2024-07-11T02:39:51,560 Created temporary directory: /tmp/pip-build-tracker-vnwd9cda 2024-07-11T02:39:51,561 Initialized build tracking at /tmp/pip-build-tracker-vnwd9cda 2024-07-11T02:39:51,561 Created build tracker: /tmp/pip-build-tracker-vnwd9cda 2024-07-11T02:39:51,562 Entered build tracker: /tmp/pip-build-tracker-vnwd9cda 2024-07-11T02:39:51,562 Created temporary directory: /tmp/pip-wheel-f6a07aik 2024-07-11T02:39:51,565 Created temporary directory: /tmp/pip-ephem-wheel-cache-p4qpgpw_ 2024-07-11T02:39:51,587 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-11T02:39:51,591 2 location(s) to search for versions of kssdtree: 2024-07-11T02:39:51,591 * https://pypi.org/simple/kssdtree/ 2024-07-11T02:39:51,591 * https://www.piwheels.org/simple/kssdtree/ 2024-07-11T02:39:51,591 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-07-11T02:39:51,592 Getting page https://pypi.org/simple/kssdtree/ 2024-07-11T02:39:51,594 Found index url https://pypi.org/simple/ 2024-07-11T02:39:51,808 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-07-11T02:39:51,810 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 2024-07-11T02:39:51,811 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 2024-07-11T02:39:51,812 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 2024-07-11T02:39:51,812 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 2024-07-11T02:39:51,813 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 2024-07-11T02:39:51,813 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 2024-07-11T02:39:51,814 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 2024-07-11T02:39:51,815 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-07-11T02:39:51,815 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-07-11T02:39:51,817 Found index url https://www.piwheels.org/simple/ 2024-07-11T02:39:51,980 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-07-11T02:39:51,989 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/) 2024-07-11T02:39:51,989 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/) 2024-07-11T02:39:51,990 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/) 2024-07-11T02:39:51,990 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/) 2024-07-11T02:39:51,991 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/) 2024-07-11T02:39:51,992 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/) 2024-07-11T02:39:51,992 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/) 2024-07-11T02:39:51,993 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/) 2024-07-11T02:39:51,993 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/) 2024-07-11T02:39:51,994 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/) 2024-07-11T02:39:51,994 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/) 2024-07-11T02:39:51,995 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/) 2024-07-11T02:39:51,995 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/) 2024-07-11T02:39:51,996 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/) 2024-07-11T02:39:51,996 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/) 2024-07-11T02:39:51,997 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/) 2024-07-11T02:39:51,997 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/) 2024-07-11T02:39:51,998 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/) 2024-07-11T02:39:51,998 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/) 2024-07-11T02:39:51,999 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/) 2024-07-11T02:39:52,000 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/) 2024-07-11T02:39:52,000 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/) 2024-07-11T02:39:52,000 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/) 2024-07-11T02:39:52,001 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/) 2024-07-11T02:39:52,001 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/) 2024-07-11T02:39:52,002 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/) 2024-07-11T02:39:52,002 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/) 2024-07-11T02:39:52,003 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/) 2024-07-11T02:39:52,003 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/) 2024-07-11T02:39:52,004 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/) 2024-07-11T02:39:52,004 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/) 2024-07-11T02:39:52,005 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/) 2024-07-11T02:39:52,005 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-07-11T02:39:52,006 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-07-11T02:39:52,026 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-07-11T02:39:52,046 Collecting kssdtree==1.1.8 2024-07-11T02:39:52,049 Created temporary directory: /tmp/pip-unpack-82u1wx76 2024-07-11T02:39:52,524 Downloading kssdtree-1.1.8.tar.gz (112 kB) 2024-07-11T02:39:52,749 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-vnwd9cda' 2024-07-11T02:39:52,750 Running setup.py (path:/tmp/pip-wheel-f6a07aik/kssdtree_baad69bfdf844dfa8f74236738c2100a/setup.py) egg_info for package kssdtree 2024-07-11T02:39:52,751 Created temporary directory: /tmp/pip-pip-egg-info-goyvqj_5 2024-07-11T02:39:52,752 Preparing metadata (setup.py): started 2024-07-11T02:39:52,753 Running command python setup.py egg_info 2024-07-11T02:39:53,887 running egg_info 2024-07-11T02:39:53,888 creating /tmp/pip-pip-egg-info-goyvqj_5/kssdtree.egg-info 2024-07-11T02:39:53,913 writing /tmp/pip-pip-egg-info-goyvqj_5/kssdtree.egg-info/PKG-INFO 2024-07-11T02:39:53,917 writing dependency_links to /tmp/pip-pip-egg-info-goyvqj_5/kssdtree.egg-info/dependency_links.txt 2024-07-11T02:39:53,919 writing requirements to /tmp/pip-pip-egg-info-goyvqj_5/kssdtree.egg-info/requires.txt 2024-07-11T02:39:53,920 writing top-level names to /tmp/pip-pip-egg-info-goyvqj_5/kssdtree.egg-info/top_level.txt 2024-07-11T02:39:53,921 writing manifest file '/tmp/pip-pip-egg-info-goyvqj_5/kssdtree.egg-info/SOURCES.txt' 2024-07-11T02:39:54,024 reading manifest file '/tmp/pip-pip-egg-info-goyvqj_5/kssdtree.egg-info/SOURCES.txt' 2024-07-11T02:39:54,025 reading manifest template 'MANIFEST.in' 2024-07-11T02:39:54,043 writing manifest file '/tmp/pip-pip-egg-info-goyvqj_5/kssdtree.egg-info/SOURCES.txt' 2024-07-11T02:39:54,162 Preparing metadata (setup.py): finished with status 'done' 2024-07-11T02:39:54,166 Source in /tmp/pip-wheel-f6a07aik/kssdtree_baad69bfdf844dfa8f74236738c2100a 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 2024-07-11T02:39:54,167 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-vnwd9cda' 2024-07-11T02:39:54,171 Created temporary directory: /tmp/pip-unpack-elfijxdx 2024-07-11T02:39:54,172 Created temporary directory: /tmp/pip-unpack-0hz_160g 2024-07-11T02:39:54,177 Building wheels for collected packages: kssdtree 2024-07-11T02:39:54,181 Created temporary directory: /tmp/pip-wheel-g9h_ucq_ 2024-07-11T02:39:54,182 Building wheel for kssdtree (setup.py): started 2024-07-11T02:39:54,183 Destination directory: /tmp/pip-wheel-g9h_ucq_ 2024-07-11T02:39:54,184 Running command python setup.py bdist_wheel 2024-07-11T02:39:55,257 running bdist_wheel 2024-07-11T02:39:55,355 running build 2024-07-11T02:39:55,356 running build_py 2024-07-11T02:39:55,383 creating build 2024-07-11T02:39:55,384 creating build/lib.linux-armv7l-cpython-311 2024-07-11T02:39:55,385 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2024-07-11T02:39:55,388 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2024-07-11T02:39:55,390 running egg_info 2024-07-11T02:39:55,451 writing kssdtree.egg-info/PKG-INFO 2024-07-11T02:39:55,454 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-07-11T02:39:55,456 writing requirements to kssdtree.egg-info/requires.txt 2024-07-11T02:39:55,457 writing top-level names to kssdtree.egg-info/top_level.txt 2024-07-11T02:39:55,485 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-11T02:39:55,488 reading manifest template 