2024-07-11T11:05:57,521 Created temporary directory: /tmp/pip-build-tracker-i25tarz5 2024-07-11T11:05:57,522 Initialized build tracking at /tmp/pip-build-tracker-i25tarz5 2024-07-11T11:05:57,523 Created build tracker: /tmp/pip-build-tracker-i25tarz5 2024-07-11T11:05:57,523 Entered build tracker: /tmp/pip-build-tracker-i25tarz5 2024-07-11T11:05:57,524 Created temporary directory: /tmp/pip-wheel-z4i2k55y 2024-07-11T11:05:57,527 Created temporary directory: /tmp/pip-ephem-wheel-cache-5se7bsyq 2024-07-11T11:05:57,549 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-11T11:05:57,553 2 location(s) to search for versions of kssdtree: 2024-07-11T11:05:57,553 * https://pypi.org/simple/kssdtree/ 2024-07-11T11:05:57,553 * https://www.piwheels.org/simple/kssdtree/ 2024-07-11T11:05:57,553 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-07-11T11:05:57,554 Getting page https://pypi.org/simple/kssdtree/ 2024-07-11T11:05:57,556 Found index url https://pypi.org/simple/ 2024-07-11T11:05:57,767 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-07-11T11:05:57,769 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 2024-07-11T11:05:57,770 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 2024-07-11T11:05:57,771 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 2024-07-11T11:05:57,771 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 2024-07-11T11:05:57,772 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 2024-07-11T11:05:57,773 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 2024-07-11T11:05:57,773 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 2024-07-11T11:05:57,774 Found link https://files.pythonhosted.org/packages/da/db/e458cca6427752c05428d2378ccdee631d32f760174fdaba65f73125e71b/kssdtree-1.1.9.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.9 2024-07-11T11:05:57,775 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-07-11T11:05:57,776 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-07-11T11:05:57,777 Found index url https://www.piwheels.org/simple/ 2024-07-11T11:05:57,951 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-07-11T11:05:57,961 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.8-cp39-cp39-linux_armv6l.whl#sha256=6b3f5b0e827056c7b589f4fb02c353408efa5892ef4df1c8a54b4cb30331754a (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T11:05:57,962 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.8-cp39-cp39-linux_armv7l.whl#sha256=6b3f5b0e827056c7b589f4fb02c353408efa5892ef4df1c8a54b4cb30331754a (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T11:05:57,962 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.8-cp311-cp311-linux_armv6l.whl#sha256=717afc6606ad3045caac8f3f1cd01a37edd2f01f1cc38bc1bc6c3320882bd392 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T11:05:57,963 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.8-cp311-cp311-linux_armv7l.whl#sha256=717afc6606ad3045caac8f3f1cd01a37edd2f01f1cc38bc1bc6c3320882bd392 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-11T11:05:57,964 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/) 2024-07-11T11:05:57,964 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/) 2024-07-11T11:05:57,965 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/) 2024-07-11T11:05:57,965 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/) 2024-07-11T11:05:57,966 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/) 2024-07-11T11:05:57,966 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/) 2024-07-11T11:05:57,967 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/) 2024-07-11T11:05:57,967 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/) 2024-07-11T11:05:57,968 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/) 2024-07-11T11:05:57,969 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/) 2024-07-11T11:05:57,969 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/) 2024-07-11T11:05:57,970 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/) 2024-07-11T11:05:57,970 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/) 2024-07-11T11:05:57,971 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/) 2024-07-11T11:05:57,971 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/) 2024-07-11T11:05:57,973 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/) 2024-07-11T11:05:57,973 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/) 2024-07-11T11:05:57,973 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/) 2024-07-11T11:05:57,974 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/) 2024-07-11T11:05:57,974 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/) 2024-07-11T11:05:57,975 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/) 2024-07-11T11:05:57,975 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/) 2024-07-11T11:05:57,976 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/) 2024-07-11T11:05:57,977 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/) 2024-07-11T11:05:57,977 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/) 2024-07-11T11:05:57,978 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/) 2024-07-11T11:05:57,979 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/) 2024-07-11T11:05:57,979 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/) 2024-07-11T11:05:57,980 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/) 2024-07-11T11:05:57,981 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/) 2024-07-11T11:05:57,981 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/) 2024-07-11T11:05:57,981 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/) 2024-07-11T11:05:57,982 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-07-11T11:05:57,982 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-07-11T11:05:58,003 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-07-11T11:05:58,023 Collecting kssdtree==1.1.9 2024-07-11T11:05:58,025 Created temporary directory: /tmp/pip-unpack-30jmcb52 2024-07-11T11:05:58,230 Downloading kssdtree-1.1.9.tar.gz (112 kB) 2024-07-11T11:05:58,443 Added kssdtree==1.1.9 from https://files.pythonhosted.org/packages/da/db/e458cca6427752c05428d2378ccdee631d32f760174fdaba65f73125e71b/kssdtree-1.1.9.tar.gz to build tracker '/tmp/pip-build-tracker-i25tarz5' 2024-07-11T11:05:58,445 Running setup.py (path:/tmp/pip-wheel-z4i2k55y/kssdtree_efd1bd3451664c8f9cdb2afb88bc0ede/setup.py) egg_info for package kssdtree 2024-07-11T11:05:58,446 Created temporary directory: /tmp/pip-pip-egg-info-od1ke6dr 2024-07-11T11:05:58,446 Preparing metadata (setup.py): started 2024-07-11T11:05:58,448 Running command python setup.py egg_info 2024-07-11T11:05:59,537 running egg_info 2024-07-11T11:05:59,538 creating /tmp/pip-pip-egg-info-od1ke6dr/kssdtree.egg-info 2024-07-11T11:05:59,564 writing /tmp/pip-pip-egg-info-od1ke6dr/kssdtree.egg-info/PKG-INFO 2024-07-11T11:05:59,567 writing dependency_links to /tmp/pip-pip-egg-info-od1ke6dr/kssdtree.egg-info/dependency_links.txt 2024-07-11T11:05:59,569 writing requirements to /tmp/pip-pip-egg-info-od1ke6dr/kssdtree.egg-info/requires.txt 2024-07-11T11:05:59,570 writing top-level names to /tmp/pip-pip-egg-info-od1ke6dr/kssdtree.egg-info/top_level.txt 2024-07-11T11:05:59,572 writing manifest file '/tmp/pip-pip-egg-info-od1ke6dr/kssdtree.egg-info/SOURCES.txt' 2024-07-11T11:05:59,674 reading manifest file '/tmp/pip-pip-egg-info-od1ke6dr/kssdtree.egg-info/SOURCES.txt' 2024-07-11T11:05:59,676 reading manifest template 'MANIFEST.in' 2024-07-11T11:05:59,693 writing manifest file '/tmp/pip-pip-egg-info-od1ke6dr/kssdtree.egg-info/SOURCES.txt' 2024-07-11T11:05:59,812 Preparing metadata (setup.py): finished with status 'done' 2024-07-11T11:05:59,816 Source in /tmp/pip-wheel-z4i2k55y/kssdtree_efd1bd3451664c8f9cdb2afb88bc0ede has version 1.1.9, which satisfies