2024-07-11T03:29:37,962 Created temporary directory: /tmp/pip-build-tracker-lgrev5rq 2024-07-11T03:29:37,963 Initialized build tracking at /tmp/pip-build-tracker-lgrev5rq 2024-07-11T03:29:37,964 Created build tracker: /tmp/pip-build-tracker-lgrev5rq 2024-07-11T03:29:37,964 Entered build tracker: /tmp/pip-build-tracker-lgrev5rq 2024-07-11T03:29:37,964 Created temporary directory: /tmp/pip-wheel-2k_t5z96 2024-07-11T03:29:37,968 Created temporary directory: /tmp/pip-ephem-wheel-cache-ek8cyj9v 2024-07-11T03:29:37,992 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-11T03:29:37,996 2 location(s) to search for versions of kssdtree: 2024-07-11T03:29:37,996 * https://pypi.org/simple/kssdtree/ 2024-07-11T03:29:37,996 * https://www.piwheels.org/simple/kssdtree/ 2024-07-11T03:29:37,996 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-07-11T03:29:37,997 Getting page https://pypi.org/simple/kssdtree/ 2024-07-11T03:29:37,998 Found index url https://pypi.org/simple/ 2024-07-11T03:29:38,049 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-07-11T03:29:38,051 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 2024-07-11T03:29:38,051 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 2024-07-11T03:29:38,051 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 2024-07-11T03:29:38,052 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 2024-07-11T03:29:38,052 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 2024-07-11T03:29:38,052 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 2024-07-11T03:29:38,052 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 2024-07-11T03:29:38,053 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-07-11T03:29:38,053 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-07-11T03:29:38,054 Found index url https://www.piwheels.org/simple/ 2024-07-11T03:29:38,117 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-07-11T03:29:38,127 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.8-cp311-cp311-linux_armv6l.whl#sha256=717afc6606ad3045caac8f3f1cd01a37edd2f01f1cc38bc1bc6c3320882bd392 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T03:29:38,127 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.8-cp311-cp311-linux_armv7l.whl#sha256=717afc6606ad3045caac8f3f1cd01a37edd2f01f1cc38bc1bc6c3320882bd392 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T03:29:38,127 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/) 2024-07-11T03:29:38,127 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/) 2024-07-11T03:29:38,128 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/) 2024-07-11T03:29:38,128 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.7-cp39-cp39-linux_armv7l.whl#sha256=e1df896451d30c12e01aceb3eb91f0f7dfe0ee6f16fd66864fdefbc21cc54856 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T03:29:38,128 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp311-cp311-linux_armv6l.whl#sha256=0901b6cf3efb240d5d32b1e88a8863f28e2986a2c0749886421c643b98a4aec2 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T03:29:38,128 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp311-cp311-linux_armv7l.whl#sha256=0901b6cf3efb240d5d32b1e88a8863f28e2986a2c0749886421c643b98a4aec2 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T03:29:38,128 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp39-cp39-linux_armv6l.whl#sha256=9defb70b5162efc2c0eb6e415a7e37c604aa9b248a006af86af8f59a3bce5d2b (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T03:29:38,129 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/) 2024-07-11T03:29:38,129 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/) 2024-07-11T03:29:38,129 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/) 2024-07-11T03:29:38,129 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/) 2024-07-11T03:29:38,129 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/) 2024-07-11T03:29:38,130 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/) 2024-07-11T03:29:38,130 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/) 2024-07-11T03:29:38,130 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/) 2024-07-11T03:29:38,130 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/) 2024-07-11T03:29:38,130 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/) 2024-07-11T03:29:38,131 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp37-cp37m-linux_armv7l.whl#sha256=d179f6c6c0ad4e0f06950e1609118b065b3476c47446325f6614bdbef5ede0d0 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T03:29:38,131 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp39-cp39-linux_armv6l.whl#sha256=6df2298fa80eefa823153fa0b9db67e35da72da7f88c5949f4f637872ff22c3b (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T03:29:38,131 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp39-cp39-linux_armv7l.whl#sha256=6df2298fa80eefa823153fa0b9db67e35da72da7f88c5949f4f637872ff22c3b (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T03:29:38,131 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv6l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T03:29:38,131 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/) 2024-07-11T03:29:38,132 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/) 2024-07-11T03:29:38,132 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/) 2024-07-11T03:29:38,132 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/) 2024-07-11T03:29:38,132 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/) 2024-07-11T03:29:38,132 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/) 2024-07-11T03:29:38,133 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/) 2024-07-11T03:29:38,133 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/) 2024-07-11T03:29:38,133 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/) 2024-07-11T03:29:38,133 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/) 2024-07-11T03:29:38,133 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/) 2024-07-11T03:29:38,134 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-07-11T03:29:38,134 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-07-11T03:29:38,152 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-07-11T03:29:38,169 Collecting kssdtree==1.1.8 2024-07-11T03:29:38,171 Created temporary directory: /tmp/pip-unpack-y5eipddq 2024-07-11T03:29:38,215 Downloading kssdtree-1.1.8.tar.gz (112 kB) 2024-07-11T03:29:38,407 Added kssdtree==1.1.8 from https://files.pythonhosted.org/packages/7e/8a/a62c8adc92df69ab8cb242827ee64a3e2b6d5c89b83425785dd00605af17/kssdtree-1.1.8.tar.gz to build tracker '/tmp/pip-build-tracker-lgrev5rq' 2024-07-11T03:29:38,409 Running setup.py (path:/tmp/pip-wheel-2k_t5z96/kssdtree_18fddeed18664dae9cf5e974a41436c3/setup.py) egg_info for package kssdtree 2024-07-11T03:29:38,410 Created temporary directory: /tmp/pip-pip-egg-info-3um3q88r 2024-07-11T03:29:38,410 Preparing metadata (setup.py): started 2024-07-11T03:29:38,411 Running command python setup.py egg_info 2024-07-11T03:29:39,537 running egg_info 2024-07-11T03:29:39,539 creating /tmp/pip-pip-egg-info-3um3q88r/kssdtree.egg-info 2024-07-11T03:29:39,563 writing /tmp/pip-pip-egg-info-3um3q88r/kssdtree.egg-info/PKG-INFO 2024-07-11T03:29:39,567 writing dependency_links to /tmp/pip-pip-egg-info-3um3q88r/kssdtree.egg-info/dependency_links.txt 2024-07-11T03:29:39,569 writing requirements to /tmp/pip-pip-egg-info-3um3q88r/kssdtree.egg-info/requires.txt 2024-07-11T03:29:39,570 writing top-level names to /tmp/pip-pip-egg-info-3um3q88r/kssdtree.egg-info/top_level.txt 2024-07-11T03:29:39,571 writing manifest file '/tmp/pip-pip-egg-info-3um3q88r/kssdtree.egg-info/SOURCES.txt' 2024-07-11T03:29:39,668 reading manifest file '/tmp/pip-pip-egg-info-3um3q88r/kssdtree.egg-info/SOURCES.txt' 2024-07-11T03:29:39,670 reading manifest template 'MANIFEST.in' 2024-07-11T03:29:39,687 writing manifest file '/tmp/pip-pip-egg-info-3um3q88r/kssdtree.egg-info/SOURCES.txt' 2024-07-11T03:29:39,783 Preparing metadata (setup.py): finished with status 'done' 2024-07-11T03:29:39,787 Source in /tmp/pip-wheel-2k_t5z96/kssdtree_18fddeed18664dae9cf5e974a41436c3 has version 1.1.8, which satisfies requirement kssdtree==1.1.8 from https://files.pythonhosted.org/packages/7e/8a/a62c8adc92df69ab8cb242827ee64a3e2b6d5c89b83425785dd00605af17/kssdtree-1.1.8.tar.gz 2024-07-11T03:29:39,788 Removed kssdtree==1.1.8 from https://files.pythonhosted.org/packages/7e/8a/a62c8adc92df69ab8cb242827ee64a3e2b6d5c89b83425785dd00605af17/kssdtree-1.1.8.tar.gz from build tracker '/tmp/pip-build-tracker-lgrev5rq' 2024-07-11T03:29:39,792 Created temporary directory: /tmp/pip-unpack-r7pf8uzv 2024-07-11T03:29:39,793 Created temporary directory: /tmp/pip-unpack-bmb4yx78 2024-07-11T03:29:39,799 Building wheels for collected packages: kssdtree 2024-07-11T03:29:39,803 Created temporary directory: /tmp/pip-wheel-yhw704re 2024-07-11T03:29:39,803 Building wheel for kssdtree (setup.py): started 2024-07-11T03:29:39,804 Destination directory: /tmp/pip-wheel-yhw704re 2024-07-11T03:29:39,804 Running command python setup.py bdist_wheel 2024-07-11T03:29:40,900 running bdist_wheel 2024-07-11T03:29:40,993 running build 2024-07-11T03:29:40,993 running build_py 2024-07-11T03:29:41,019 creating build 2024-07-11T03:29:41,020 creating build/lib.linux-armv7l-cpython-39 2024-07-11T03:29:41,021 copying kssdtree.py -> build/lib.linux-armv7l-cpython-39 2024-07-11T03:29:41,024 copying toolutils.py -> build/lib.linux-armv7l-cpython-39 2024-07-11T03:29:41,026 running egg_info 2024-07-11T03:29:41,080 writing kssdtree.egg-info/PKG-INFO 2024-07-11T03:29:41,083 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-07-11T03:29:41,085 writing requirements to kssdtree.egg-info/requires.txt 2024-07-11T03:29:41,087 writing top-level names to kssdtree.egg-info/top_level.txt 2024-07-11T03:29:41,113 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-11T03:29:41,116 reading manifest template 'MANIFEST.in' 2024-07-11T03:29:41,134 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-11T03:29:41,136 running build_ext 2024-07-11T03:29:41,639 building 'kssd' extension 2024-07-11T03:29:41,640 creating build/temp.linux-armv7l-cpython-39 2024-07-11T03:29:41,641 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 2024-07-11T03:29:41,805 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-07-11T03:29:41,805 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T03:29:41,805 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-07-11T03:29:41,805 | ^ 2024-07-11T03:29:41,807 co2mco.c: In function ‘co2unitllmco’: 2024-07-11T03:29:41,808 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T03:29:41,808 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-07-11T03:29:41,808 | ^ 2024-07-11T03:29:42,444 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 2024-07-11T03:29:43,000 command_composite.c: In function ‘get_species_abundance’: 2024-07-11T03:29:43,001 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-11T03:29:43,001 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-07-11T03:29:43,001 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,002 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-11T03:29:43,002 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-07-11T03:29:43,002 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,002 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:43,002 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-11T03:29:43,002 | ^ 2024-07-11T03:29:43,002 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-11T03:29:43,003 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-11T03:29:43,003 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,003 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:43,003 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-11T03:29:43,003 | ^ 2024-07-11T03:29:43,003 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-11T03:29:43,003 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-11T03:29:43,004 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,004 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:43,004 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-11T03:29:43,004 | ^ 2024-07-11T03:29:43,004 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-11T03:29:43,004 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-11T03:29:43,005 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,005 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:43,005 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-11T03:29:43,005 | ^ 2024-07-11T03:29:43,005 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-11T03:29:43,005 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-11T03:29:43,005 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,006 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:43,006 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-11T03:29:43,006 | ^ 2024-07-11T03:29:43,006 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-07-11T03:29:43,006 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-11T03:29:43,006 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,240 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist.c -o build/temp.linux-armv7l-cpython-39/command_dist.o -fopenmp 2024-07-11T03:29:43,442 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-11T03:29:43,443 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=] 2024-07-11T03:29:43,443 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T03:29:43,444 | ~~^ 2024-07-11T03:29:43,444 | | 2024-07-11T03:29:43,444 | long unsigned int 2024-07-11T03:29:43,444 | %u 2024-07-11T03:29:43,444 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T03:29:43,444 | ~~~~~~~ 2024-07-11T03:29:43,444 | | 2024-07-11T03:29:43,444 | size_t {aka unsigned int} 2024-07-11T03:29:43,445 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=] 2024-07-11T03:29:43,445 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T03:29:43,445 | ~~^ 2024-07-11T03:29:43,445 | | 2024-07-11T03:29:43,445 | long unsigned int 2024-07-11T03:29:43,445 | %u 2024-07-11T03:29:43,445 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T03:29:43,445 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T03:29:43,446 | ~~~~~~~~~ 2024-07-11T03:29:43,446 | | 2024-07-11T03:29:43,446 | size_t {aka unsigned int} 2024-07-11T03:29:43,446 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-11T03:29:43,446 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T03:29:43,446 | ~~^ 2024-07-11T03:29:43,446 | | 2024-07-11T03:29:43,447 | long unsigned