'MANIFEST.in' 2024-07-11T02:39:55,505 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-11T02:39:55,507 running build_ext 2024-07-11T02:39:55,970 building 'kssd' extension 2024-07-11T02:39:55,971 creating build/temp.linux-armv7l-cpython-311 2024-07-11T02:39:55,972 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c co2mco.c -o build/temp.linux-armv7l-cpython-311/co2mco.o -fopenmp 2024-07-11T02:39:56,156 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-07-11T02:39:56,157 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T02:39:56,157 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-07-11T02:39:56,158 | ^ 2024-07-11T02:39:56,161 co2mco.c: In function ‘co2unitllmco’: 2024-07-11T02:39:56,161 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T02:39:56,162 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-07-11T02:39:56,162 | ^ 2024-07-11T02:39:56,865 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_composite.c -o build/temp.linux-armv7l-cpython-311/command_composite.o -fopenmp 2024-07-11T02:39:57,243 command_composite.c: In function ‘get_species_abundance’: 2024-07-11T02:39:57,244 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-11T02:39:57,245 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-07-11T02:39:57,245 | ^~ 2024-07-11T02:39:57,246 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-11T02:39:57,246 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-07-11T02:39:57,247 | ^~ 2024-07-11T02:39:57,247 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:39:57,248 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-11T02:39:57,249 | ^ 2024-07-11T02:39:57,249 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:39:57,250 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-11T02:39:57,250 | ^~~~~~~~~~ 2024-07-11T02:39:57,251 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-11T02:39:57,251 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-11T02:39:57,252 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:57,253 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:39:57,253 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-11T02:39:57,254 | ^ 2024-07-11T02:39:57,254 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:39:57,255 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-11T02:39:57,256 | ^~~~~~~~~~ 2024-07-11T02:39:57,256 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-11T02:39:57,257 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-11T02:39:57,257 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:57,258 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:39:57,259 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-11T02:39:57,259 | ^ 2024-07-11T02:39:57,260 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:39:57,260 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-11T02:39:57,261 | ^~~~~~~~~~ 2024-07-11T02:39:57,261 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-11T02:39:57,262 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-11T02:39:57,262 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:57,263 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:39:57,263 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-11T02:39:57,264 | ^ 2024-07-11T02:39:57,264 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:39:57,265 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-11T02:39:57,265 | ^~~~~~~~~~ 2024-07-11T02:39:57,266 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-11T02:39:57,266 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-11T02:39:57,267 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:57,268 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:39:57,268 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-11T02:39:57,269 | ^ 2024-07-11T02:39:57,269 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:39:57,270 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-11T02:39:57,271 | ^~~~~~~~~~~~ 2024-07-11T02:39:57,271 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2024-07-11T02:39:57,272 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-11T02:39:57,272 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:57,501 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist.c -o build/temp.linux-armv7l-cpython-311/command_dist.o -fopenmp 2024-07-11T02:39:57,736 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-11T02:39:57,738 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=] 2024-07-11T02:39:57,738 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T02:39:57,739 | ~~^ 2024-07-11T02:39:57,739 | | 2024-07-11T02:39:57,740 | long unsigned int 2024-07-11T02:39:57,740 | %u 2024-07-11T02:39:57,741 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T02:39:57,741 | ~~~~~~~ 2024-07-11T02:39:57,741 | | 2024-07-11T02:39:57,742 | size_t {aka unsigned int} 2024-07-11T02:39:57,743 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=] 2024-07-11T02:39:57,743 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T02:39:57,744 | ~~^ 2024-07-11T02:39:57,744 | | 2024-07-11T02:39:57,744 | long unsigned int 2024-07-11T02:39:57,745 | %u 2024-07-11T02:39:57,745 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T02:39:57,746 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T02:39:57,746 | ~~~~~~~~~ 2024-07-11T02:39:57,746 | | 2024-07-11T02:39:57,747 | size_t {aka unsigned int} 2024-07-11T02:39:57,748 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-11T02:39:57,748 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T02:39:57,749 | ~~^ 2024-07-11T02:39:57,749 | | 2024-07-11T02:39:57,750 | long unsigned int 2024-07-11T02:39:57,750 | %u 2024-07-11T02:39:57,751 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T02:39:57,751 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T02:39:57,752 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:57,753 | | 2024-07-11T02:39:57,753 | unsigned int 2024-07-11T02:39:57,756 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-11T02:39:57,756 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-07-11T02:39:57,757 | ^ 2024-07-11T02:39:57,765 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-11T02:39:57,767 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=] 2024-07-11T02:39:57,768 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-11T02:39:57,768 | ~~^ ~~~~~~~ 2024-07-11T02:39:57,769 | | | 2024-07-11T02:39:57,769 | long unsigned int size_t {aka unsigned int} 2024-07-11T02:39:57,770 | %u 2024-07-11T02:39:57,771 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=] 2024-07-11T02:39:57,772 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-11T02:39:57,772 | ~~^ 2024-07-11T02:39:57,773 | | 2024-07-11T02:39:57,773 | long unsigned int 2024-07-11T02:39:57,773 | %u 2024-07-11T02:39:57,774 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-11T02:39:57,774 | ~~~~~~~~~ 2024-07-11T02:39:57,775 | | 2024-07-11T02:39:57,775 | size_t {aka unsigned int} 2024-07-11T02:39:57,776 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-11T02:39:57,777 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-11T02:39:57,778 | ~~^ 2024-07-11T02:39:57,778 | | 2024-07-11T02:39:57,779 | long unsigned int 2024-07-11T02:39:57,779 | %u 2024-07-11T02:39:57,780 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-11T02:39:57,780 865 | (size_t) b * unitsz_distf_mapped); 2024-07-11T02:39:57,781 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:57,781 | | 2024-07-11T02:39:57,782 | unsigned int 2024-07-11T02:39:57,784 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-07-11T02:39:57,785 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-07-11T02:39:57,785 | ^~~~~~~ 2024-07-11T02:39:57,786 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-07-11T02:39:57,787 809 | struct stat cbd_fcode_stat; 2024-07-11T02:39:57,787 | ^~~~~~~~~~~~~~ 2024-07-11T02:39:57,788 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-07-11T02:39:57,789 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-11T02:39:57,789 