requirement kssdtree==1.1.9 from https://files.pythonhosted.org/packages/da/db/e458cca6427752c05428d2378ccdee631d32f760174fdaba65f73125e71b/kssdtree-1.1.9.tar.gz 2024-07-11T11:05:59,817 Removed kssdtree==1.1.9 from https://files.pythonhosted.org/packages/da/db/e458cca6427752c05428d2378ccdee631d32f760174fdaba65f73125e71b/kssdtree-1.1.9.tar.gz from build tracker '/tmp/pip-build-tracker-i25tarz5' 2024-07-11T11:05:59,821 Created temporary directory: /tmp/pip-unpack-tdowj397 2024-07-11T11:05:59,822 Created temporary directory: /tmp/pip-unpack-wnqk9ni7 2024-07-11T11:05:59,827 Building wheels for collected packages: kssdtree 2024-07-11T11:05:59,831 Created temporary directory: /tmp/pip-wheel-j1jn8q9z 2024-07-11T11:05:59,832 Building wheel for kssdtree (setup.py): started 2024-07-11T11:05:59,833 Destination directory: /tmp/pip-wheel-j1jn8q9z 2024-07-11T11:05:59,834 Running command python setup.py bdist_wheel 2024-07-11T11:06:00,896 running bdist_wheel 2024-07-11T11:06:00,992 running build 2024-07-11T11:06:00,993 running build_py 2024-07-11T11:06:01,019 creating build 2024-07-11T11:06:01,020 creating build/lib.linux-armv7l-cpython-311 2024-07-11T11:06:01,021 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2024-07-11T11:06:01,025 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2024-07-11T11:06:01,027 running egg_info 2024-07-11T11:06:01,087 writing kssdtree.egg-info/PKG-INFO 2024-07-11T11:06:01,089 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-07-11T11:06:01,091 writing requirements to kssdtree.egg-info/requires.txt 2024-07-11T11:06:01,092 writing top-level names to kssdtree.egg-info/top_level.txt 2024-07-11T11:06:01,120 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-11T11:06:01,123 reading manifest template 'MANIFEST.in' 2024-07-11T11:06:01,139 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-11T11:06:01,141 running build_ext 2024-07-11T11:06:01,620 building 'kssd' extension 2024-07-11T11:06:01,620 creating build/temp.linux-armv7l-cpython-311 2024-07-11T11:06:01,621 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 2024-07-11T11:06:01,804 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-07-11T11:06:01,805 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T11:06:01,806 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-07-11T11:06:01,807 | ^ 2024-07-11T11:06:01,810 co2mco.c: In function ‘co2unitllmco’: 2024-07-11T11:06:01,811 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T11:06:01,811 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-07-11T11:06:01,812 | ^ 2024-07-11T11:06:02,515 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 2024-07-11T11:06:02,898 command_composite.c: In function ‘get_species_abundance’: 2024-07-11T11:06:02,898 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-11T11:06:02,899 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-07-11T11:06:02,900 | ^~ 2024-07-11T11:06:02,900 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-11T11:06:02,901 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-07-11T11:06:02,902 | ^~ 2024-07-11T11:06:02,902 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:02,903 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-11T11:06:02,904 | ^ 2024-07-11T11:06:02,904 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:02,905 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-11T11:06:02,906 | ^~~~~~~~~~ 2024-07-11T11:06:02,907 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-11T11:06:02,907 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-11T11:06:02,908 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:02,909 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:02,909 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-11T11:06:02,910 | ^ 2024-07-11T11:06:02,910 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:02,911 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-11T11:06:02,911 | ^~~~~~~~~~ 2024-07-11T11:06:02,912 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-11T11:06:02,912 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-11T11:06:02,913 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:02,913 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:02,914 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-11T11:06:02,914 | ^ 2024-07-11T11:06:02,915 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:02,916 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-11T11:06:02,917 | ^~~~~~~~~~ 2024-07-11T11:06:02,917 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-11T11:06:02,918 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-11T11:06:02,919 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:02,920 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:02,920 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-11T11:06:02,921 | ^ 2024-07-11T11:06:02,922 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:02,923 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-11T11:06:02,923 | ^~~~~~~~~~ 2024-07-11T11:06:02,924 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-11T11:06:02,924 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-11T11:06:02,925 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:02,926 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:02,926 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-11T11:06:02,927 | ^ 2024-07-11T11:06:02,928 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:02,929 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-11T11:06:02,929 | ^~~~~~~~~~~~ 2024-07-11T11:06:02,930 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2024-07-11T11:06:02,931 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-11T11:06:02,931 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:03,158 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 2024-07-11T11:06:03,401 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-11T11:06:03,402 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=] 2024-07-11T11:06:03,403 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T11:06:03,403 | ~~^ 2024-07-11T11:06:03,404 | | 2024-07-11T11:06:03,404 | long unsigned int 2024-07-11T11:06:03,405 | %u 2024-07-11T11:06:03,405 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T11:06:03,405 | ~~~~~~~ 2024-07-11T11:06:03,406 | | 2024-07-11T11:06:03,406 | size_t {aka unsigned int} 2024-07-11T11:06:03,407 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=] 2024-07-11T11:06:03,408 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T11:06:03,408 | ~~^ 2024-07-11T11:06:03,409 | | 2024-07-11T11:06:03,409 | long unsigned int 2024-07-11T11:06:03,410 | %u 2024-07-11T11:06:03,411 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T11:06:03,412 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T11:06:03,412 | ~~~~~~~~~ 2024-07-11T11:06:03,413 | | 2024-07-11T11:06:03,414 | size_t {aka unsigned int} 2024-07-11T11:06:03,414 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-11T11:06:03,415 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T11:06:03,415 | ~~^ 2024-07-11T11:06:03,416 | | 2024-07-11T11:06:03,417 | long unsigned int 2024-07-11T11:06:03,417 | %u 2024-07-11T11:06:03,418 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T11:06:03,419 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T11:06:03,420 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:03,420 | | 2024-07-11T11:06:03,421 | unsigned int 2024-07-11T11:06:03,421 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-11T11:06:03,422 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-07-11T11:06:03,422 | ^ 2024-07-11T11:06:03,429 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-11T11:06:03,431 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=] 2024-07-11T11:06:03,432 