int 2024-07-11T03:29:43,447 | %u 2024-07-11T03:29:43,447 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T03:29:43,447 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T03:29:43,447 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,447 | | 2024-07-11T03:29:43,447 | unsigned int 2024-07-11T03:29:43,448 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-11T03:29:43,448 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-07-11T03:29:43,448 | ^ 2024-07-11T03:29:43,454 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-11T03:29:43,455 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=] 2024-07-11T03:29:43,456 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-11T03:29:43,456 | ~~^ ~~~~~~~ 2024-07-11T03:29:43,456 | | | 2024-07-11T03:29:43,456 | long unsigned int size_t {aka unsigned int} 2024-07-11T03:29:43,456 | %u 2024-07-11T03:29:43,457 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=] 2024-07-11T03:29:43,457 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-11T03:29:43,457 | ~~^ 2024-07-11T03:29:43,457 | | 2024-07-11T03:29:43,457 | long unsigned int 2024-07-11T03:29:43,457 | %u 2024-07-11T03:29:43,458 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-11T03:29:43,458 | ~~~~~~~~~ 2024-07-11T03:29:43,458 | | 2024-07-11T03:29:43,458 | size_t {aka unsigned int} 2024-07-11T03:29:43,458 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-11T03:29:43,458 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-11T03:29:43,459 | ~~^ 2024-07-11T03:29:43,459 | | 2024-07-11T03:29:43,459 | long unsigned int 2024-07-11T03:29:43,459 | %u 2024-07-11T03:29:43,459 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-11T03:29:43,459 865 | (size_t) b * unitsz_distf_mapped); 2024-07-11T03:29:43,459 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,459 | | 2024-07-11T03:29:43,460 | unsigned int 2024-07-11T03:29:43,460 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-07-11T03:29:43,461 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-07-11T03:29:43,461 | ^~~~~~~ 2024-07-11T03:29:43,461 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-07-11T03:29:43,461 809 | struct stat cbd_fcode_stat; 2024-07-11T03:29:43,461 | ^~~~~~~~~~~~~~ 2024-07-11T03:29:43,461 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-07-11T03:29:43,462 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-11T03:29:43,462 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,462 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-07-11T03:29:43,462 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-11T03:29:43,462 | ^~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,468 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-11T03:29:43,469 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=] 2024-07-11T03:29:43,469 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T03:29:43,469 | ~~^ 2024-07-11T03:29:43,469 | | 2024-07-11T03:29:43,470 | long unsigned int 2024-07-11T03:29:43,470 | %u 2024-07-11T03:29:43,470 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T03:29:43,470 | ~~~~~~~ 2024-07-11T03:29:43,470 | | 2024-07-11T03:29:43,470 | size_t {aka unsigned int} 2024-07-11T03:29:43,471 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=] 2024-07-11T03:29:43,471 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T03:29:43,471 | ~~^ 2024-07-11T03:29:43,471 | | 2024-07-11T03:29:43,471 | long unsigned int 2024-07-11T03:29:43,471 | %u 2024-07-11T03:29:43,472 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T03:29:43,472 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T03:29:43,472 | ~~~~~~~~~ 2024-07-11T03:29:43,472 | | 2024-07-11T03:29:43,472 | size_t {aka unsigned int} 2024-07-11T03:29:43,472 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-11T03:29:43,473 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T03:29:43,473 | ~~^ 2024-07-11T03:29:43,473 | | 2024-07-11T03:29:43,473 | long unsigned int 2024-07-11T03:29:43,473 | %u 2024-07-11T03:29:43,473 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T03:29:43,473 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T03:29:43,474 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,474 | | 2024-07-11T03:29:43,474 | unsigned int 2024-07-11T03:29:43,474 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:43,474 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-07-11T03:29:43,475 | ^ 2024-07-11T03:29:43,477 command_dist.c: In function ‘mco_co_dist_core’: 2024-07-11T03:29:43,478 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-11T03:29:43,478 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-07-11T03:29:43,478 | ^ 2024-07-11T03:29:43,484 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-07-11T03:29:43,484 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:43,485 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-07-11T03:29:43,485 | ^ 2024-07-11T03:29:43,486 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:43,486 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-11T03:29:43,486 | ^ 2024-07-11T03:29:43,491 command_dist.c: In function ‘dist_print_nobin’: 2024-07-11T03:29:43,492 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:43,492 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-07-11T03:29:43,492 | ^ 2024-07-11T03:29:43,494 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:43,494 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-11T03:29:43,494 | ^ 2024-07-11T03:29:43,496 command_dist.c:1380:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:43,496 1380 | for (int rid = 0; rid < ref_num; rid++) 2024-07-11T03:29:43,496 | ^ 2024-07-11T03:29:43,496 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:43,497 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-07-11T03:29:43,497 | ^ 2024-07-11T03:29:43,747 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-07-11T03:29:43,747 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-07-11T03:29:43,747 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-07-11T03:29:43,748 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:43,748 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-07-11T03:29:43,748 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-07-11T03:29:43,748 | ^~~~~~~~~~~~ 2024-07-11T03:29:44,471 command_dist.c: In function ‘get_dim_shuffle’: 2024-07-11T03:29:44,471 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-07-11T03:29:44,472 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-11T03:29:44,472 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:44,472 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-07-11T03:29:44,472 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-11T03:29:44,472 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,254 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-11T03:29:45,254 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:45,254 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T03:29:45,255 | ^~ ~~~~~~~~~ 2024-07-11T03:29:45,255 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-11T03:29:45,255 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T03:29:45,255 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,255 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T03:29:45,256 