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:57,790 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-07-11T02:39:57,790 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-11T02:39:57,791 | ^~~~~~~~~~~~~~~~~ 2024-07-11T02:39:57,798 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-11T02:39:57,801 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=] 2024-07-11T02:39:57,801 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T02:39:57,802 | ~~^ 2024-07-11T02:39:57,802 | | 2024-07-11T02:39:57,803 | long unsigned int 2024-07-11T02:39:57,803 | %u 2024-07-11T02:39:57,804 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T02:39:57,804 | ~~~~~~~ 2024-07-11T02:39:57,804 | | 2024-07-11T02:39:57,805 | size_t {aka unsigned int} 2024-07-11T02:39:57,806 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=] 2024-07-11T02:39:57,807 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T02:39:57,807 | ~~^ 2024-07-11T02:39:57,808 | | 2024-07-11T02:39:57,808 | long unsigned int 2024-07-11T02:39:57,809 | %u 2024-07-11T02:39:57,809 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T02:39:57,810 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T02:39:57,810 | ~~~~~~~~~ 2024-07-11T02:39:57,810 | | 2024-07-11T02:39:57,811 | size_t {aka unsigned int} 2024-07-11T02:39:57,812 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-11T02:39:57,813 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T02:39:57,813 | ~~^ 2024-07-11T02:39:57,814 | | 2024-07-11T02:39:57,814 | long unsigned int 2024-07-11T02:39:57,815 | %u 2024-07-11T02:39:57,816 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T02:39:57,816 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T02:39:57,817 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:57,817 | | 2024-07-11T02:39:57,818 | unsigned int 2024-07-11T02:39:57,819 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-07-11T02:39:57,820 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-07-11T02:39:57,821 | ^ 2024-07-11T02:39:57,825 command_dist.c: In function ‘mco_co_dist_core’: 2024-07-11T02:39:57,827 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-11T02:39:57,827 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-07-11T02:39:57,828 | ^ 2024-07-11T02:39:57,835 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-07-11T02:39:57,837 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T02:39:57,838 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-07-11T02:39:57,838 | ^ 2024-07-11T02:39:57,840 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T02:39:57,841 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-11T02:39:57,841 | ^ 2024-07-11T02:39:57,848 command_dist.c: In function ‘dist_print_nobin’: 2024-07-11T02:39:57,850 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T02:39:57,850 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-07-11T02:39:57,851 | ^ 2024-07-11T02:39:57,854 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T02:39:57,855 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-11T02:39:57,855 | ^ 2024-07-11T02:39:57,858 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T02:39:57,859 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-07-11T02:39:57,859 | ^ 2024-07-11T02:39:58,221 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-07-11T02:39:58,222 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T02:39:58,222 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-07-11T02:39:58,223 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:58,223 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-07-11T02:39:58,224 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-07-11T02:39:58,224 | ^~~~~~~~~~~~ 2024-07-11T02:39:59,059 command_dist.c: In function ‘get_dim_shuffle’: 2024-07-11T02:39:59,060 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-07-11T02:39:59,061 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-11T02:39:59,061 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:59,062 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-07-11T02:39:59,063 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-11T02:39:59,063 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:59,961 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-11T02:39:59,963 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:39:59,963 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T02:39:59,964 | ^~ ~~~~~~~~~ 2024-07-11T02:39:59,965 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-11T02:39:59,965 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T02:39:59,966 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:59,967 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T02:39:59,967 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T02:39:59,968 | ^~~~~~~~~~~~~~~ 2024-07-11T02:39:59,968 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-11T02:39:59,969 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T02:39:59,969 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:59,971 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T02:39:59,972 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T02:39:59,972 | ^~~~~~~~~~~ 2024-07-11T02:39:59,973 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:39:59,974 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T02:39:59,974 | ^~~~~~~~~~~~~~~~~ 2024-07-11T02:39:59,975 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-11T02:39:59,976 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T02:39:59,976 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:39:59,977 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T02:39:59,978 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T02:39:59,978 | ^~~~~ 2024-07-11T02:39:59,979 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:39:59,979 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T02:39:59,980 | ^~~~~~~~~~~ 2024-07-11T02:39:59,981 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T02:39:59,981 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T02:39:59,982 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,221 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-11T02:40:00,223 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:00,224 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T02:40:00,224 | ^~ ~~~~~~~~~ 2024-07-11T02:40:00,225 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-11T02:40:00,226 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T02:40:00,226 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,228 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T02:40:00,228 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T02:40:00,229 | ^~~~~~~~~~~~~~~ 2024-07-11T02:40:00,230 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-11T02:40:00,230 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T02:40:00,231 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,232 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T02:40:00,232 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T02:40:00,233 | ^~~~~~~~~~~~~ 2024-07-11T02:40:00,234 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-11T02:40:00,234 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T02:40:00,235 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,236 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:00,237 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-11T02:40:00,237 | ^ 2024-07-11T02:40:00,238 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-07-11T02:40:00,239 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-11T02:40:00,239 | ^~~~~~~~~~ 2024-07-11T02:40:00,240 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-11T02:40:00,241 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-11T02:40:00,241 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,242 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:00,243 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-11T02:40:00,244 | ^ 2024-07-11T02:40:00,244 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-07-11T02:40:00,245 