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-11T11:06:03,432 | ~~^ ~~~~~~~ 2024-07-11T11:06:03,432 | | | 2024-07-11T11:06:03,433 | long unsigned int size_t {aka unsigned int} 2024-07-11T11:06:03,433 | %u 2024-07-11T11:06:03,435 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=] 2024-07-11T11:06:03,435 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-11T11:06:03,436 | ~~^ 2024-07-11T11:06:03,437 | | 2024-07-11T11:06:03,437 | long unsigned int 2024-07-11T11:06:03,438 | %u 2024-07-11T11:06:03,438 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-11T11:06:03,439 | ~~~~~~~~~ 2024-07-11T11:06:03,440 | | 2024-07-11T11:06:03,441 | size_t {aka unsigned int} 2024-07-11T11:06:03,441 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-11T11:06:03,442 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-11T11:06:03,442 | ~~^ 2024-07-11T11:06:03,443 | | 2024-07-11T11:06:03,444 | long unsigned int 2024-07-11T11:06:03,444 | %u 2024-07-11T11:06:03,445 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-11T11:06:03,446 865 | (size_t) b * unitsz_distf_mapped); 2024-07-11T11:06:03,446 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:03,447 | | 2024-07-11T11:06:03,447 | unsigned int 2024-07-11T11:06:03,448 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-07-11T11:06:03,448 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-07-11T11:06:03,448 | ^~~~~~~ 2024-07-11T11:06:03,449 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-07-11T11:06:03,449 809 | struct stat cbd_fcode_stat; 2024-07-11T11:06:03,450 | ^~~~~~~~~~~~~~ 2024-07-11T11:06:03,450 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-07-11T11:06:03,450 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-11T11:06:03,451 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:03,451 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-07-11T11:06:03,452 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-11T11:06:03,452 | ^~~~~~~~~~~~~~~~~ 2024-07-11T11:06:03,459 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-11T11:06:03,462 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=] 2024-07-11T11:06:03,462 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T11:06:03,463 | ~~^ 2024-07-11T11:06:03,463 | | 2024-07-11T11:06:03,464 | long unsigned int 2024-07-11T11:06:03,465 | %u 2024-07-11T11:06:03,465 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T11:06:03,466 | ~~~~~~~ 2024-07-11T11:06:03,466 | | 2024-07-11T11:06:03,467 | size_t {aka unsigned int} 2024-07-11T11:06:03,468 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=] 2024-07-11T11:06:03,468 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T11:06:03,469 | ~~^ 2024-07-11T11:06:03,470 | | 2024-07-11T11:06:03,470 | long unsigned int 2024-07-11T11:06:03,471 | %u 2024-07-11T11:06:03,471 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T11:06:03,472 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T11:06:03,472 | ~~~~~~~~~ 2024-07-11T11:06:03,473 | | 2024-07-11T11:06:03,474 | size_t {aka unsigned int} 2024-07-11T11:06:03,474 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-11T11:06:03,475 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-11T11:06:03,476 | ~~^ 2024-07-11T11:06:03,477 | | 2024-07-11T11:06:03,477 | long unsigned int 2024-07-11T11:06:03,478 | %u 2024-07-11T11:06:03,478 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-11T11:06:03,479 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-11T11:06:03,479 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:03,480 | | 2024-07-11T11:06:03,480 | unsigned int 2024-07-11T11:06:03,481 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-07-11T11:06:03,481 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-07-11T11:06:03,482 | ^ 2024-07-11T11:06:03,482 command_dist.c: In function ‘mco_co_dist_core’: 2024-07-11T11:06:03,483 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-11T11:06:03,484 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-07-11T11:06:03,484 | ^ 2024-07-11T11:06:03,491 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-07-11T11:06:03,492 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T11:06:03,493 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-07-11T11:06:03,493 | ^ 2024-07-11T11:06:03,495 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T11:06:03,495 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-11T11:06:03,496 | ^ 2024-07-11T11:06:03,501 command_dist.c: In function ‘dist_print_nobin’: 2024-07-11T11:06:03,503 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T11:06:03,504 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-07-11T11:06:03,504 | ^ 2024-07-11T11:06:03,506 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T11:06:03,507 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-11T11:06:03,507 | ^ 2024-07-11T11:06:03,509 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T11:06:03,510 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-07-11T11:06:03,510 | ^ 2024-07-11T11:06:03,874 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-07-11T11:06:03,875 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-11T11:06:03,875 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-07-11T11:06:03,876 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:03,877 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-07-11T11:06:03,878 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-07-11T11:06:03,878 | ^~~~~~~~~~~~ 2024-07-11T11:06:04,712 command_dist.c: In function ‘get_dim_shuffle’: 2024-07-11T11:06:04,713 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-07-11T11:06:04,714 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-11T11:06:04,714 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:04,715 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-07-11T11:06:04,715 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-11T11:06:04,716 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:05,619 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-11T11:06:05,620 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:05,621 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T11:06:05,621 | ^~ ~~~~~~~~~ 2024-07-11T11:06:05,622 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-11T11:06:05,622 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T11:06:05,623 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:05,623 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T11:06:05,624 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T11:06:05,625 | ^~~~~~~~~~~~~~~ 2024-07-11T11:06:05,625 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-11T11:06:05,626 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T11:06:05,627 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:05,627 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T11:06:05,628 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T11:06:05,629 | ^~~~~~~~~~~ 2024-07-11T11:06:05,630 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:05,630 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T11:06:05,631 | ^~~~~~~~~~~~~~~~~ 2024-07-11T11:06:05,632 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-11T11:06:05,633 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T11:06:05,633 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:05,634 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T11:06:05,635 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T11:06:05,635 | ^~~~~ 2024-07-11T11:06:05,636 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:05,637 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T11:06:05,638 | ^~~~~~~~~~~ 2024-07-11T11:06:05,638 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T11:06:05,639 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T11:06:05,640 