ 2024-07-17T05:30:08,421 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-07-17T05:30:08,422 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-07-17T05:30:08,422 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-07-17T05:30:08,422 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:08,422 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-07-17T05:30:08,422 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-07-17T05:30:08,422 | ^~~~~~~~~~~~ 2024-07-17T05:30:09,143 command_dist.c: In function ‘get_dim_shuffle’: 2024-07-17T05:30:09,144 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-07-17T05:30:09,144 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-17T05:30:09,144 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:09,144 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-07-17T05:30:09,144 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-17T05:30:09,145 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:09,925 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-17T05:30:09,926 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:09,926 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-17T05:30:09,926 | ^~ ~~~~~~~~~ 2024-07-17T05:30:09,926 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-17T05:30:09,926 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-17T05:30:09,926 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:09,927 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-17T05:30:09,927 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-17T05:30:09,927 | ^~~~~~~~~~~~~~~ 2024-07-17T05:30:09,927 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-17T05:30:09,927 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-17T05:30:09,927 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:09,928 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-17T05:30:09,929 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-17T05:30:09,929 | ^~~~~~~~~~~ 2024-07-17T05:30:09,929 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-17T05:30:09,929 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-17T05:30:09,929 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:09,929 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-17T05:30:09,929 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-17T05:30:09,930 | ^~~~~ 2024-07-17T05:30:09,930 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-17T05:30:09,930 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-17T05:30:09,930 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,136 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-17T05:30:10,136 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:10,137 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-17T05:30:10,137 | ^~ ~~~~~~~~~ 2024-07-17T05:30:10,137 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-17T05:30:10,137 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-17T05:30:10,137 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,138 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-17T05:30:10,138 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-17T05:30:10,138 | ^~~~~~~~~~~~~~~ 2024-07-17T05:30:10,138 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-17T05:30:10,138 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-17T05:30:10,138 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,139 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-17T05:30:10,139 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-17T05:30:10,139 | ^~~~~~~~~~~~~ 2024-07-17T05:30:10,139 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-17T05:30:10,140 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-17T05:30:10,140 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,141 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:10,141 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-17T05:30:10,141 | ^ 2024-07-17T05:30:10,141 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-07-17T05:30:10,141 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-17T05:30:10,141 | ^~~~~~~~~~ 2024-07-17T05:30:10,142 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-17T05:30:10,142 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-17T05:30:10,142 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,142 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:10,143 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-17T05:30:10,143 | ^ 2024-07-17T05:30:10,143 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-07-17T05:30:10,143 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-17T05:30:10,143 | ^~~~~~~~~~ 2024-07-17T05:30:10,143 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-17T05:30:10,144 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-17T05:30:10,144 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,381 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-17T05:30:10,381 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:10,382 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-17T05:30:10,382 | ^~ ~~~~~~~~~ 2024-07-17T05:30:10,382 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-17T05:30:10,382 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-17T05:30:10,382 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,383 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-17T05:30:10,383 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-17T05:30:10,383 | ^~~~~~~~~~~~~~~ 2024-07-17T05:30:10,384 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-17T05:30:10,384 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-17T05:30:10,384 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,384 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-17T05:30:10,385 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-17T05:30:10,385 | ^~~~~~~~~~~~~ 2024-07-17T05:30:10,385 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-17T05:30:10,385 