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-11T02:40:00,245 | ^~~~~~~~~~ 2024-07-11T02:40:00,246 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-11T02:40:00,247 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-11T02:40:00,248 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,513 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-11T02:40:00,516 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:00,516 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T02:40:00,517 | ^~ ~~~~~~~~~ 2024-07-11T02:40:00,518 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-11T02:40:00,518 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T02:40:00,519 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,520 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T02:40:00,521 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T02:40:00,521 | ^~~~~~~~~~~~~~~ 2024-07-11T02:40:00,522 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-11T02:40:00,523 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T02:40:00,524 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,525 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T02:40:00,525 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T02:40:00,526 | ^~~~~~~~~~~~~ 2024-07-11T02:40:00,527 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-11T02:40:00,528 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T02:40:00,528 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,530 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T02:40:00,531 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T02:40:00,531 | ^~~~~~~~~~~ 2024-07-11T02:40:00,533 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:00,533 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T02:40:00,534 | ^~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,535 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-11T02:40:00,535 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T02:40:00,536 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,537 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T02:40:00,538 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T02:40:00,538 | ^~~~~ 2024-07-11T02:40:00,539 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:00,540 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T02:40:00,540 | ^~~~~~~~~~~ 2024-07-11T02:40:00,541 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T02:40:00,542 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T02:40:00,543 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,817 command_dist.c: In function ‘combine_queries’: 2024-07-11T02:40:00,819 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T02:40:00,819 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-11T02:40:00,820 | ^ 2024-07-11T02:40:00,822 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T02:40:00,822 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-11T02:40:00,823 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,825 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T02:40:00,825 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-11T02:40:00,826 | ^ 2024-07-11T02:40:00,827 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T02:40:00,828 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-11T02:40:00,829 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:00,832 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:00,832 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-11T02:40:00,833 | ^~ ~~~~~~~~ 2024-07-11T02:40:00,835 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-11T02:40:00,835 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-11T02:40:00,836 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:01,317 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o -fopenmp 2024-07-11T02:40:01,491 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_set.c -o build/temp.linux-armv7l-cpython-311/command_set.o -fopenmp 2024-07-11T02:40:01,663 command_set.c: In function ‘sketch_operate’: 2024-07-11T02:40:01,664 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-11T02:40:01,665 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-07-11T02:40:01,665 | ^ 2024-07-11T02:40:01,677 command_set.c: In function ‘combin_subset_pans’: 2024-07-11T02:40:01,677 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-11T02:40:01,678 458 | free(co_dstat_fpath); 2024-07-11T02:40:01,679 | ^~~~~~~~~~~~~~ 2024-07-11T02:40:01,679 In file included from kssdheaders/global_basic.h:159, 2024-07-11T02:40:01,680 from command_set.c:15: 2024-07-11T02:40:01,680 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-11T02:40:01,681 568 | extern void free (void *__ptr) __THROW; 2024-07-11T02:40:01,681 | ~~~~~~^~~~~ 2024-07-11T02:40:01,684 command_set.c: In function ‘grouping_genomes’: 2024-07-11T02:40:01,685 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-11T02:40:01,685 563 | free(co_dstat_fpath); 2024-07-11T02:40:01,686 | ^~~~~~~~~~~~~~ 2024-07-11T02:40:01,686 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-11T02:40:01,687 568 | extern void free (void *__ptr) __THROW; 2024-07-11T02:40:01,688 | ~~~~~~^~~~~ 2024-07-11T02:40:01,852 command_set.c: In function ‘sketch_union’: 2024-07-11T02:40:01,853 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T02:40:01,854 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:01,855 | ^ 2024-07-11T02:40:01,855 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T02:40:01,856 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:01,856 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:01,857 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:01,858 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T02:40:01,859 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:01,859 command_set.c:83:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:01,860 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T02:40:01,860 | ^~~~~~~~~~ 2024-07-11T02:40:01,861 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T02:40:01,861 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T02:40:01,862 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:01,862 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:01,863 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-11T02:40:01,864 | ^~ ~~~~~~~~~~ 2024-07-11T02:40:01,864 command_set.c:93:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:01,865 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-11T02:40:01,865 | ^~~~~~~~~~ 2024-07-11T02:40:01,866 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T02:40:01,866 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-11T02:40:01,867 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:01,984 command_set.c: In function ‘sketch_operate’: 2024-07-11T02:40:01,985 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:01,985 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-11T02:40:01,986 | ^~ ~~~~~~~~~~ 2024-07-11T02:40:01,986 command_set.c:154:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:01,987 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-11T02:40:01,987 | ^~~~~~~~~~ 2024-07-11T02:40:01,988 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T02:40:01,988 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-11T02:40:01,989 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:01,990 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:01,990 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-11T02:40:01,991 | ^~ ~~~~~~~~~~~~~~~ 2024-07-11T02:40:01,991 command_set.c:156:29: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:01,992 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-11T02:40:01,993 | ^~~~~~~~~~ 2024-07-11T02:40:01,993 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-11T02:40:01,994 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-11T02:40:01,994 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:01,995 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:01,996 