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:05,874 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-11T11:06:05,876 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:05,876 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T11:06:05,876 | ^~ ~~~~~~~~~ 2024-07-11T11:06:05,877 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-11T11:06:05,877 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T11:06:05,878 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:05,878 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T11:06:05,879 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T11:06:05,879 | ^~~~~~~~~~~~~~~ 2024-07-11T11:06:05,880 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-11T11:06:05,880 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T11:06:05,881 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:05,881 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T11:06:05,882 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T11:06:05,883 | ^~~~~~~~~~~~~ 2024-07-11T11:06:05,883 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-11T11:06:05,884 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T11:06:05,884 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:05,885 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:05,885 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-11T11:06:05,886 | ^ 2024-07-11T11:06:05,887 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-07-11T11:06:05,887 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-11T11:06:05,888 | ^~~~~~~~~~ 2024-07-11T11:06:05,889 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-11T11:06:05,889 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-11T11:06:05,890 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:05,891 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:05,891 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-11T11:06:05,892 | ^ 2024-07-11T11:06:05,893 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-07-11T11:06:05,893 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-11T11:06:05,894 | ^~~~~~~~~~ 2024-07-11T11:06:05,895 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-11T11:06:05,896 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-11T11:06:05,897 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:06,157 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-11T11:06:06,158 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:06,159 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T11:06:06,159 | ^~ ~~~~~~~~~ 2024-07-11T11:06:06,159 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-11T11:06:06,160 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-11T11:06:06,160 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:06,161 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T11:06:06,161 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T11:06:06,162 | ^~~~~~~~~~~~~~~ 2024-07-11T11:06:06,162 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-11T11:06:06,163 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-11T11:06:06,163 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:06,164 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T11:06:06,164 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T11:06:06,165 | ^~~~~~~~~~~~~ 2024-07-11T11:06:06,165 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-11T11:06:06,166 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-11T11:06:06,167 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:06,167 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T11:06:06,168 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T11:06:06,169 | ^~~~~~~~~~~ 2024-07-11T11:06:06,169 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:06,170 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T11:06:06,171 | ^~~~~~~~~~~~~~~~~ 2024-07-11T11:06:06,171 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-11T11:06:06,172 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-11T11:06:06,173 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:06,173 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-11T11:06:06,174 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T11:06:06,174 | ^~~~~ 2024-07-11T11:06:06,175 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:06,176 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T11:06:06,176 | ^~~~~~~~~~~ 2024-07-11T11:06:06,177 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T11:06:06,178 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-11T11:06:06,179 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:06,454 command_dist.c: In function ‘combine_queries’: 2024-07-11T11:06:06,455 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T11:06:06,456 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-11T11:06:06,456 | ^ 2024-07-11T11:06:06,457 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T11:06:06,458 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-11T11:06:06,458 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:06,459 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T11:06:06,459 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-11T11:06:06,460 | ^ 2024-07-11T11:06:06,461 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T11:06:06,461 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-11T11:06:06,462 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:06,464 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:06,464 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-11T11:06:06,465 | ^~ ~~~~~~~~ 2024-07-11T11:06:06,466 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-11T11:06:06,467 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-11T11:06:06,467 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:06,950 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 2024-07-11T11:06:07,128 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 2024-07-11T11:06:07,301 command_set.c: In function ‘sketch_operate’: 2024-07-11T11:06:07,302 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-11T11:06:07,302 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-07-11T11:06:07,303 | ^ 2024-07-11T11:06:07,315 command_set.c: In function ‘combin_subset_pans’: 2024-07-11T11:06:07,315 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-11T11:06:07,316 458 | free(co_dstat_fpath); 2024-07-11T11:06:07,317 | ^~~~~~~~~~~~~~ 2024-07-11T11:06:07,317 In file included from kssdheaders/global_basic.h:159, 2024-07-11T11:06:07,318 from command_set.c:15: 2024-07-11T11:06:07,319 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-11T11:06:07,319 568 | extern void free (void *__ptr) __THROW; 2024-07-11T11:06:07,320 | ~~~~~~^~~~~ 2024-07-11T11:06:07,323 command_set.c: In function ‘grouping_genomes’: 2024-07-11T11:06:07,323 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-11T11:06:07,325 563 | free(co_dstat_fpath); 2024-07-11T11:06:07,326 | ^~~~~~~~~~~~~~ 2024-07-11T11:06:07,326 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-11T11:06:07,327 568 | extern void free (void *__ptr) __THROW; 2024-07-11T11:06:07,327 | ~~~~~~^~~~~ 2024-07-11T11:06:07,495 command_set.c: In function ‘sketch_union’: 2024-07-11T11:06:07,496 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T11:06:07,497 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:07,497 | ^ 2024-07-11T11:06:07,498 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T11:06:07,498 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:07,499 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,499 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,500 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T11:06:07,501 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:07,501 command_set.c:83:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:07,502 