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T03:29:45,256 | ^~~~~~~~~~~~~~~ 2024-07-11T03:29:45,256 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-11T03:29:45,256 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T03:29:45,256 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,257 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T03:29:45,257 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T03:29:45,257 | ^~~~~~~~~~~ 2024-07-11T03:29:45,258 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-11T03:29:45,258 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T03:29:45,258 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,258 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T03:29:45,258 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T03:29:45,258 | ^~~~~ 2024-07-11T03:29:45,258 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T03:29:45,259 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T03:29:45,259 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,466 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-11T03:29:45,467 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:45,467 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T03:29:45,467 | ^~ ~~~~~~~~~ 2024-07-11T03:29:45,468 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-11T03:29:45,468 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T03:29:45,468 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,468 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T03:29:45,468 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T03:29:45,469 | ^~~~~~~~~~~~~~~ 2024-07-11T03:29:45,469 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-11T03:29:45,469 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T03:29:45,469 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,470 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T03:29:45,470 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T03:29:45,470 | ^~~~~~~~~~~~~ 2024-07-11T03:29:45,470 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-11T03:29:45,470 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T03:29:45,470 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,471 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:45,471 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-11T03:29:45,472 | ^ 2024-07-11T03:29:45,472 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-07-11T03:29:45,472 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-11T03:29:45,472 | ^~~~~~~~~~ 2024-07-11T03:29:45,472 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-11T03:29:45,472 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-11T03:29:45,473 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,473 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:45,473 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-11T03:29:45,473 | ^ 2024-07-11T03:29:45,474 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-07-11T03:29:45,474 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-11T03:29:45,474 | ^~~~~~~~~~ 2024-07-11T03:29:45,474 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-11T03:29:45,474 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-11T03:29:45,474 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,711 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-11T03:29:45,711 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:45,712 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T03:29:45,712 | ^~ ~~~~~~~~~ 2024-07-11T03:29:45,712 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-11T03:29:45,712 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T03:29:45,712 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,713 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T03:29:45,713 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T03:29:45,713 | ^~~~~~~~~~~~~~~ 2024-07-11T03:29:45,714 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-11T03:29:45,714 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T03:29:45,714 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,714 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T03:29:45,715 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T03:29:45,715 | ^~~~~~~~~~~~~ 2024-07-11T03:29:45,715 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-11T03:29:45,715 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T03:29:45,715 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,717 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T03:29:45,717 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T03:29:45,717 | ^~~~~~~~~~~ 2024-07-11T03:29:45,717 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-11T03:29:45,717 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T03:29:45,718 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,718 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T03:29:45,718 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T03:29:45,718 | ^~~~~ 2024-07-11T03:29:45,719 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T03:29:45,719 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T03:29:45,719 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,966 command_dist.c: In function ‘combine_queries’: 2024-07-11T03:29:45,967 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T03:29:45,967 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-11T03:29:45,967 | ^ 2024-07-11T03:29:45,968 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T03:29:45,968 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-11T03:29:45,968 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,969 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T03:29:45,969 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-11T03:29:45,969 | ^ 2024-07-11T03:29:45,970 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T03:29:45,970 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-11T03:29:45,970 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:45,972 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:45,972 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-11T03:29:45,972 | ^~ ~~~~~~~~ 2024-07-11T03:29:45,973 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-11T03:29:45,973 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-11T03:29:45,973 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:46,443 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 2024-07-11T03:29:46,610 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 2024-07-11T03:29:46,757 command_set.c: In function ‘sketch_operate’: 2024-07-11T03:29:46,757 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-11T03:29:46,757 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-07-11T03:29:46,758 | ^ 2024-07-11T03:29:46,767 command_set.c: In function ‘combin_subset_pans’: 2024-07-11T03:29:46,767 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-11T03:29:46,767 458 | free(co_dstat_fpath); 2024-07-11T03:29:46,767 | ^~~~~~~~~~~~~~ 2024-07-11T03:29:46,768 In file included from kssdheaders/global_basic.h:159, 2024-07-11T03:29:46,768 from command_set.c:15: 2024-07-11T03:29:46,768 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-11T03:29:46,768 565 | extern void free (void *__ptr) __THROW; 2024-07-11T03:29:46,768 | ~~~~~~^~~~~ 