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T02:40:01,996 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:01,997 command_set.c:166:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:01,997 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T02:40:01,998 | ^~~~~~~~~~~~~~~~ 2024-07-11T02:40:01,999 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T02:40:01,999 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T02:40:02,000 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,000 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,001 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T02:40:02,001 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:02,002 command_set.c:170:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,003 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T02:40:02,003 | ^~~~~~~~~~ 2024-07-11T02:40:02,004 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T02:40:02,004 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T02:40:02,005 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,005 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,006 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T02:40:02,007 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:02,007 command_set.c:175:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,008 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T02:40:02,008 | ^~~~~~~~~~ 2024-07-11T02:40:02,009 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T02:40:02,010 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T02:40:02,011 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,011 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,012 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T02:40:02,013 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:02,013 command_set.c:188:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,014 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T02:40:02,014 | ^~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,015 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T02:40:02,016 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T02:40:02,016 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,017 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T02:40:02,018 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:02,018 | ^ 2024-07-11T02:40:02,019 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T02:40:02,020 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:02,020 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,161 command_set.c: In function ‘uniq_sketch_union’: 2024-07-11T02:40:02,161 command_set.c:220:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T02:40:02,162 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-07-11T02:40:02,162 | ^ 2024-07-11T02:40:02,163 command_set.c:220:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2024-07-11T02:40:02,163 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-07-11T02:40:02,164 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,164 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T02:40:02,165 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:02,165 | ^ 2024-07-11T02:40:02,166 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T02:40:02,167 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:02,167 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,168 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,168 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T02:40:02,169 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:02,170 command_set.c:248:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,170 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T02:40:02,171 | ^~~~~~~~~~ 2024-07-11T02:40:02,171 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T02:40:02,172 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T02:40:02,172 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,173 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,174 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-11T02:40:02,174 | ^~ ~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,175 command_set.c:260:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,175 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-11T02:40:02,176 | ^~~~~~~~~~ 2024-07-11T02:40:02,177 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-11T02:40:02,177 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-11T02:40:02,178 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,310 command_set.c: In function ‘combin_pans’: 2024-07-11T02:40:02,311 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,311 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T02:40:02,312 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:02,312 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-07-11T02:40:02,313 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T02:40:02,314 | ^~~~~~~~~~ 2024-07-11T02:40:02,314 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-07-11T02:40:02,315 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T02:40:02,316 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,316 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,317 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T02:40:02,317 | ^~ ~~~~~~~~~~ 2024-07-11T02:40:02,318 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-07-11T02:40:02,318 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T02:40:02,319 | ^~~~~~~~~~ 2024-07-11T02:40:02,319 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-07-11T02:40:02,320 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T02:40:02,320 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,321 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T02:40:02,321 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:02,322 | ^ 2024-07-11T02:40:02,323 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T02:40:02,323 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:02,324 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,527 command_set.c: In function ‘combin_subset_pans’: 2024-07-11T02:40:02,528 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,529 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T02:40:02,529 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:02,530 command_set.c:470:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,530 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T02:40:02,531 | ^~~~~~~~~~ 2024-07-11T02:40:02,531 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T02:40:02,532 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T02:40:02,532 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,533 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,533 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T02:40:02,534 | ^~ ~~~~~~~~~~ 2024-07-11T02:40:02,534 command_set.c:476:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,535 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T02:40:02,535 | ^~~~~~~~~~ 2024-07-11T02:40:02,536 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T02:40:02,536 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T02:40:02,537 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,537 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,538 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T02:40:02,539 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:02,539 command_set.c:482:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,540 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T02:40:02,540 | ^~~~~~~~~~ 2024-07-11T02:40:02,541 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T02:40:02,541 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T02:40:02,542 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,542 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,543 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T02:40:02,543 | ^~ ~~~~~~~~~~ 2024-07-11T02:40:02,544 command_set.c:513:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,544 