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T11:06:07,503 | ^~~~~~~~~~ 2024-07-11T11:06:07,503 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T11:06:07,504 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T11:06:07,505 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,506 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,506 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-11T11:06:07,507 | ^~ ~~~~~~~~~~ 2024-07-11T11:06:07,508 command_set.c:93:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:07,508 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-11T11:06:07,509 | ^~~~~~~~~~ 2024-07-11T11:06:07,510 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T11:06:07,510 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-11T11:06:07,511 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,629 command_set.c: In function ‘sketch_operate’: 2024-07-11T11:06:07,630 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,630 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-11T11:06:07,631 | ^~ ~~~~~~~~~~ 2024-07-11T11:06:07,631 command_set.c:154:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:07,632 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-11T11:06:07,633 | ^~~~~~~~~~ 2024-07-11T11:06:07,633 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-11T11:06:07,634 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-11T11:06:07,635 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,636 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,636 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-11T11:06:07,637 | ^~ ~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,637 command_set.c:156:29: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:07,638 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-11T11:06:07,638 | ^~~~~~~~~~ 2024-07-11T11:06:07,639 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-11T11:06:07,639 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-11T11:06:07,640 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,641 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,641 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T11:06:07,642 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:07,642 command_set.c:166:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:07,643 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T11:06:07,643 | ^~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,644 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T11:06:07,645 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T11:06:07,645 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,646 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,647 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T11:06:07,648 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:07,648 command_set.c:170:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:07,649 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T11:06:07,650 | ^~~~~~~~~~ 2024-07-11T11:06:07,650 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T11:06:07,651 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-11T11:06:07,652 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,653 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,653 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T11:06:07,654 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:07,654 command_set.c:175:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:07,655 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T11:06:07,656 | ^~~~~~~~~~ 2024-07-11T11:06:07,656 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T11:06:07,657 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T11:06:07,658 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,659 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,659 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T11:06:07,660 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:07,661 command_set.c:188:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:07,661 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T11:06:07,662 | ^~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,662 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T11:06:07,663 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-11T11:06:07,663 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,664 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T11:06:07,664 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:07,665 | ^ 2024-07-11T11:06:07,666 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T11:06:07,666 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:07,667 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,810 command_set.c: In function ‘uniq_sketch_union’: 2024-07-11T11:06:07,810 command_set.c:220:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T11:06:07,811 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-07-11T11:06:07,812 | ^ 2024-07-11T11:06:07,813 command_set.c:220:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2024-07-11T11:06:07,813 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-07-11T11:06:07,814 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,815 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T11:06:07,815 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:07,816 | ^ 2024-07-11T11:06:07,817 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T11:06:07,818 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:07,818 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,819 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,820 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T11:06:07,820 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:07,821 command_set.c:248:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:07,822 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T11:06:07,822 | ^~~~~~~~~~ 2024-07-11T11:06:07,823 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T11:06:07,824 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-11T11:06:07,824 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,825 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,826 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-11T11:06:07,827 | ^~ ~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,827 command_set.c:260:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:07,828 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-11T11:06:07,828 | ^~~~~~~~~~ 2024-07-11T11:06:07,829 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-11T11:06:07,829 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-11T11:06:07,830 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,963 command_set.c: In function ‘combin_pans’: 2024-07-11T11:06:07,963 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,964 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T11:06:07,964 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:07,965 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-07-11T11:06:07,965 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T11:06:07,966 | ^~~~~~~~~~ 2024-07-11T11:06:07,966 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-07-11T11:06:07,967 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T11:06:07,968 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,968 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:07,969 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T11:06:07,970 | ^~ ~~~~~~~~~~ 2024-07-11T11:06:07,971 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-07-11T11:06:07,971 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T11:06:07,972 | ^~~~~~~~~~ 2024-07-11T11:06:07,973 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-07-11T11:06:07,973 