2024-07-10T11:14:54,566 Created temporary directory: /tmp/pip-build-tracker-9hbkm2xf 2024-07-10T11:14:54,567 Initialized build tracking at /tmp/pip-build-tracker-9hbkm2xf 2024-07-10T11:14:54,567 Created build tracker: /tmp/pip-build-tracker-9hbkm2xf 2024-07-10T11:14:54,568 Entered build tracker: /tmp/pip-build-tracker-9hbkm2xf 2024-07-10T11:14:54,569 Created temporary directory: /tmp/pip-wheel-w4qaucj2 2024-07-10T11:14:54,572 Created temporary directory: /tmp/pip-ephem-wheel-cache-3rzm72r3 2024-07-10T11:14:54,594 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-10T11:14:54,597 2 location(s) to search for versions of kssdtree: 2024-07-10T11:14:54,597 * https://pypi.org/simple/kssdtree/ 2024-07-10T11:14:54,597 * https://www.piwheels.org/simple/kssdtree/ 2024-07-10T11:14:54,598 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-07-10T11:14:54,599 Getting page https://pypi.org/simple/kssdtree/ 2024-07-10T11:14:54,600 Found index url https://pypi.org/simple/ 2024-07-10T11:14:54,810 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-07-10T11:14:54,812 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 2024-07-10T11:14:54,813 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 2024-07-10T11:14:54,814 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 2024-07-10T11:14:54,814 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 2024-07-10T11:14:54,815 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 2024-07-10T11:14:54,816 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 2024-07-10T11:14:54,817 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-07-10T11:14:54,817 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-07-10T11:14:54,819 Found index url https://www.piwheels.org/simple/ 2024-07-10T11:14:54,978 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-07-10T11:14:54,986 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/) 2024-07-10T11:14:54,986 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/) 2024-07-10T11:14:54,987 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/) 2024-07-10T11:14:54,987 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/) 2024-07-10T11:14:54,988 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/) 2024-07-10T11:14:54,989 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/) 2024-07-10T11:14:54,990 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/) 2024-07-10T11:14:54,990 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/) 2024-07-10T11:14:54,990 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/) 2024-07-10T11:14:54,991 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/) 2024-07-10T11:14:54,991 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/) 2024-07-10T11:14:54,992 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/) 2024-07-10T11:14:54,992 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/) 2024-07-10T11:14:54,993 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/) 2024-07-10T11:14:54,993 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/) 2024-07-10T11:14:54,994 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/) 2024-07-10T11:14:54,995 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/) 2024-07-10T11:14:54,995 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/) 2024-07-10T11:14:54,996 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/) 2024-07-10T11:14:54,996 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/) 2024-07-10T11:14:54,997 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/) 2024-07-10T11:14:54,997 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/) 2024-07-10T11:14:54,998 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/) 2024-07-10T11:14:54,998 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/) 2024-07-10T11:14:54,999 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/) 2024-07-10T11:14:54,999 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/) 2024-07-10T11:14:55,000 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/) 2024-07-10T11:14:55,000 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/) 2024-07-10T11:14:55,001 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-07-10T11:14:55,001 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-07-10T11:14:55,022 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-07-10T11:14:55,042 Collecting kssdtree==1.1.7 2024-07-10T11:14:55,044 Created temporary directory: /tmp/pip-unpack-fhfu8hsy 2024-07-10T11:14:55,250 Downloading kssdtree-1.1.7.tar.gz (112 kB) 2024-07-10T11:14:55,470 Added kssdtree==1.1.7 from https://files.pythonhosted.org/packages/cd/4b/d886cbcc573ff0969da7d9c756049925b86141e60ee6708dfbbe0644d008/kssdtree-1.1.7.tar.gz to build tracker '/tmp/pip-build-tracker-9hbkm2xf' 2024-07-10T11:14:55,472 Running setup.py (path:/tmp/pip-wheel-w4qaucj2/kssdtree_240fcd3b1f174b75841d1085642e703b/setup.py) egg_info for package kssdtree 2024-07-10T11:14:55,473 Created temporary directory: /tmp/pip-pip-egg-info-6jbda1g0 2024-07-10T11:14:55,474 Preparing metadata (setup.py): started 2024-07-10T11:14:55,475 Running command python setup.py egg_info 2024-07-10T11:14:56,428 running egg_info 2024-07-10T11:14:56,429 creating /tmp/pip-pip-egg-info-6jbda1g0/kssdtree.egg-info 2024-07-10T11:14:56,456 writing /tmp/pip-pip-egg-info-6jbda1g0/kssdtree.egg-info/PKG-INFO 2024-07-10T11:14:56,460 writing dependency_links to /tmp/pip-pip-egg-info-6jbda1g0/kssdtree.egg-info/dependency_links.txt 2024-07-10T11:14:56,462 writing requirements to /tmp/pip-pip-egg-info-6jbda1g0/kssdtree.egg-info/requires.txt 2024-07-10T11:14:56,463 writing top-level names to /tmp/pip-pip-egg-info-6jbda1g0/kssdtree.egg-info/top_level.txt 2024-07-10T11:14:56,464 writing manifest file '/tmp/pip-pip-egg-info-6jbda1g0/kssdtree.egg-info/SOURCES.txt' 2024-07-10T11:14:56,572 reading manifest file '/tmp/pip-pip-egg-info-6jbda1g0/kssdtree.egg-info/SOURCES.txt' 2024-07-10T11:14:56,574 reading manifest template 'MANIFEST.in' 2024-07-10T11:14:56,590 writing manifest file '/tmp/pip-pip-egg-info-6jbda1g0/kssdtree.egg-info/SOURCES.txt' 2024-07-10T11:14:56,699 Preparing metadata (setup.py): finished with status 'done' 2024-07-10T11:14:56,703 Source in /tmp/pip-wheel-w4qaucj2/kssdtree_240fcd3b1f174b75841d1085642e703b has version 1.1.7, which satisfies requirement kssdtree==1.1.7 from https://files.pythonhosted.org/packages/cd/4b/d886cbcc573ff0969da7d9c756049925b86141e60ee6708dfbbe0644d008/kssdtree-1.1.7.tar.gz 2024-07-10T11:14:56,703 Removed kssdtree==1.1.7 from https://files.pythonhosted.org/packages/cd/4b/d886cbcc573ff0969da7d9c756049925b86141e60ee6708dfbbe0644d008/kssdtree-1.1.7.tar.gz from build tracker '/tmp/pip-build-tracker-9hbkm2xf' 2024-07-10T11:14:56,707 Created temporary directory: /tmp/pip-unpack-810qbxsz 2024-07-10T11:14:56,708 Created temporary directory: /tmp/pip-unpack-l6cjtblj 2024-07-10T11:14:56,713 Building wheels for collected packages: kssdtree 2024-07-10T11:14:56,717 Created temporary directory: /tmp/pip-wheel-zrz45_fx 2024-07-10T11:14:56,718 Building wheel for kssdtree (setup.py): started 2024-07-10T11:14:56,719 Destination directory: /tmp/pip-wheel-zrz45_fx 2024-07-10T11:14:56,719 Running command python setup.py bdist_wheel 2024-07-10T11:14:57,588 running bdist_wheel 2024-07-10T11:14:57,724 running build 2024-07-10T11:14:57,724 running build_py 2024-07-10T11:14:57,752 creating build 2024-07-10T11:14:57,752 creating build/lib.linux-armv7l-cpython-311 2024-07-10T11:14:57,753 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2024-07-10T11:14:57,756 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2024-07-10T11:14:57,758 running egg_info 2024-07-10T11:14:57,784 writing kssdtree.egg-info/PKG-INFO 2024-07-10T11:14:57,786 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-07-10T11:14:57,788 writing requirements to kssdtree.egg-info/requires.txt 2024-07-10T11:14:57,789 writing top-level names to kssdtree.egg-info/top_level.txt 2024-07-10T11:14:57,818 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-10T11:14:57,822 reading manifest template 'MANIFEST.in' 2024-07-10T11:14:57,837 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-10T11:14:57,839 running build_ext 2024-07-10T11:14:58,309 building 'kssd' extension 2024-07-10T11:14:58,310 creating build/temp.linux-armv7l-cpython-311 2024-07-10T11:14:58,311 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 2024-07-10T11:14:58,501 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-07-10T11:14:58,502 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T11:14:58,503 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-07-10T11:14:58,503 | ^ 2024-07-10T11:14:58,507 co2mco.c: In function ‘co2unitllmco’: 2024-07-10T11:14:58,508 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T11:14:58,508 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-07-10T11:14:58,509 | ^ 2024-07-10T11:14:59,210 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 2024-07-10T11:14:59,592 command_composite.c: In function ‘get_species_abundance’: 2024-07-10T11:14:59,593 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-10T11:14:59,594 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-07-10T11:14:59,594 | ^~ 2024-07-10T11:14:59,595 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-10T11:14:59,595 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-07-10T11:14:59,596 | ^~ 2024-07-10T11:14:59,596 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:14:59,597 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-10T11:14:59,597 | ^ 2024-07-10T11:14:59,598 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:14:59,599 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-10T11:14:59,600 | ^~~~~~~~~~ 2024-07-10T11:14:59,600 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-10T11:14:59,601 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-10T11:14:59,602 