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T02:40:02,545 | ^~~~~~~~~~ 2024-07-11T02:40:02,545 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T02:40:02,546 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T02:40:02,546 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,547 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T02:40:02,547 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:02,548 | ^ 2024-07-11T02:40:02,548 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T02:40:02,549 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:02,549 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,773 command_set.c: In function ‘grouping_genomes’: 2024-07-11T02:40:02,774 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,775 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T02:40:02,775 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:02,776 command_set.c:575:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,776 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T02:40:02,777 | ^~~~~~~~~~ 2024-07-11T02:40:02,777 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T02:40:02,778 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T02:40:02,778 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,779 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,779 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T02:40:02,780 | ^~ ~~~~~~~~~~ 2024-07-11T02:40:02,780 command_set.c:581:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,781 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T02:40:02,782 | ^~~~~~~~~~ 2024-07-11T02:40:02,782 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T02:40:02,783 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T02:40:02,783 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,784 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,784 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T02:40:02,785 | ^~ ~~~~~~~~~~~ 2024-07-11T02:40:02,785 command_set.c:613:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,786 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T02:40:02,786 | ^~~~~~~~~~ 2024-07-11T02:40:02,787 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T02:40:02,787 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T02:40:02,788 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,789 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T02:40:02,789 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T02:40:02,790 | ^~ ~~~~~~~~~~ 2024-07-11T02:40:02,790 command_set.c:635:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T02:40:02,791 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T02:40:02,791 | ^~~~~~~~~~ 2024-07-11T02:40:02,792 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T02:40:02,793 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T02:40:02,793 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:02,794 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T02:40:02,794 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:02,795 | ^ 2024-07-11T02:40:02,795 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T02:40:02,796 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T02:40:02,796 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:03,073 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-311/command_shuffle.o -fopenmp 2024-07-11T02:40:03,396 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c global_basic.c -o build/temp.linux-armv7l-cpython-311/global_basic.o -fopenmp 2024-07-11T02:40:03,563 global_basic.c: In function ‘organize_infile_list’: 2024-07-11T02:40:03,564 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-07-11T02:40:03,565 195 | while (isspace(*buf)) buf++; 2024-07-11T02:40:03,565 | ^~~~~~~ 2024-07-11T02:40:03,566 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2024-07-11T02:40:03,566 34 | #include 2024-07-11T02:40:03,567 +++ |+#include 2024-07-11T02:40:03,568 35 | 2024-07-11T02:40:03,568 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=] 2024-07-11T02:40:03,569 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-11T02:40:03,569 | ~~^ 2024-07-11T02:40:03,570 | | 2024-07-11T02:40:03,570 | long unsigned int 2024-07-11T02:40:03,571 | %u 2024-07-11T02:40:03,571 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-11T02:40:03,572 | ~~~~~~~~~~~ 2024-07-11T02:40:03,573 | | 2024-07-11T02:40:03,573 | size_t {aka unsigned int} 2024-07-11T02:40:03,574 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=] 2024-07-11T02:40:03,574 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-11T02:40:03,575 | ~~^ 2024-07-11T02:40:03,575 | | 2024-07-11T02:40:03,576 | long unsigned int 2024-07-11T02:40:03,576 | %u 2024-07-11T02:40:03,577 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-11T02:40:03,577 | ~~~~~~~~~~~ 2024-07-11T02:40:03,578 | | 2024-07-11T02:40:03,579 | size_t {aka unsigned int} 2024-07-11T02:40:04,362 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-311/iseq2comem.o -fopenmp 2024-07-11T02:40:04,538 iseq2comem.c: In function ‘reads2mco’: 2024-07-11T02:40:04,539 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,540 156 | if (base > TL) { 2024-07-11T02:40:04,540 | ^ 2024-07-11T02:40:04,541 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,541 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T02:40:04,542 | ^~ 2024-07-11T02:40:04,543 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,544 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T02:40:04,545 | ^ 2024-07-11T02:40:04,546 iseq2comem.c: In function ‘fasta2co’: 2024-07-11T02:40:04,547 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,547 239 | if (base > TL) { 2024-07-11T02:40:04,548 | ^ 2024-07-11T02:40:04,549 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,549 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T02:40:04,550 | ^~ 2024-07-11T02:40:04,550 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,551 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T02:40:04,551 | ^ 2024-07-11T02:40:04,552 iseq2comem.c: In function ‘fastq2co’: 2024-07-11T02:40:04,552 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-07-11T02:40:04,553 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-07-11T02:40:04,553 | ^~ 2024-07-11T02:40:04,555 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,556 318 | if (base > TL) { 2024-07-11T02:40:04,556 | ^ 2024-07-11T02:40:04,557 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,557 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T02:40:04,558 | ^~ 2024-07-11T02:40:04,558 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,559 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T02:40:04,560 | ^ 2024-07-11T02:40:04,562 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,562 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-07-11T02:40:04,563 | ^ 2024-07-11T02:40:04,565 iseq2comem.c: In function ‘fastq2koc’: 2024-07-11T02:40:04,566 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,566 402 | if (base > TL) { 2024-07-11T02:40:04,567 | ^ 2024-07-11T02:40:04,567 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,568 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T02:40:04,568 | ^~ 2024-07-11T02:40:04,569 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,570 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T02:40:04,570 | ^ 2024-07-11T02:40:04,577 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-07-11T02:40:04,578 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,578 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T02:40:04,579 | ^~ 2024-07-11T02:40:04,580 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:04,581 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T02:40:04,581 | ^ 2024-07-11T02:40:05,922 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2024-07-11T02:40:05,978 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mytime.c -o build/temp.linux-armv7l-cpython-311/mytime.o -fopenmp 2024-07-11T02:40:06,104 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c pykssd.c -o build/temp.linux-armv7l-cpython-311/pykssd.o -fopenmp 2024-07-11T02:40:06,500 pykssd.c: In function ‘py_dist_dispatch’: 2024-07-11T02:40:06,501 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-07-11T02:40:06,501 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-07-11T02:40:06,502 | ^~~~~~ 2024-07-11T02:40:06,503 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-07-11T02:40:06,504 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-07-11T02:40:06,504 | ^~~~~~ 2024-07-11T02:40:06,506 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-07-11T02:40:06,507 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-07-11T02:40:06,507 | ^~~~~~ 2024-07-11T02:40:07,073 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/co2mco.o build/temp.linux-armv7l-cpython-311/command_composite.o build/temp.linux-armv7l-cpython-311/command_dist.o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o build/temp.linux-armv7l-cpython-311/command_set.o build/temp.linux-armv7l-cpython-311/command_shuffle.o build/temp.linux-armv7l-cpython-311/global_basic.o build/temp.linux-armv7l-cpython-311/iseq2comem.