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-17T05:30:10,385 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,387 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-17T05:30:10,387 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-17T05:30:10,387 | ^~~~~~~~~~~ 2024-07-17T05:30:10,387 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-17T05:30:10,387 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-17T05:30:10,387 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,388 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-17T05:30:10,388 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-17T05:30:10,388 | ^~~~~ 2024-07-17T05:30:10,389 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-17T05:30:10,389 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-17T05:30:10,389 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,635 command_dist.c: In function ‘combine_queries’: 2024-07-17T05:30:10,636 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-17T05:30:10,636 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-17T05:30:10,636 | ^ 2024-07-17T05:30:10,637 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-17T05:30:10,637 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-17T05:30:10,637 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,638 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-17T05:30:10,638 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-17T05:30:10,638 | ^ 2024-07-17T05:30:10,639 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-17T05:30:10,639 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-17T05:30:10,639 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:10,641 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:10,641 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-17T05:30:10,641 | ^~ ~~~~~~~~ 2024-07-17T05:30:10,642 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-17T05:30:10,642 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-17T05:30:10,642 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,117 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o -fopenmp 2024-07-17T05:30:11,289 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_set.c -o build/temp.linux-armv7l-cpython-39/command_set.o -fopenmp 2024-07-17T05:30:11,437 command_set.c: In function ‘sketch_operate’: 2024-07-17T05:30:11,438 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-17T05:30:11,438 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-07-17T05:30:11,438 | ^ 2024-07-17T05:30:11,447 command_set.c: In function ‘combin_subset_pans’: 2024-07-17T05:30:11,448 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-17T05:30:11,448 458 | free(co_dstat_fpath); 2024-07-17T05:30:11,448 | ^~~~~~~~~~~~~~ 2024-07-17T05:30:11,448 In file included from kssdheaders/global_basic.h:159, 2024-07-17T05:30:11,449 from command_set.c:15: 2024-07-17T05:30:11,449 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-17T05:30:11,449 565 | extern void free (void *__ptr) __THROW; 2024-07-17T05:30:11,449 | ~~~~~~^~~~~ 2024-07-17T05:30:11,453 command_set.c: In function ‘grouping_genomes’: 2024-07-17T05:30:11,453 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-17T05:30:11,453 563 | free(co_dstat_fpath); 2024-07-17T05:30:11,453 | ^~~~~~~~~~~~~~ 2024-07-17T05:30:11,453 In file included from kssdheaders/global_basic.h:159, 2024-07-17T05:30:11,454 from command_set.c:15: 2024-07-17T05:30:11,454 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-17T05:30:11,454 565 | extern void free (void *__ptr) __THROW; 2024-07-17T05:30:11,454 | ~~~~~~^~~~~ 2024-07-17T05:30:11,570 command_set.c: In function ‘sketch_union’: 2024-07-17T05:30:11,570 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-17T05:30:11,570 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:11,570 | ^ 2024-07-17T05:30:11,570 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-17T05:30:11,571 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:11,571 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,571 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,571 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-17T05:30:11,571 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:11,571 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-17T05:30:11,571 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-17T05:30:11,572 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,572 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,572 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-17T05:30:11,572 | ^~ ~~~~~~~~~~ 2024-07-17T05:30:11,572 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-17T05:30:11,572 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-17T05:30:11,572 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,683 command_set.c: In function ‘sketch_operate’: 2024-07-17T05:30:11,683 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,684 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-17T05:30:11,684 | ^~ ~~~~~~~~~~ 2024-07-17T05:30:11,684 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-17T05:30:11,684 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-17T05:30:11,684 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,684 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,684 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-17T05:30:11,685 | ^~ ~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,685 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-17T05:30:11,685 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-17T05:30:11,685 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,685 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,685 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-17T05:30:11,685 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:11,685 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-17T05:30:11,686 