2024-07-11T03:29:46,772 command_set.c: In function ‘grouping_genomes’: 2024-07-11T03:29:46,772 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-11T03:29:46,773 563 | free(co_dstat_fpath); 2024-07-11T03:29:46,773 | ^~~~~~~~~~~~~~ 2024-07-11T03:29:46,773 In file included from kssdheaders/global_basic.h:159, 2024-07-11T03:29:46,773 from command_set.c:15: 2024-07-11T03:29:46,773 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-11T03:29:46,773 565 | extern void free (void *__ptr) __THROW; 2024-07-11T03:29:46,773 | ~~~~~~^~~~~ 2024-07-11T03:29:46,888 command_set.c: In function ‘sketch_union’: 2024-07-11T03:29:46,889 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T03:29:46,889 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:46,889 | ^ 2024-07-11T03:29:46,889 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T03:29:46,889 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:46,889 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:46,889 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:46,890 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T03:29:46,890 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:46,890 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T03:29:46,890 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T03:29:46,890 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:46,890 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:46,890 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-11T03:29:46,891 | ^~ ~~~~~~~~~~ 2024-07-11T03:29:46,891 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T03:29:46,891 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-11T03:29:46,891 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,002 command_set.c: In function ‘sketch_operate’: 2024-07-11T03:29:47,002 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,002 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-11T03:29:47,002 | ^~ ~~~~~~~~~~ 2024-07-11T03:29:47,003 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T03:29:47,003 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-11T03:29:47,003 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,003 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,003 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-11T03:29:47,003 | ^~ ~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,003 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-11T03:29:47,003 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-11T03:29:47,004 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,004 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,004 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T03:29:47,004 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:47,004 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T03:29:47,004 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T03:29:47,004 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,005 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,005 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T03:29:47,005 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:47,005 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T03:29:47,005 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T03:29:47,005 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,005 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,006 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T03:29:47,006 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:47,006 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T03:29:47,006 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T03:29:47,006 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,006 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,006 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T03:29:47,006 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:47,007 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T03:29:47,007 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T03:29:47,007 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,007 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T03:29:47,007 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:47,007 | ^ 2024-07-11T03:29:47,007 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T03:29:47,008 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:47,008 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,155 command_set.c: In function ‘uniq_sketch_union’: 2024-07-11T03:29:47,155 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T03:29:47,155 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:47,155 | ^ 2024-07-11T03:29:47,156 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T03:29:47,156 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:47,156 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,156 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,156 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T03:29:47,156 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:47,156 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T03:29:47,157 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T03:29:47,157 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,157 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,157 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-11T03:29:47,157 | ^~ ~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,157 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-11T03:29:47,157 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-11T03:29:47,157 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,282 command_set.c: In function ‘combin_pans’: 2024-07-11T03:29:47,282 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,282 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T03:29:47,282 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:47,283 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-07-11T03:29:47,283 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T03:29:47,283 | ^~~~~~~~~~ 2024-07-11T03:29:47,283 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-07-11T03:29:47,283 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T03:29:47,283 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,283 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,283 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T03:29:47,284 | ^~ ~~~~~~~~~~ 2024-07-11T03:29:47,284 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-07-11T03:29:47,284 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T03:29:47,284 | ^~~~~~~~~~ 2024-07-11T03:29:47,284 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-07-11T03:29:47,284 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T03:29:47,284 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,285 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T03:29:47,285 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:47,285 | ^ 2024-07-11T03:29:47,285 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T03:29:47,285 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:47,285 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,469 command_set.c: In function ‘combin_subset_pans’: 2024-07-11T03:29:47,470 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,470 