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/mytime.o build/temp.linux-armv7l-cpython-311/pykssd.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -fopenmp 2024-07-11T02:40:07,219 building 'nj' extension 2024-07-11T02:40:07,220 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c align.c -o build/temp.linux-armv7l-cpython-311/align.o 2024-07-11T02:40:07,711 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c buildtree.c -o build/temp.linux-armv7l-cpython-311/buildtree.o 2024-07-11T02:40:07,858 buildtree.c: In function ‘UPGMA_buildtree’: 2024-07-11T02:40:07,858 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T02:40:07,859 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-11T02:40:07,860 | ^~ 2024-07-11T02:40:07,861 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T02:40:07,862 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-11T02:40:07,862 | ^~ 2024-07-11T02:40:08,523 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c cluster.c -o build/temp.linux-armv7l-cpython-311/cluster.o 2024-07-11T02:40:08,894 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c distancemat.c -o build/temp.linux-armv7l-cpython-311/distancemat.o 2024-07-11T02:40:09,029 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-07-11T02:40:09,030 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T02:40:09,030 226 | for( i=0; i < dest->size; i++) { 2024-07-11T02:40:09,031 | ^ 2024-07-11T02:40:09,031 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-07-11T02:40:09,032 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T02:40:09,032 260 | for( i=0; i < mat->size; i++) { 2024-07-11T02:40:09,033 | ^ 2024-07-11T02:40:09,034 distancemat.c: In function ‘print_DistanceMatrix’: 2024-07-11T02:40:09,035 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T02:40:09,035 349 | for(row=0; row < mat->size; row++) { 2024-07-11T02:40:09,036 | ^ 2024-07-11T02:40:09,037 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-07-11T02:40:09,038 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-07-11T02:40:09,038 410 | while(c = fgetc(handle)) { 2024-07-11T02:40:09,039 | ^ 2024-07-11T02:40:09,426 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c pynj.c -o build/temp.linux-armv7l-cpython-311/pynj.o 2024-07-11T02:40:09,863 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c sequence.c -o build/temp.linux-armv7l-cpython-311/sequence.o 2024-07-11T02:40:10,079 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c tree.c -o build/temp.linux-armv7l-cpython-311/tree.o 2024-07-11T02:40:10,888 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c util.c -o build/temp.linux-armv7l-cpython-311/util.o 2024-07-11T02:40:11,064 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/align.o build/temp.linux-armv7l-cpython-311/buildtree.o build/temp.linux-armv7l-cpython-311/cluster.o build/temp.linux-armv7l-cpython-311/distancemat.o build/temp.linux-armv7l-cpython-311/pynj.o build/temp.linux-armv7l-cpython-311/sequence.o build/temp.linux-armv7l-cpython-311/tree.o build/temp.linux-armv7l-cpython-311/util.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so 2024-07-11T02:40:11,170 building 'dnj' extension 2024-07-11T02:40:11,171 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c bytescale.c -o build/temp.linux-armv7l-cpython-311/bytescale.o -fopenmp 2024-07-11T02:40:11,227 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c dnj.c -o build/temp.linux-armv7l-cpython-311/dnj.o -fopenmp 2024-07-11T02:40:11,362 dnj.c: In function ‘minQpair’: 2024-07-11T02:40:11,362 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,363 70 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,363 | ^~~ 2024-07-11T02:40:11,364 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,364 126 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,365 | ^~~ 2024-07-11T02:40:11,365 dnj.c: In function ‘maxQpair’: 2024-07-11T02:40:11,366 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,366 157 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,367 | ^~~ 2024-07-11T02:40:11,368 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,368 213 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,369 | ^~~ 2024-07-11T02:40:11,369 dnj.c: In function ‘UPGMApair’: 2024-07-11T02:40:11,370 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,370 237 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,371 | ^~~ 2024-07-11T02:40:11,371 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,372 284 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,373 | ^~~ 2024-07-11T02:40:11,373 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,374 291 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,374 | ^~~ 2024-07-11T02:40:11,375 dnj.c: In function ‘minQrow’: 2024-07-11T02:40:11,375 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,376 374 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,376 | ^~~ 2024-07-11T02:40:11,377 dnj.c: In function ‘maxQrow’: 2024-07-11T02:40:11,378 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,378 435 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,379 | ^~~ 2024-07-11T02:40:11,379 dnj.c: In function ‘UPGMArow’: 2024-07-11T02:40:11,380 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,380 488 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,381 | ^~~ 2024-07-11T02:40:11,382 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,382 494 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,383 | ^~~ 2024-07-11T02:40:11,383 dnj.c: In function ‘minQ_thread’: 2024-07-11T02:40:11,384 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:11,384 553 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:11,385 | ^~~ 2024-07-11T02:40:12,738 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c filebuff.c -o build/temp.linux-armv7l-cpython-311/filebuff.o -fopenmp 2024-07-11T02:40:12,856 filebuff.c: In function ‘BuffgzFileBuff’: 2024-07-11T02:40:12,857 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:12,857 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-07-11T02:40:12,858 | ^~ 2024-07-11T02:40:13,188 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c hclust.c -o build/temp.linux-armv7l-cpython-311/hclust.o -fopenmp 2024-07-11T02:40:13,322 hclust.c: In function ‘minQ’: 2024-07-11T02:40:13,323 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T02:40:13,323 364 | while(++i < Q->n) { 2024-07-11T02:40:13,324 | ^ 2024-07-11T02:40:13,324 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:13,325 377 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:13,325 | ^~~ 2024-07-11T02:40:13,326 hclust.c: In function ‘maxQ’: 2024-07-11T02:40:13,326 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T02:40:13,326 394 | while(++i < Q->n) { 2024-07-11T02:40:13,327 | ^ 2024-07-11T02:40:13,327 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:13,328 