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-17T05:30:11,686 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,686 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,686 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-17T05:30:11,686 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:11,686 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-17T05:30:11,687 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-17T05:30:11,687 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,687 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,687 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-17T05:30:11,687 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:11,687 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-17T05:30:11,687 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-17T05:30:11,688 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,688 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,688 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-17T05:30:11,688 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:11,688 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-17T05:30:11,688 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-17T05:30:11,688 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,689 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-17T05:30:11,689 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:11,689 | ^ 2024-07-17T05:30:11,689 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-17T05:30:11,689 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:11,689 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,836 command_set.c: In function ‘uniq_sketch_union’: 2024-07-17T05:30:11,837 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-17T05:30:11,837 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:11,837 | ^ 2024-07-17T05:30:11,837 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-17T05:30:11,837 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:11,837 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,838 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,838 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-17T05:30:11,838 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:11,838 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-17T05:30:11,838 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-17T05:30:11,838 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,838 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,839 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-17T05:30:11,839 | ^~ ~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,839 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-17T05:30:11,839 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-17T05:30:11,839 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,963 command_set.c: In function ‘combin_pans’: 2024-07-17T05:30:11,963 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,963 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-17T05:30:11,963 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:11,963 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-07-17T05:30:11,964 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-17T05:30:11,964 | ^~~~~~~~~~ 2024-07-17T05:30:11,964 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-07-17T05:30:11,964 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-17T05:30:11,964 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,964 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:11,964 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-17T05:30:11,965 | ^~ ~~~~~~~~~~ 2024-07-17T05:30:11,965 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-07-17T05:30:11,965 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-17T05:30:11,965 | ^~~~~~~~~~ 2024-07-17T05:30:11,965 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-07-17T05:30:11,965 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-17T05:30:11,965 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:11,965 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-17T05:30:11,966 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:11,966 | ^ 2024-07-17T05:30:11,966 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-17T05:30:11,966 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:11,966 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,148 command_set.c: In function ‘combin_subset_pans’: 2024-07-17T05:30:12,149 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:12,149 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-17T05:30:12,149 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:12,149 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-17T05:30:12,149 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-17T05:30:12,149 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,150 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:12,150 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-17T05:30:12,150 | ^~ ~~~~~~~~~~ 2024-07-17T05:30:12,150 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-17T05:30:12,150 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-17T05:30:12,150 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,150 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:12,151 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-17T05:30:12,151 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:12,151 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-17T05:30:12,151 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-17T05:30:12,151 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,152 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:12,153 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-17T05:30:12,153 | ^~ ~~~~~~~~~~ 2024-07-17T05:30:12,153 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-17T05:30:12,153 