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T03:29:47,470 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:47,470 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T03:29:47,470 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T03:29:47,470 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,470 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,471 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T03:29:47,471 | ^~ ~~~~~~~~~~ 2024-07-11T03:29:47,471 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T03:29:47,471 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T03:29:47,471 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,471 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,471 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T03:29:47,472 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:47,472 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T03:29:47,472 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T03:29:47,472 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,473 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,473 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T03:29:47,474 | ^~ ~~~~~~~~~~ 2024-07-11T03:29:47,474 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T03:29:47,474 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T03:29:47,474 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,474 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T03:29:47,474 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:47,474 | ^ 2024-07-11T03:29:47,475 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T03:29:47,475 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:47,475 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,677 command_set.c: In function ‘grouping_genomes’: 2024-07-11T03:29:47,677 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,678 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T03:29:47,678 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:47,678 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T03:29:47,678 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T03:29:47,678 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,679 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,679 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T03:29:47,679 | ^~ ~~~~~~~~~~ 2024-07-11T03:29:47,679 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T03:29:47,679 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T03:29:47,679 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,681 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,681 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T03:29:47,681 | ^~ ~~~~~~~~~~~ 2024-07-11T03:29:47,681 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T03:29:47,681 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T03:29:47,681 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,682 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T03:29:47,682 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T03:29:47,682 | ^~ ~~~~~~~~~~ 2024-07-11T03:29:47,683 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T03:29:47,683 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T03:29:47,683 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,683 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T03:29:47,683 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:47,683 | ^ 2024-07-11T03:29:47,684 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T03:29:47,684 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T03:29:47,684 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:47,957 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 2024-07-11T03:29:48,234 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 2024-07-11T03:29:48,384 global_basic.c: In function ‘organize_infile_list’: 2024-07-11T03:29:48,384 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-07-11T03:29:48,384 195 | while (isspace(*buf)) buf++; 2024-07-11T03:29:48,385 | ^~~~~~~ 2024-07-11T03:29:48,385 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=] 2024-07-11T03:29:48,385 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-11T03:29:48,385 | ~~^ 2024-07-11T03:29:48,385 | | 2024-07-11T03:29:48,385 | long unsigned int 2024-07-11T03:29:48,386 | %u 2024-07-11T03:29:48,386 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-11T03:29:48,386 | ~~~~~~~~~~~ 2024-07-11T03:29:48,386 | | 2024-07-11T03:29:48,386 | size_t {aka unsigned int} 2024-07-11T03:29:48,386 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=] 2024-07-11T03:29:48,386 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-11T03:29:48,387 | ~~^ 2024-07-11T03:29:48,387 | | 2024-07-11T03:29:48,387 | long unsigned int 2024-07-11T03:29:48,387 | %u 2024-07-11T03:29:48,387 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-11T03:29:48,387 | ~~~~~~~~~~~ 2024-07-11T03:29:48,387 | | 2024-07-11T03:29:48,388 | size_t {aka unsigned int} 2024-07-11T03:29:49,057 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 2024-07-11T03:29:49,208 iseq2comem.c: In function ‘reads2mco’: 2024-07-11T03:29:49,208 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,208 156 | if (base > TL) { 2024-07-11T03:29:49,209 | ^ 2024-07-11T03:29:49,209 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,209 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T03:29:49,209 | ^~ 2024-07-11T03:29:49,209 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,209 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T03:29:49,209 | ^ 2024-07-11T03:29:49,210 iseq2comem.c: In function ‘fasta2co’: 2024-07-11T03:29:49,211 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,211 239 | if (base > TL) { 2024-07-11T03:29:49,211 | ^ 2024-07-11T03:29:49,211 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,211 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T03:29:49,211 | ^~ 2024-07-11T03:29:49,211 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,212 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T03:29:49,212 | ^ 2024-07-11T03:29:49,212 iseq2comem.c: In function ‘fastq2co’: 2024-07-11T03:29:49,212 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-07-11T03:29:49,212 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-07-11T03:29:49,212 | ^~ 2024-07-11T03:29:49,213 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,213 318 | if (base > TL) { 2024-07-11T03:29:49,213 | ^ 2024-07-11T03:29:49,214 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,214 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T03:29:49,214 | ^~ 2024-07-11T03:29:49,214 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,214 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T03:29:49,214 | ^ 2024-07-11T03:29:49,215 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,215 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-07-11T03:29:49,215 | ^ 2024-07-11T03:29:49,216 iseq2comem.c: In function ‘fastq2koc’: 2024-07-11T03:29:49,217 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,217 402 | if (base > TL) { 2024-07-11T03:29:49,217 | ^ 2024-07-11T03:29:49,217 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,217 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T03:29:49,217 | ^~ 