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T11:06:07,974 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:07,975 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T11:06:07,975 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:07,976 | ^ 2024-07-11T11:06:07,977 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T11:06:07,977 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:07,978 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,184 command_set.c: In function ‘combin_subset_pans’: 2024-07-11T11:06:08,185 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:08,186 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T11:06:08,187 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:08,187 command_set.c:470:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:08,188 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T11:06:08,189 | ^~~~~~~~~~ 2024-07-11T11:06:08,190 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T11:06:08,190 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T11:06:08,191 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,191 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:08,191 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T11:06:08,192 | ^~ ~~~~~~~~~~ 2024-07-11T11:06:08,192 command_set.c:476:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:08,193 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T11:06:08,193 | ^~~~~~~~~~ 2024-07-11T11:06:08,194 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T11:06:08,194 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T11:06:08,194 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,195 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:08,195 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T11:06:08,196 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:08,196 command_set.c:482:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:08,197 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T11:06:08,197 | ^~~~~~~~~~ 2024-07-11T11:06:08,198 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T11:06:08,199 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T11:06:08,200 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,200 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:08,201 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T11:06:08,202 | ^~ ~~~~~~~~~~ 2024-07-11T11:06:08,203 command_set.c:513:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:08,203 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T11:06:08,204 | ^~~~~~~~~~ 2024-07-11T11:06:08,205 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T11:06:08,205 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T11:06:08,206 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,207 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T11:06:08,207 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:08,208 | ^ 2024-07-11T11:06:08,209 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T11:06:08,209 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:08,210 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,438 command_set.c: In function ‘grouping_genomes’: 2024-07-11T11:06:08,440 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:08,440 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T11:06:08,441 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:08,442 command_set.c:575:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:08,442 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T11:06:08,443 | ^~~~~~~~~~ 2024-07-11T11:06:08,443 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T11:06:08,443 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-11T11:06:08,444 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,444 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:08,445 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T11:06:08,445 | ^~ ~~~~~~~~~~ 2024-07-11T11:06:08,446 command_set.c:581:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:08,446 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T11:06:08,447 | ^~~~~~~~~~ 2024-07-11T11:06:08,447 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T11:06:08,447 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-11T11:06:08,448 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,448 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:08,449 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T11:06:08,450 | ^~ ~~~~~~~~~~~ 2024-07-11T11:06:08,450 command_set.c:613:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:08,451 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T11:06:08,451 | ^~~~~~~~~~ 2024-07-11T11:06:08,452 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-11T11:06:08,453 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-11T11:06:08,454 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,455 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-11T11:06:08,455 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T11:06:08,456 | ^~ ~~~~~~~~~~ 2024-07-11T11:06:08,457 command_set.c:635:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-11T11:06:08,457 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T11:06:08,458 | ^~~~~~~~~~ 2024-07-11T11:06:08,459 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-11T11:06:08,459 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-11T11:06:08,460 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,460 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-11T11:06:08,461 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:08,462 | ^ 2024-07-11T11:06:08,463 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-11T11:06:08,464 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-11T11:06:08,464 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:08,743 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 2024-07-11T11:06:09,058 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 2024-07-11T11:06:09,227 global_basic.c: In function ‘organize_infile_list’: 2024-07-11T11:06:09,227 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-07-11T11:06:09,228 195 | while (isspace(*buf)) buf++; 2024-07-11T11:06:09,228 | ^~~~~~~ 2024-07-11T11:06:09,229 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2024-07-11T11:06:09,229 34 | #include 2024-07-11T11:06:09,230 +++ |+#include 2024-07-11T11:06:09,230 35 | 2024-07-11T11:06:09,231 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=] 2024-07-11T11:06:09,231 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-11T11:06:09,232 | ~~^ 2024-07-11T11:06:09,233 | | 2024-07-11T11:06:09,233 | long unsigned int 2024-07-11T11:06:09,234 | %u 2024-07-11T11:06:09,235 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-11T11:06:09,235 | ~~~~~~~~~~~ 2024-07-11T11:06:09,236 | | 2024-07-11T11:06:09,237 | size_t {aka unsigned int} 2024-07-11T11:06:09,238 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=] 2024-07-11T11:06:09,238 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-11T11:06:09,239 | ~~^ 2024-07-11T11:06:09,240 | | 2024-07-11T11:06:09,241 | long unsigned int 2024-07-11T11:06:09,241 | %u 2024-07-11T11:06:09,242 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-11T11:06:09,243 | ~~~~~~~~~~~ 2024-07-11T11:06:09,243 | | 2024-07-11T11:06:09,244 | size_t {aka unsigned int} 2024-07-11T11:06:09,997 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 2024-07-11T11:06:10,175 iseq2comem.c: In function ‘reads2mco’: 2024-07-11T11:06:10,176 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,176 156 | if (base > TL) { 2024-07-11T11:06:10,177 | ^ 2024-07-11T11:06:10,177 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,178 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T11:06:10,178 | ^~ 2024-07-11T11:06:10,179 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,179 