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-17T05:30:12,153 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,153 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-17T05:30:12,153 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:12,153 | ^ 2024-07-17T05:30:12,154 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-17T05:30:12,154 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:12,154 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,355 command_set.c: In function ‘grouping_genomes’: 2024-07-17T05:30:12,356 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:12,356 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-17T05:30:12,356 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:12,356 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-17T05:30:12,356 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-17T05:30:12,357 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,357 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:12,357 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-17T05:30:12,357 | ^~ ~~~~~~~~~~ 2024-07-17T05:30:12,357 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-17T05:30:12,357 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-17T05:30:12,358 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,359 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:12,359 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-17T05:30:12,359 | ^~ ~~~~~~~~~~~ 2024-07-17T05:30:12,360 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-17T05:30:12,360 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-17T05:30:12,360 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,361 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-17T05:30:12,361 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-17T05:30:12,361 | ^~ ~~~~~~~~~~ 2024-07-17T05:30:12,361 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-17T05:30:12,361 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-17T05:30:12,361 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,362 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-17T05:30:12,362 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:12,362 | ^ 2024-07-17T05:30:12,362 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-17T05:30:12,362 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-17T05:30:12,362 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:12,634 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-39/command_shuffle.o -fopenmp 2024-07-17T05:30:12,913 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c global_basic.c -o build/temp.linux-armv7l-cpython-39/global_basic.o -fopenmp 2024-07-17T05:30:13,061 global_basic.c: In function ‘organize_infile_list’: 2024-07-17T05:30:13,061 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-07-17T05:30:13,061 195 | while (isspace(*buf)) buf++; 2024-07-17T05:30:13,061 | ^~~~~~~ 2024-07-17T05:30:13,062 global_basic.c:201:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-17T05:30:13,062 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-17T05:30:13,062 | ~~^ 2024-07-17T05:30:13,062 | | 2024-07-17T05:30:13,062 | long unsigned int 2024-07-17T05:30:13,062 | %u 2024-07-17T05:30:13,063 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-17T05:30:13,063 | ~~~~~~~~~~~ 2024-07-17T05:30:13,063 | | 2024-07-17T05:30:13,063 | size_t {aka unsigned int} 2024-07-17T05:30:13,063 global_basic.c:233:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-17T05:30:13,063 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-17T05:30:13,063 | ~~^ 2024-07-17T05:30:13,064 | | 2024-07-17T05:30:13,064 | long unsigned int 2024-07-17T05:30:13,064 | %u 2024-07-17T05:30:13,064 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-17T05:30:13,064 | ~~~~~~~~~~~ 2024-07-17T05:30:13,064 | | 2024-07-17T05:30:13,064 | size_t {aka unsigned int} 2024-07-17T05:30:13,751 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-39/iseq2comem.o -fopenmp 2024-07-17T05:30:13,926 iseq2comem.c: In function ‘reads2mco’: 2024-07-17T05:30:13,927 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,928 156 | if (base > TL) { 2024-07-17T05:30:13,928 | ^ 2024-07-17T05:30:13,928 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,928 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-17T05:30:13,928 | ^~ 2024-07-17T05:30:13,928 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,929 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-17T05:30:13,929 | ^ 2024-07-17T05:30:13,929 iseq2comem.c: In function ‘fasta2co’: 2024-07-17T05:30:13,929 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,929 239 | if (base > TL) { 2024-07-17T05:30:13,930 | ^ 2024-07-17T05:30:13,930 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,930 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-17T05:30:13,930 | ^~ 2024-07-17T05:30:13,930 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,931 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-17T05:30:13,931 | ^ 2024-07-17T05:30:13,931 iseq2comem.c: In function ‘fastq2co’: 2024-07-17T05:30:13,931 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-07-17T05:30:13,931 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-07-17T05:30:13,931 | ^~ 2024-07-17T05:30:13,932 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,932 318 | if (base > TL) { 2024-07-17T05:30:13,933 | ^ 2024-07-17T05:30:13,933 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,933 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-17T05:30:13,933 | ^~ 2024-07-17T05:30:13,933 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,933 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-17T05:30:13,934 | ^ 2024-07-17T05:30:13,934 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,934 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-07-17T05:30:13,934 | ^ 2024-07-17T05:30:13,935 iseq2comem.c: In function ‘fastq2koc’: 2024-07-17T05:30:13,935 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,936 402 | if (base > TL) { 2024-07-17T05:30:13,936 | ^ 2024-07-17T05:30:13,936 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,936 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-17T05:30:13,936 | ^~ 2024-07-17T05:30:13,937 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,937 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-17T05:30:13,937 | ^ 2024-07-17T05:30:13,943 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-07-17T05:30:13,943 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,943 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-17T05:30:13,943 | ^~ 2024-07-17T05:30:13,944 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:13,944 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-17T05:30:13,944 | ^ 2024-07-17T05:30:15,105 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-07-17T05:30:15,172 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mytime.c -o build/temp.linux-armv7l-cpython-39/mytime.o -fopenmp 2024-07-17T05:30:15,296 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c pykssd.c -o build/temp.linux-armv7l-cpython-39/pykssd.o -fopenmp 2024-07-17T05:30:15,628 pykssd.c: In function ‘py_dist_dispatch’: 2024-07-17T05:30:15,628 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-07-17T05:30:15,628 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-07-17T05:30:15,629 | ^~~~~~ 2024-07-17T05:30:15,630 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-07-17T05:30:15,630 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-07-17T05:30:15,630 | ^~~~~~ 2024-07-17T05:30:15,633 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-07-17T05:30:15,633 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-07-17T05:30:15,633 | ^~~~~~ 2024-07-17T05:30:15,794 pykssd.c: In function ‘rename_file’: 2024-07-17T05:30:15,795 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-07-17T05:30:15,795 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-07-17T05:30:15,795 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-17T05:30:15,795 pykssd.c:41:15: note: length computed here 2024-07-17T05:30:15,795 41 | int len = strlen(p1); 2024-07-17T05:30:15,795 | ^~~~~~~~~~ 2024-07-17T05:30:16,389 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/co2mco.o build/temp.linux-armv7l-cpython-39/command_composite.o build/temp.linux-armv7l-cpython-39/command_dist.o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o build/temp.linux-armv7l-cpython-39/command_set.o build/temp.linux-armv7l-cpython-39/command_shuffle.o build/temp.linux-armv7l-cpython-39/global_basic.o build/temp.linux-armv7l-cpython-39/iseq2comem.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/mytime.o build/temp.linux-armv7l-cpython-39/pykssd.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-07-17T05:30:16,554 building 'nj' extension 2024-07-17T05:30:16,555 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c align.c -o build/temp.linux-armv7l-cpython-39/align.o 2024-07-17T05:30:16,961 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c buildtree.c -o build/temp.linux-armv7l-cpython-39/buildtree.o 2024-07-17T05:30:17,087 buildtree.c: In function ‘UPGMA_buildtree’: 2024-07-17T05:30:17,087 buildtree.c:716:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:17,088 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-17T05:30:17,088 | ^~ 2024-07-17T05:30:17,088 buildtree.c:716:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:17,088 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-17T05:30:17,088 | ^~ 2024-07-17T05:30:17,649 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c cluster.c -o build/temp.linux-armv7l-cpython-39/cluster.o 2024-07-17T05:30:17,972 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c distancemat.c -o build/temp.linux-armv7l-cpython-39/distancemat.o 2024-07-17T05:30:18,091 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-07-17T05:30:18,091 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-17T05:30:18,091 226 | for( i=0; i < dest->size; i++) { 2024-07-17T05:30:18,091 | ^ 2024-07-17T05:30:18,092 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-07-17T05:30:18,092 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-17T05:30:18,092 260 | for( i=0; i < mat->size; i++) { 2024-07-17T05:30:18,092 | ^ 2024-07-17T05:30:18,092 distancemat.c: In function ‘print_DistanceMatrix’: 2024-07-17T05:30:18,092 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-17T05:30:18,093 349 | for(row=0; row < mat->size; row++) { 2024-07-17T05:30:18,093 | ^ 2024-07-17T05:30:18,093 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-07-17T05:30:18,093 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-07-17T05:30:18,093 410 | while(c = fgetc(handle)) { 2024-07-17T05:30:18,094 | ^ 2024-07-17T05:30:18,428 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c pynj.c -o build/temp.linux-armv7l-cpython-39/pynj.o 2024-07-17T05:30:18,816 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c sequence.c -o build/temp.linux-armv7l-cpython-39/sequence.o 2024-07-17T05:30:19,013 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c tree.c -o build/temp.linux-armv7l-cpython-39/tree.o 2024-07-17T05:30:19,746 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c util.c -o build/temp.linux-armv7l-cpython-39/util.o 2024-07-17T05:30:19,916 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/align.o build/temp.linux-armv7l-cpython-39/buildtree.o build/temp.linux-armv7l-cpython-39/cluster.o build/temp.linux-armv7l-cpython-39/distancemat.o build/temp.linux-armv7l-cpython-39/pynj.o build/temp.linux-armv7l-cpython-39/sequence.o build/temp.linux-armv7l-cpython-39/tree.o build/temp.linux-armv7l-cpython-39/util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so 2024-07-17T05:30:20,032 building 'dnj' extension 