2024-07-11T03:29:49,217 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,218 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T03:29:49,218 | ^ 2024-07-11T03:29:49,223 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-07-11T03:29:49,223 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,223 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T03:29:49,223 | ^~ 2024-07-11T03:29:49,223 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:49,224 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T03:29:49,224 | ^ 2024-07-11T03:29:50,386 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 2024-07-11T03:29:50,449 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 2024-07-11T03:29:50,570 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 2024-07-11T03:29:50,947 pykssd.c: In function ‘py_dist_dispatch’: 2024-07-11T03:29:50,948 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-07-11T03:29:50,948 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-07-11T03:29:50,948 | ^~~~~~ 2024-07-11T03:29:50,948 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-07-11T03:29:50,948 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-07-11T03:29:50,949 | ^~~~~~ 2024-07-11T03:29:50,950 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-07-11T03:29:50,950 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-07-11T03:29:50,950 | ^~~~~~ 2024-07-11T03:29:51,087 pykssd.c: In function ‘rename_file’: 2024-07-11T03:29:51,087 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-07-11T03:29:51,088 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-07-11T03:29:51,088 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T03:29:51,088 pykssd.c:41:15: note: length computed here 2024-07-11T03:29:51,088 41 | int len = strlen(p1); 2024-07-11T03:29:51,088 | ^~~~~~~~~~ 2024-07-11T03:29:51,452 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 2024-07-11T03:29:51,611 building 'nj' extension 2024-07-11T03:29:51,612 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 2024-07-11T03:29:52,019 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 2024-07-11T03:29:52,145 buildtree.c: In function ‘UPGMA_buildtree’: 2024-07-11T03:29:52,145 buildtree.c:716:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:52,145 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-11T03:29:52,145 | ^~ 2024-07-11T03:29:52,145 buildtree.c:716:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:52,145 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-11T03:29:52,146 | ^~ 2024-07-11T03:29:52,743 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 2024-07-11T03:29:53,065 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 2024-07-11T03:29:53,182 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-07-11T03:29:53,183 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T03:29:53,183 226 | for( i=0; i < dest->size; i++) { 2024-07-11T03:29:53,183 | ^ 2024-07-11T03:29:53,184 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-07-11T03:29:53,184 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T03:29:53,184 260 | for( i=0; i < mat->size; i++) { 2024-07-11T03:29:53,185 | ^ 2024-07-11T03:29:53,186 distancemat.c: In function ‘print_DistanceMatrix’: 2024-07-11T03:29:53,186 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T03:29:53,186 349 | for(row=0; row < mat->size; row++) { 2024-07-11T03:29:53,186 | ^ 2024-07-11T03:29:53,187 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-07-11T03:29:53,188 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-07-11T03:29:53,188 410 | while(c = fgetc(handle)) { 2024-07-11T03:29:53,188 | ^ 2024-07-11T03:29:53,522 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 2024-07-11T03:29:53,891 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 2024-07-11T03:29:55,917 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 2024-07-11T03:29:56,663 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 2024-07-11T03:29:56,830 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 2024-07-11T03:29:56,946 building 'dnj' extension 2024-07-11T03:29:56,947 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 2024-07-11T03:29:57,012 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 2024-07-11T03:29:57,135 dnj.c: In function ‘minQpair’: 2024-07-11T03:29:57,135 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,135 70 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,136 | ^~~ 2024-07-11T03:29:57,136 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,136 126 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,137 | ^~~ 2024-07-11T03:29:57,137 dnj.c: In function ‘maxQpair’: 2024-07-11T03:29:57,137 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,137 157 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,137 | ^~~ 2024-07-11T03:29:57,138 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,138 213 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,138 | ^~~ 2024-07-11T03:29:57,138 dnj.c: In function ‘UPGMApair’: 2024-07-11T03:29:57,138 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,138 237 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,139 | ^~~ 2024-07-11T03:29:57,139 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,139 284 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,139 | ^~~ 2024-07-11T03:29:57,139 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,140 291 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,140 | ^~~ 2024-07-11T03:29:57,140 dnj.c: In function ‘minQrow’: 2024-07-11T03:29:57,141 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,141 374 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,141 | ^~~ 2024-07-11T03:29:57,142 dnj.c: In function ‘maxQrow’: 2024-07-11T03:29:57,142 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,142 435 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,142 | ^~~ 2024-07-11T03:29:57,143 dnj.c: In function ‘UPGMArow’: 2024-07-11T03:29:57,143 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,143 488 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,143 | ^~~ 2024-07-11T03:29:57,144 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,144 494 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,144 | ^~~ 2024-07-11T03:29:57,145 dnj.c: In function ‘minQ_thread’: 2024-07-11T03:29:57,145 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:57,145 553 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:57,145 | ^~~ 2024-07-11T03:29:58,313 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c filebuff.c -o build/temp.linux-armv7l-cpython-39/filebuff.o -fopenmp 2024-07-11T03:29:58,418 filebuff.c: In function ‘BuffgzFileBuff’: 2024-07-11T03:29:58,418 filebuff.c:99:47: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:29:58,419 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-07-11T03:29:58,419 | ^~ 2024-07-11T03:29:58,702 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 2024-07-11T03:29:58,826 hclust.c: In function ‘minQ’: 2024-07-11T03:29:58,826 hclust.c:364:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:58,827 364 | while(++i < Q->n) { 2024-07-11T03:29:58,827 | ^ 2024-07-11T03:29:58,827 hclust.c:377:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:58,827 377 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:58,827 | ^~~ 2024-07-11T03:29:58,827 hclust.c: In function ‘maxQ’: 2024-07-11T03:29:58,827 hclust.c:394:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T03:29:58,828 394 | while(++i < Q->n) { 2024-07-11T03:29:58,828 | ^ 2024-07-11T03:29:58,828 hclust.c:407:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:29:58,828 407 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:29:58,828 | ^~~ 2024-07-11T03:30:00,890 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c matrix.c -o build/temp.linux-armv7l-cpython-39/matrix.o -fopenmp 2024-07-11T03:30:01,011 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-07-11T03:30:01,011 matrix.c:538:9: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T03:30:01,011 538 | if(pos != n) { 2024-07-11T03:30:01,011 | ^~ 2024-07-11T03:30:01,764 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 2024-07-11T03:30:01,827 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 2024-07-11T03:30:01,949 nj.c: In function ‘initQ’: 2024-07-11T03:30:01,949 nj.c:243:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:30:01,949 243 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:30:01,949 | ^~~ 2024-07-11T03:30:01,951 nj.c: In function ‘initQ_MN’: 2024-07-11T03:30:01,951 nj.c:358:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:30:01,951 358 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:30:01,951 | ^~~ 2024-07-11T03:30:01,954 nj.c: In function ‘minD’: 2024-07-11T03:30:01,954 nj.c:559:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:30:01,955 559 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:30:01,955 | ^~~ 2024-07-11T03:30:01,956 nj.c: In function ‘maxD’: 2024-07-11T03:30:01,956 nj.c:642:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:30:01,956 642 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:30:01,956 | ^~~ 2024-07-11T03:30:01,959 nj.c: In function ‘minPair’: 2024-07-11T03:30:01,960 nj.c:826:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T03:30:01,960 826 | pos <<= sizeof(unsigned) * 8; 2024-07-11T03:30:01,960 | ^~~ 2024-07-11T03:30:03,973 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 2024-07-11T03:30:04,438 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 2024-07-11T03:30:04,524 pherror.c: In function ‘cfread’: 2024-07-11T03:30:04,525 pherror.c:58:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T03:30:04,525 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-07-11T03:30:04,525 | ^~ 2024-07-11T03:30:04,616 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 2024-07-11T03:30:05,534 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pydnj.c -o build/temp.linux-armv7l-cpython-39/pydnj.o -fopenmp 2024-07-11T03:30:05,840 In file included from pydnj.c:11: 2024-07-11T03:30:05,840 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-07-11T03:30:05,841 20 | #define _XOPEN_SOURCE 600 2024-07-11T03:30:05,841 | 2024-07-11T03:30:05,841 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-07-11T03:30:05,841 from /usr/include/limits.h:26, 2024-07-11T03:30:05,841 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:195, 2024-07-11T03:30:05,842 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/syslimits.h:7, 2024-07-11T03:30:05,842 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:34, 2024-07-11T03:30:05,842 from /usr/include/python3.9/Python.h:11, 2024-07-11T03:30:05,842 from pydnj.c:1: 2024-07-11T03:30:05,842 /usr/include/features.h:207: note: this is the location of the previous definition 2024-07-11T03:30:05,842 207 | # define _XOPEN_SOURCE 700 2024-07-11T03:30:05,843 | 2024-07-11T03:30:05,855 pydnj.c: In function ‘py_build’: 2024-07-11T03:30:05,856 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-07-11T03:30:05,856 165 | p = omp_get_num_procs(); 2024-07-11T03:30:05,856 | ^~~~~~~~~~~~~~~~~ 2024-07-11T03:30:06,037 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 2024-07-11T03:30:06,227 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 2024-07-11T03:30:06,336 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 2024-07-11T03:30:06,519 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 2024-07-11T03:30:06,673 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 2024-07-11T03:30:06,852 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-07-11T03:30:06,852 !! 2024-07-11T03:30:06,853 ******************************************************************************** 2024-07-11T03:30:06,853 Please avoid running ``setup.py`` directly. 2024-07-11T03:30:06,853 Instead, use pypa/build, pypa/installer or other 2024-07-11T03:30:06,853 standards-based tools. 2024-07-11T03:30:06,853 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-07-11T03:30:06,853 ******************************************************************************** 2024-07-11T03:30:06,854 !! 2024-07-11T03:30:06,854 self.initialize_options() 2024-07-11T03:30:06,877 installing to build/bdist.linux-armv7l/wheel 2024-07-11T03:30:06,878 running install 2024-07-11T03:30:06,903 running install_lib 2024-07-11T03:30:06,927 creating build/bdist.linux-armv7l 2024-07-11T03:30:06,928 creating build/bdist.linux-armv7l/wheel 2024-07-11T03:30:06,929 copying build/lib.linux-armv7l-cpython-39/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-07-11T03:30:06,932 copying build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-11T03:30:06,937 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-11T03:30:06,947 copying build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-11T03:30:06,954 copying build/lib.linux-armv7l-cpython-39/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-07-11T03:30:06,957 running install_egg_info 2024-07-11T03:30:06,986 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-1.1.8-py3.9.egg-info 2024-07-11T03:30:06,999 running install_scripts 2024-07-11T03:30:07,015 creating build/bdist.linux-armv7l/wheel/kssdtree-1.1.8.dist-info/WHEEL 2024-07-11T03:30:07,018 creating '/tmp/pip-wheel-yhw704re/kssdtree-1.1.8-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-07-11T03:30:07,098 adding 'dnj.cpython-39-arm-linux-gnueabihf.so' 2024-07-11T03:30:07,192 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2024-07-11T03:30:07,198 adding 'kssdtree.py' 2024-07-11T03:30:07,220 adding 'nj.cpython-39-arm-linux-gnueabihf.so' 2024-07-11T03:30:07,223 adding 'toolutils.py' 2024-07-11T03:30:07,225 adding 'kssdtree-1.1.8.dist-info/METADATA' 2024-07-11T03:30:07,227 adding 'kssdtree-1.1.8.dist-info/WHEEL' 2024-07-11T03:30:07,228 adding 'kssdtree-1.1.8.dist-info/dependency_links.txt' 2024-07-11T03:30:07,229 adding 'kssdtree-1.1.8.dist-info/top_level.txt' 2024-07-11T03:30:07,230 adding 'kssdtree-1.1.8.dist-info/RECORD' 2024-07-11T03:30:07,236 removing build/bdist.linux-armv7l/wheel 2024-07-11T03:30:07,375 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-07-11T03:30:07,381 Created wheel for kssdtree: filename=kssdtree-1.1.8-cp39-cp39-linux_armv7l.whl size=375695 sha256=6b3f5b0e827056c7b589f4fb02c353408efa5892ef4df1c8a54b4cb30331754a 2024-07-11T03:30:07,383 Stored in directory: /tmp/pip-ephem-wheel-cache-ek8cyj9v/wheels/81/b2/c9/1fcd6bbf2cec3a321b30bbe082c81e650b34c60f27b27d2aac 2024-07-11T03:30:07,393 Successfully built kssdtree 2024-07-11T03:30:07,405 Removed build tracker: '/tmp/pip-build-tracker-lgrev5rq'