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T11:06:10,180 | ^ 2024-07-11T11:06:10,180 iseq2comem.c: In function ‘fasta2co’: 2024-07-11T11:06:10,181 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,181 239 | if (base > TL) { 2024-07-11T11:06:10,182 | ^ 2024-07-11T11:06:10,182 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,183 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T11:06:10,183 | ^~ 2024-07-11T11:06:10,184 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,185 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T11:06:10,185 | ^ 2024-07-11T11:06:10,186 iseq2comem.c: In function ‘fastq2co’: 2024-07-11T11:06:10,187 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-07-11T11:06:10,187 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-07-11T11:06:10,188 | ^~ 2024-07-11T11:06:10,189 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,189 318 | if (base > TL) { 2024-07-11T11:06:10,190 | ^ 2024-07-11T11:06:10,191 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,191 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T11:06:10,192 | ^~ 2024-07-11T11:06:10,193 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,193 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T11:06:10,194 | ^ 2024-07-11T11:06:10,195 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,195 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-07-11T11:06:10,196 | ^ 2024-07-11T11:06:10,197 iseq2comem.c: In function ‘fastq2koc’: 2024-07-11T11:06:10,198 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,198 402 | if (base > TL) { 2024-07-11T11:06:10,198 | ^ 2024-07-11T11:06:10,199 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,199 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T11:06:10,200 | ^~ 2024-07-11T11:06:10,201 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,202 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T11:06:10,202 | ^ 2024-07-11T11:06:10,203 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-07-11T11:06:10,204 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,204 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T11:06:10,205 | ^~ 2024-07-11T11:06:10,205 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:10,206 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-11T11:06:10,207 | ^ 2024-07-11T11:06:11,582 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 2024-07-11T11:06:11,637 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 2024-07-11T11:06:11,760 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 2024-07-11T11:06:12,147 pykssd.c: In function ‘py_dist_dispatch’: 2024-07-11T11:06:12,147 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-07-11T11:06:12,148 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-07-11T11:06:12,149 | ^~~~~~ 2024-07-11T11:06:12,150 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-07-11T11:06:12,150 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-07-11T11:06:12,151 | ^~~~~~ 2024-07-11T11:06:12,152 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-07-11T11:06:12,152 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-07-11T11:06:12,153 | ^~~~~~ 2024-07-11T11:06:12,720 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 2024-07-11T11:06:12,867 building 'nj' extension 2024-07-11T11:06:12,868 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 2024-07-11T11:06:13,327 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 2024-07-11T11:06:13,473 buildtree.c: In function ‘UPGMA_buildtree’: 2024-07-11T11:06:13,474 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T11:06:13,474 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-11T11:06:13,475 | ^~ 2024-07-11T11:06:13,475 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T11:06:13,476 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-11T11:06:13,476 | ^~ 2024-07-11T11:06:14,134 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 2024-07-11T11:06:14,504 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 2024-07-11T11:06:14,639 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-07-11T11:06:14,640 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T11:06:14,640 226 | for( i=0; i < dest->size; i++) { 2024-07-11T11:06:14,641 | ^ 2024-07-11T11:06:14,642 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-07-11T11:06:14,642 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T11:06:14,643 260 | for( i=0; i < mat->size; i++) { 2024-07-11T11:06:14,644 | ^ 2024-07-11T11:06:14,644 distancemat.c: In function ‘print_DistanceMatrix’: 2024-07-11T11:06:14,645 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T11:06:14,646 349 | for(row=0; row < mat->size; row++) { 2024-07-11T11:06:14,646 | ^ 2024-07-11T11:06:14,647 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-07-11T11:06:14,648 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-07-11T11:06:14,649 410 | while(c = fgetc(handle)) { 2024-07-11T11:06:14,649 | ^ 2024-07-11T11:06:15,070 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 2024-07-11T11:06:15,517 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 2024-07-11T11:06:15,734 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 2024-07-11T11:06:16,556 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 2024-07-11T11:06:16,731 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 2024-07-11T11:06:16,839 building 'dnj' extension 2024-07-11T11:06:16,840 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 bytescale.c -o build/temp.linux-armv7l-cpython-311/bytescale.o -fopenmp 2024-07-11T11:06:16,896 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 2024-07-11T11:06:17,062 dnj.c: In function ‘minQpair’: 2024-07-11T11:06:17,063 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,064 70 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,064 | ^~~ 2024-07-11T11:06:17,065 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,066 126 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,067 | ^~~ 2024-07-11T11:06:17,067 dnj.c: In function ‘maxQpair’: 2024-07-11T11:06:17,068 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,069 157 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,069 | ^~~ 2024-07-11T11:06:17,070 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,071 213 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,071 | ^~~ 2024-07-11T11:06:17,072 dnj.c: In function ‘UPGMApair’: 2024-07-11T11:06:17,073 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,073 237 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,074 | ^~~ 2024-07-11T11:06:17,074 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,075 284 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,076 | ^~~ 2024-07-11T11:06:17,076 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,077 291 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,078 | ^~~ 2024-07-11T11:06:17,078 dnj.c: In function ‘minQrow’: 2024-07-11T11:06:17,079 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,080 374 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,081 | ^~~ 2024-07-11T11:06:17,082 dnj.c: In function ‘maxQrow’: 2024-07-11T11:06:17,082 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,083 435 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,083 | ^~~ 2024-07-11T11:06:17,084 dnj.c: In function ‘UPGMArow’: 2024-07-11T11:06:17,084 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,085 488 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,085 | ^~~ 2024-07-11T11:06:17,086 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,087 494 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,087 | ^~~ 2024-07-11T11:06:17,088 dnj.c: In function ‘minQ_thread’: 2024-07-11T11:06:17,088 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:17,089 553 