407 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:13,329 | ^~~ 2024-07-11T02:40:15,701 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c matrix.c -o build/temp.linux-armv7l-cpython-311/matrix.o -fopenmp 2024-07-11T02:40:15,832 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-07-11T02:40:15,833 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T02:40:15,834 538 | if(pos != n) { 2024-07-11T02:40:15,834 | ^~ 2024-07-11T02:40:16,707 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2024-07-11T02:40:16,761 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nj.c -o build/temp.linux-armv7l-cpython-311/nj.o -fopenmp 2024-07-11T02:40:16,891 nj.c: In function ‘initQ’: 2024-07-11T02:40:16,892 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:16,892 243 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:16,893 | ^~~ 2024-07-11T02:40:16,895 nj.c: In function ‘initQ_MN’: 2024-07-11T02:40:16,896 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:16,896 358 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:16,897 | ^~~ 2024-07-11T02:40:16,902 nj.c: In function ‘minD’: 2024-07-11T02:40:16,902 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:16,903 559 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:16,903 | ^~~ 2024-07-11T02:40:16,905 nj.c: In function ‘maxD’: 2024-07-11T02:40:16,906 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:16,907 642 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:16,907 | ^~~ 2024-07-11T02:40:16,912 nj.c: In function ‘minPair’: 2024-07-11T02:40:16,913 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T02:40:16,913 826 | pos <<= sizeof(unsigned) * 8; 2024-07-11T02:40:16,914 | ^~~ 2024-07-11T02:40:19,269 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nwck.c -o build/temp.linux-armv7l-cpython-311/nwck.o -fopenmp 2024-07-11T02:40:19,840 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pherror.c -o build/temp.linux-armv7l-cpython-311/pherror.o -fopenmp 2024-07-11T02:40:19,933 pherror.c: In function ‘cfread’: 2024-07-11T02:40:19,933 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T02:40:19,934 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-07-11T02:40:19,935 | ^~ 2024-07-11T02:40:20,025 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c phy.c -o build/temp.linux-armv7l-cpython-311/phy.o -fopenmp 2024-07-11T02:40:21,119 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pydnj.c -o build/temp.linux-armv7l-cpython-311/pydnj.o -fopenmp 2024-07-11T02:40:21,497 In file included from pydnj.c:11: 2024-07-11T02:40:21,498 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-07-11T02:40:21,498 20 | #define _XOPEN_SOURCE 600 2024-07-11T02:40:21,499 | 2024-07-11T02:40:21,499 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-07-11T02:40:21,500 from /usr/include/stdlib.h:26, 2024-07-11T02:40:21,501 from /usr/include/python3.11/Python.h:23, 2024-07-11T02:40:21,501 from pydnj.c:1: 2024-07-11T02:40:21,502 /usr/include/features.h:214: note: this is the location of the previous definition 2024-07-11T02:40:21,502 214 | # define _XOPEN_SOURCE 700 2024-07-11T02:40:21,503 | 2024-07-11T02:40:21,522 pydnj.c: In function ‘py_build’: 2024-07-11T02:40:21,523 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-07-11T02:40:21,524 165 | p = omp_get_num_procs(); 2024-07-11T02:40:21,525 | ^~~~~~~~~~~~~~~~~ 2024-07-11T02:40:21,642 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2024-07-11T02:40:21,643 169 | free(file); 2024-07-11T02:40:21,644 | ^~~~~~~~~~ 2024-07-11T02:40:21,644 pydnj.c:125:12: note: returned from ‘fopen’ 2024-07-11T02:40:21,645 125 | file = fopen(inputfilename, "r"); 2024-07-11T02:40:21,646 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T02:40:21,716 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c qseqs.c -o build/temp.linux-armv7l-cpython-311/qseqs.o -fopenmp 2024-07-11T02:40:21,923 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c str.c -o build/temp.linux-armv7l-cpython-311/str.o -fopenmp 2024-07-11T02:40:22,031 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c tmp.c -o build/temp.linux-armv7l-cpython-311/tmp.o -fopenmp 2024-07-11T02:40:22,226 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c vector.c -o build/temp.linux-armv7l-cpython-311/vector.o -fopenmp 2024-07-11T02:40:22,385 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/bytescale.o build/temp.linux-armv7l-cpython-311/dnj.o build/temp.linux-armv7l-cpython-311/filebuff.o build/temp.linux-armv7l-cpython-311/hclust.o build/temp.linux-armv7l-cpython-311/matrix.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/nj.o build/temp.linux-armv7l-cpython-311/nwck.o build/temp.linux-armv7l-cpython-311/pherror.o build/temp.linux-armv7l-cpython-311/phy.o build/temp.linux-armv7l-cpython-311/pydnj.o build/temp.linux-armv7l-cpython-311/qseqs.o build/temp.linux-armv7l-cpython-311/str.o build/temp.linux-armv7l-cpython-311/tmp.o build/temp.linux-armv7l-cpython-311/vector.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -fopenmp 2024-07-11T02:40:22,551 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-07-11T02:40:22,551 !! 2024-07-11T02:40:22,552 ******************************************************************************** 2024-07-11T02:40:22,553 Please avoid running ``setup.py`` directly. 2024-07-11T02:40:22,553 Instead, use pypa/build, pypa/installer or other 2024-07-11T02:40:22,554 standards-based tools. 2024-07-11T02:40:22,555 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-07-11T02:40:22,555 ******************************************************************************** 2024-07-11T02:40:22,556 !! 2024-07-11T02:40:22,557 self.initialize_options() 2024-07-11T02:40:22,577 installing to build/bdist.linux-armv7l/wheel 2024-07-11T02:40:22,577 running install 2024-07-11T02:40:22,602 running install_lib 2024-07-11T02:40:22,639 creating build/bdist.linux-armv7l 2024-07-11T02:40:22,640 creating build/bdist.linux-armv7l/wheel 2024-07-11T02:40:22,642 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-07-11T02:40:22,645 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-11T02:40:22,657 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-11T02:40:22,662 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-11T02:40:22,675 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-07-11T02:40:22,677 running install_egg_info 2024-07-11T02:40:22,720 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-1.1.8-py3.11.egg-info 2024-07-11T02:40:22,733 running install_scripts 2024-07-11T02:40:22,786 creating build/bdist.linux-armv7l/wheel/kssdtree-1.1.8.dist-info/WHEEL 2024-07-11T02:40:22,789 creating '/tmp/pip-wheel-g9h_ucq_/kssdtree-1.1.8-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-07-11T02:40:22,855 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T02:40:22,940 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T02:40:22,944 adding 'kssdtree.py' 2024-07-11T02:40:22,965 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T02:40:22,967 adding 'toolutils.py' 2024-07-11T02:40:22,969 adding 'kssdtree-1.1.8.dist-info/METADATA' 2024-07-11T02:40:22,970 adding 'kssdtree-1.1.8.dist-info/WHEEL' 2024-07-11T02:40:22,971 adding 'kssdtree-1.1.8.dist-info/dependency_links.txt' 2024-07-11T02:40:22,972 adding 'kssdtree-1.1.8.dist-info/top_level.txt' 2024-07-11T02:40:22,973 adding 'kssdtree-1.1.8.dist-info/RECORD' 2024-07-11T02:40:22,978 removing build/bdist.linux-armv7l/wheel 2024-07-11T02:40:23,135 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-07-11T02:40:23,141 Created wheel for kssdtree: filename=kssdtree-1.1.8-cp311-cp311-linux_armv7l.whl size=379684 sha256=717afc6606ad3045caac8f3f1cd01a37edd2f01f1cc38bc1bc6c3320882bd392 2024-07-11T02:40:23,142 Stored in directory: /tmp/pip-ephem-wheel-cache-p4qpgpw_/wheels/49/97/83/06285c41d58501f1c4d61587a59126a875308e9445ab4ebbc8 2024-07-11T02:40:23,151 Successfully built kssdtree 2024-07-11T02:40:23,167 Removed build tracker: '/tmp/pip-build-tracker-vnwd9cda'