2024-07-17T05:30:20,033 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c bytescale.c -o build/temp.linux-armv7l-cpython-39/bytescale.o -fopenmp 2024-07-17T05:30:20,098 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c dnj.c -o build/temp.linux-armv7l-cpython-39/dnj.o -fopenmp 2024-07-17T05:30:20,220 dnj.c: In function ‘minQpair’: 2024-07-17T05:30:20,220 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,220 70 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,220 | ^~~ 2024-07-17T05:30:20,221 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,221 126 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,221 | ^~~ 2024-07-17T05:30:20,222 dnj.c: In function ‘maxQpair’: 2024-07-17T05:30:20,222 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,222 157 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,222 | ^~~ 2024-07-17T05:30:20,222 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,223 213 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,223 | ^~~ 2024-07-17T05:30:20,223 dnj.c: In function ‘UPGMApair’: 2024-07-17T05:30:20,223 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,223 237 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,223 | ^~~ 2024-07-17T05:30:20,224 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,224 284 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,224 | ^~~ 2024-07-17T05:30:20,224 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,224 291 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,224 | ^~~ 2024-07-17T05:30:20,225 dnj.c: In function ‘minQrow’: 2024-07-17T05:30:20,225 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,226 374 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,226 | ^~~ 2024-07-17T05:30:20,227 dnj.c: In function ‘maxQrow’: 2024-07-17T05:30:20,227 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,227 435 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,227 | ^~~ 2024-07-17T05:30:20,228 dnj.c: In function ‘UPGMArow’: 2024-07-17T05:30:20,228 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,228 488 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,228 | ^~~ 2024-07-17T05:30:20,229 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,229 494 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,229 | ^~~ 2024-07-17T05:30:20,230 dnj.c: In function ‘minQ_thread’: 2024-07-17T05:30:20,230 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:20,230 553 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:20,230 | ^~~ 2024-07-17T05:30:21,395 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c filebuff.c -o build/temp.linux-armv7l-cpython-39/filebuff.o -fopenmp 2024-07-17T05:30:21,498 filebuff.c: In function ‘BuffgzFileBuff’: 2024-07-17T05:30:21,499 filebuff.c:99:47: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:21,499 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-07-17T05:30:21,499 | ^~ 2024-07-17T05:30:21,786 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c hclust.c -o build/temp.linux-armv7l-cpython-39/hclust.o -fopenmp 2024-07-17T05:30:21,904 hclust.c: In function ‘minQ’: 2024-07-17T05:30:21,904 hclust.c:364:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:21,905 364 | while(++i < Q->n) { 2024-07-17T05:30:21,905 | ^ 2024-07-17T05:30:21,905 hclust.c:377:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:21,905 377 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:21,905 | ^~~ 2024-07-17T05:30:21,905 hclust.c: In function ‘maxQ’: 2024-07-17T05:30:21,906 hclust.c:394:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-17T05:30:21,906 394 | while(++i < Q->n) { 2024-07-17T05:30:21,906 | ^ 2024-07-17T05:30:21,906 hclust.c:407:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:21,906 407 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:21,906 | ^~~ 2024-07-17T05:30:23,944 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c matrix.c -o build/temp.linux-armv7l-cpython-39/matrix.o -fopenmp 2024-07-17T05:30:24,063 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-07-17T05:30:24,064 matrix.c:538:9: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-17T05:30:24,064 538 | if(pos != n) { 2024-07-17T05:30:24,064 | ^~ 2024-07-17T05:30:24,846 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-07-17T05:30:24,906 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c nj.c -o build/temp.linux-armv7l-cpython-39/nj.o -fopenmp 2024-07-17T05:30:25,027 nj.c: In function ‘initQ’: 2024-07-17T05:30:25,028 nj.c:243:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:25,028 243 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:25,028 | ^~~ 2024-07-17T05:30:25,029 nj.c: In function ‘initQ_MN’: 2024-07-17T05:30:25,030 nj.c:358:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:25,030 358 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:25,030 | ^~~ 2024-07-17T05:30:25,033 nj.c: In function ‘minD’: 2024-07-17T05:30:25,033 nj.c:559:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:25,033 559 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:25,033 | ^~~ 2024-07-17T05:30:25,035 nj.c: In function ‘maxD’: 2024-07-17T05:30:25,035 nj.c:642:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:25,035 642 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:25,035 | ^~~ 2024-07-17T05:30:25,038 nj.c: In function ‘minPair’: 2024-07-17T05:30:25,039 nj.c:826:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-17T05:30:25,039 826 | pos <<= sizeof(unsigned) * 8; 2024-07-17T05:30:25,039 | ^~~ 2024-07-17T05:30:27,063 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c nwck.c -o build/temp.linux-armv7l-cpython-39/nwck.o -fopenmp 2024-07-17T05:30:27,530 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pherror.c -o build/temp.linux-armv7l-cpython-39/pherror.o -fopenmp 2024-07-17T05:30:27,627 pherror.c: In function ‘cfread’: 2024-07-17T05:30:27,627 