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:17,089 | ^~~ 2024-07-11T11:06:18,440 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 2024-07-11T11:06:18,560 filebuff.c: In function ‘BuffgzFileBuff’: 2024-07-11T11:06:18,561 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:18,561 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-07-11T11:06:18,562 | ^~ 2024-07-11T11:06:18,886 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 2024-07-11T11:06:19,020 hclust.c: In function ‘minQ’: 2024-07-11T11:06:19,021 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T11:06:19,022 364 | while(++i < Q->n) { 2024-07-11T11:06:19,022 | ^ 2024-07-11T11:06:19,023 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:19,024 377 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:19,024 | ^~~ 2024-07-11T11:06:19,025 hclust.c: In function ‘maxQ’: 2024-07-11T11:06:19,026 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-11T11:06:19,026 394 | while(++i < Q->n) { 2024-07-11T11:06:19,027 | ^ 2024-07-11T11:06:19,028 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:19,028 407 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:19,029 | ^~~ 2024-07-11T11:06:21,419 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 2024-07-11T11:06:21,552 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-07-11T11:06:21,552 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-11T11:06:21,553 538 | if(pos != n) { 2024-07-11T11:06:21,554 | ^~ 2024-07-11T11:06:22,432 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 2024-07-11T11:06:22,486 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 2024-07-11T11:06:22,615 nj.c: In function ‘initQ’: 2024-07-11T11:06:22,616 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:22,616 243 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:22,617 | ^~~ 2024-07-11T11:06:22,619 nj.c: In function ‘initQ_MN’: 2024-07-11T11:06:22,620 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:22,621 358 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:22,621 | ^~~ 2024-07-11T11:06:22,626 nj.c: In function ‘minD’: 2024-07-11T11:06:22,627 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:22,627 559 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:22,628 | ^~~ 2024-07-11T11:06:22,630 nj.c: In function ‘maxD’: 2024-07-11T11:06:22,631 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:22,631 642 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:22,632 | ^~~ 2024-07-11T11:06:22,637 nj.c: In function ‘minPair’: 2024-07-11T11:06:22,638 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-11T11:06:22,638 826 | pos <<= sizeof(unsigned) * 8; 2024-07-11T11:06:22,639 | ^~~ 2024-07-11T11:06:24,998 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 2024-07-11T11:06:25,545 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 2024-07-11T11:06:25,640 pherror.c: In function ‘cfread’: 2024-07-11T11:06:25,641 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-11T11:06:25,641 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-07-11T11:06:25,642 | ^~ 2024-07-11T11:06:25,735 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 2024-07-11T11:06:26,808 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 2024-07-11T11:06:27,180 In file included from pydnj.c:11: 2024-07-11T11:06:27,181 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-07-11T11:06:27,182 20 | #define _XOPEN_SOURCE 600 2024-07-11T11:06:27,182 | 2024-07-11T11:06:27,183 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-07-11T11:06:27,183 from /usr/include/stdlib.h:26, 2024-07-11T11:06:27,184 from /usr/include/python3.11/Python.h:23, 2024-07-11T11:06:27,185 from pydnj.c:1: 2024-07-11T11:06:27,186 /usr/include/features.h:214: note: this is the location of the previous definition 2024-07-11T11:06:27,186 214 | # define _XOPEN_SOURCE 700 2024-07-11T11:06:27,187 | 2024-07-11T11:06:27,206 pydnj.c: In function ‘py_build’: 2024-07-11T11:06:27,206 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-07-11T11:06:27,207 165 | p = omp_get_num_procs(); 2024-07-11T11:06:27,208 | ^~~~~~~~~~~~~~~~~ 2024-07-11T11:06:27,327 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2024-07-11T11:06:27,327 169 | free(file); 2024-07-11T11:06:27,328 | ^~~~~~~~~~ 2024-07-11T11:06:27,329 pydnj.c:125:12: note: returned from ‘fopen’ 2024-07-11T11:06:27,329 125 | file = fopen(inputfilename, "r"); 2024-07-11T11:06:27,329 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-11T11:06:27,402 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 2024-07-11T11:06:27,609 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 2024-07-11T11:06:27,719 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 2024-07-11T11:06:27,919 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 2024-07-11T11:06:28,079 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 2024-07-11T11:06:28,241 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-07-11T11:06:28,241 !! 2024-07-11T11:06:28,242 ******************************************************************************** 2024-07-11T11:06:28,243 Please avoid running ``setup.py`` directly. 2024-07-11T11:06:28,243 Instead, use pypa/build, pypa/installer or other 2024-07-11T11:06:28,244 standards-based tools. 2024-07-11T11:06:28,245 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-07-11T11:06:28,246 ******************************************************************************** 2024-07-11T11:06:28,247 !! 2024-07-11T11:06:28,247 self.initialize_options() 2024-07-11T11:06:28,269 installing to build/bdist.linux-armv7l/wheel 2024-07-11T11:06:28,270 running install 2024-07-11T11:06:28,294 running install_lib 2024-07-11T11:06:28,319 creating build/bdist.linux-armv7l 2024-07-11T11:06:28,320 creating build/bdist.linux-armv7l/wheel 2024-07-11T11:06:28,322 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-07-11T11:06:28,325 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-11T11:06:28,329 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-11T11:06:28,337 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-07-11T11:06:28,339 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-11T11:06:28,347 running install_egg_info 2024-07-11T11:06:28,377 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-1.1.9-py3.11.egg-info 2024-07-11T11:06:28,389 running install_scripts 2024-07-11T11:06:28,464 creating build/bdist.linux-armv7l/wheel/kssdtree-1.1.9.dist-info/WHEEL 2024-07-11T11:06:28,467 creating '/tmp/pip-wheel-j1jn8q9z/kssdtree-1.1.9-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-07-11T11:06:28,549 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T11:06:28,634 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T11:06:28,639 adding 'kssdtree.py' 2024-07-11T11:06:28,659 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2024-07-11T11:06:28,662 adding 'toolutils.py' 2024-07-11T11:06:28,665 adding 'kssdtree-1.1.9.dist-info/METADATA' 2024-07-11T11:06:28,666 adding 'kssdtree-1.1.9.dist-info/WHEEL' 2024-07-11T11:06:28,667 adding 'kssdtree-1.1.9.dist-info/dependency_links.txt' 2024-07-11T11:06:28,669 adding 'kssdtree-1.1.9.dist-info/top_level.txt' 2024-07-11T11:06:28,670 adding 'kssdtree-1.1.9.dist-info/RECORD' 2024-07-11T11:06:28,676 removing build/bdist.linux-armv7l/wheel 2024-07-11T11:06:28,834 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-07-11T11:06:28,840 Created wheel for kssdtree: filename=kssdtree-1.1.9-cp311-cp311-linux_armv7l.whl size=379901 sha256=d4c397f5fcb0af48dbb11b9fb7d7b399cc180d65355b794a8fcc7327e9a7dde1 2024-07-11T11:06:28,841 Stored in directory: /tmp/pip-ephem-wheel-cache-5se7bsyq/wheels/bf/32/a7/c6c79b7b7f1bd13ec623d44690ed43f08c563df92ddbf237d7 2024-07-11T11:06:28,850 Successfully built kssdtree 2024-07-11T11:06:28,868 Removed build tracker: '/tmp/pip-build-tracker-i25tarz5'