pherror.c:58:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-17T05:30:27,627 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-07-17T05:30:27,627 | ^~ 2024-07-17T05:30:27,718 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c phy.c -o build/temp.linux-armv7l-cpython-39/phy.o -fopenmp 2024-07-17T05:30:28,645 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pydnj.c -o build/temp.linux-armv7l-cpython-39/pydnj.o -fopenmp 2024-07-17T05:30:28,950 In file included from pydnj.c:11: 2024-07-17T05:30:28,951 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-07-17T05:30:28,951 20 | #define _XOPEN_SOURCE 600 2024-07-17T05:30:28,951 | 2024-07-17T05:30:28,951 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-07-17T05:30:28,951 from /usr/include/limits.h:26, 2024-07-17T05:30:28,951 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:195, 2024-07-17T05:30:28,951 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/syslimits.h:7, 2024-07-17T05:30:28,952 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:34, 2024-07-17T05:30:28,952 from /usr/include/python3.9/Python.h:11, 2024-07-17T05:30:28,952 from pydnj.c:1: 2024-07-17T05:30:28,952 /usr/include/features.h:207: note: this is the location of the previous definition 2024-07-17T05:30:28,952 207 | # define _XOPEN_SOURCE 700 2024-07-17T05:30:28,952 | 2024-07-17T05:30:28,966 pydnj.c: In function ‘py_build’: 2024-07-17T05:30:28,966 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-07-17T05:30:28,966 165 | p = omp_get_num_procs(); 2024-07-17T05:30:28,966 | ^~~~~~~~~~~~~~~~~ 2024-07-17T05:30:29,153 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c qseqs.c -o build/temp.linux-armv7l-cpython-39/qseqs.o -fopenmp 2024-07-17T05:30:29,350 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c str.c -o build/temp.linux-armv7l-cpython-39/str.o -fopenmp 2024-07-17T05:30:29,460 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c tmp.c -o build/temp.linux-armv7l-cpython-39/tmp.o -fopenmp 2024-07-17T05:30:29,656 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c vector.c -o build/temp.linux-armv7l-cpython-39/vector.o -fopenmp 2024-07-17T05:30:29,815 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/bytescale.o build/temp.linux-armv7l-cpython-39/dnj.o build/temp.linux-armv7l-cpython-39/filebuff.o build/temp.linux-armv7l-cpython-39/hclust.o build/temp.linux-armv7l-cpython-39/matrix.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/nj.o build/temp.linux-armv7l-cpython-39/nwck.o build/temp.linux-armv7l-cpython-39/pherror.o build/temp.linux-armv7l-cpython-39/phy.o build/temp.linux-armv7l-cpython-39/pydnj.o build/temp.linux-armv7l-cpython-39/qseqs.o build/temp.linux-armv7l-cpython-39/str.o build/temp.linux-armv7l-cpython-39/tmp.o build/temp.linux-armv7l-cpython-39/vector.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-07-17T05:30:29,999 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-07-17T05:30:29,999 !! 2024-07-17T05:30:29,999 ******************************************************************************** 2024-07-17T05:30:29,999 Please avoid running ``setup.py`` directly. 2024-07-17T05:30:30,000 Instead, use pypa/build, pypa/installer or other 2024-07-17T05:30:30,000 standards-based tools. 2024-07-17T05:30:30,000 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-07-17T05:30:30,000 ******************************************************************************** 2024-07-17T05:30:30,000 !! 2024-07-17T05:30:30,001 self.initialize_options() 2024-07-17T05:30:30,023 installing to build/bdist.linux-armv7l/wheel 2024-07-17T05:30:30,024 running install 2024-07-17T05:30:30,050 running install_lib 2024-07-17T05:30:30,074 creating build/bdist.linux-armv7l 2024-07-17T05:30:30,075 creating build/bdist.linux-armv7l/wheel 2024-07-17T05:30:30,076 copying build/lib.linux-armv7l-cpython-39/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-07-17T05:30:30,079 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-17T05:30:30,092 copying build/lib.linux-armv7l-cpython-39/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-07-17T05:30:30,095 copying build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-17T05:30:30,110 copying build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-17T05:30:30,116 running install_egg_info 2024-07-17T05:30:30,159 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-2.0.2-py3.9.egg-info 2024-07-17T05:30:30,176 running install_scripts 2024-07-17T05:30:30,199 creating build/bdist.linux-armv7l/wheel/kssdtree-2.0.2.dist-info/WHEEL 2024-07-17T05:30:30,201 creating '/tmp/pip-wheel-myg2ix8q/kssdtree-2.0.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-07-17T05:30:30,279 adding 'dnj.cpython-39-arm-linux-gnueabihf.so' 2024-07-17T05:30:30,376 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2024-07-17T05:30:30,381 adding 'kssdtree.py' 2024-07-17T05:30:30,403 adding 'nj.cpython-39-arm-linux-gnueabihf.so' 2024-07-17T05:30:30,406 adding 'toolutils.py' 2024-07-17T05:30:30,408 adding 'kssdtree-2.0.2.dist-info/METADATA' 2024-07-17T05:30:30,409 adding 'kssdtree-2.0.2.dist-info/WHEEL' 2024-07-17T05:30:30,410 adding 'kssdtree-2.0.2.dist-info/dependency_links.txt' 2024-07-17T05:30:30,411 adding 'kssdtree-2.0.2.dist-info/top_level.txt' 2024-07-17T05:30:30,411 adding 'kssdtree-2.0.2.dist-info/RECORD' 2024-07-17T05:30:30,420 removing build/bdist.linux-armv7l/wheel 2024-07-17T05:30:30,560 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-07-17T05:30:30,566 Created wheel for kssdtree: filename=kssdtree-2.0.2-cp39-cp39-linux_armv7l.whl size=375957 sha256=599ca3576cae9c0ef5ce475baaee98faa1478f8fd034062ddf88f823c9c91b10 2024-07-17T05:30:30,567 Stored in directory: /tmp/pip-ephem-wheel-cache-k8dtr1q8/wheels/be/b9/4f/c59a0af4f74b6355ed3e9da49953a01ba324353aa8ab892a0c 2024-07-17T05:30:30,578 Successfully built kssdtree 2024-07-17T05:30:30,595 Removed build tracker: '/tmp/pip-build-tracker-eotfeqtf'