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:14:59,602 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:14:59,603 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-10T11:14:59,604 | ^ 2024-07-10T11:14:59,605 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:14:59,605 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-10T11:14:59,606 | ^~~~~~~~~~ 2024-07-10T11:14:59,607 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-10T11:14:59,607 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-10T11:14:59,608 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:14:59,609 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:14:59,609 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-10T11:14:59,610 | ^ 2024-07-10T11:14:59,611 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:14:59,611 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-10T11:14:59,612 | ^~~~~~~~~~ 2024-07-10T11:14:59,612 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-10T11:14:59,613 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-10T11:14:59,614 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:14:59,614 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:14:59,615 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-10T11:14:59,616 | ^ 2024-07-10T11:14:59,617 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:14:59,617 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-10T11:14:59,618 | ^~~~~~~~~~ 2024-07-10T11:14:59,618 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-10T11:14:59,619 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-10T11:14:59,619 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:14:59,620 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:14:59,620 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-10T11:14:59,621 | ^ 2024-07-10T11:14:59,621 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:14:59,622 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-10T11:14:59,622 | ^~~~~~~~~~~~ 2024-07-10T11:14:59,623 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2024-07-10T11:14:59,623 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-10T11:14:59,624 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:14:59,851 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 2024-07-10T11:15:00,079 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-10T11:15:00,080 command_dist.c:678:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T11:15:00,081 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T11:15:00,082 | ~~^ 2024-07-10T11:15:00,082 | | 2024-07-10T11:15:00,083 | long unsigned int 2024-07-10T11:15:00,083 | %u 2024-07-10T11:15:00,084 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T11:15:00,085 | ~~~~~~~ 2024-07-10T11:15:00,085 | | 2024-07-10T11:15:00,086 | size_t {aka unsigned int} 2024-07-10T11:15:00,087 command_dist.c:678:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T11:15:00,087 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T11:15:00,088 | ~~^ 2024-07-10T11:15:00,089 | | 2024-07-10T11:15:00,089 | long unsigned int 2024-07-10T11:15:00,090 | %u 2024-07-10T11:15:00,091 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T11:15:00,092 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T11:15:00,092 | ~~~~~~~~~ 2024-07-10T11:15:00,093 | | 2024-07-10T11:15:00,093 | size_t {aka unsigned int} 2024-07-10T11:15:00,094 command_dist.c:678:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-10T11:15:00,094 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T11:15:00,095 | ~~^ 2024-07-10T11:15:00,095 | | 2024-07-10T11:15:00,096 | long unsigned int 2024-07-10T11:15:00,096 | %u 2024-07-10T11:15:00,096 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T11:15:00,097 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T11:15:00,097 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:00,098 | | 2024-07-10T11:15:00,098 | unsigned int 2024-07-10T11:15:00,099 command_dist.c:716:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-10T11:15:00,099 716 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-07-10T11:15:00,100 | ^ 2024-07-10T11:15:00,100 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-10T11:15:00,101 command_dist.c:864:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T11:15:00,102 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-10T11:15:00,102 | ~~^ ~~~~~~~ 2024-07-10T11:15:00,103 | | | 2024-07-10T11:15:00,104 | long unsigned int size_t {aka unsigned int} 2024-07-10T11:15:00,104 | %u 2024-07-10T11:15:00,105 command_dist.c:864:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T11:15:00,105 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-10T11:15:00,106 | ~~^ 2024-07-10T11:15:00,106 | | 2024-07-10T11:15:00,107 | long unsigned int 2024-07-10T11:15:00,107 | %u 2024-07-10T11:15:00,108 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-10T11:15:00,109 | ~~~~~~~~~ 2024-07-10T11:15:00,110 | | 2024-07-10T11:15:00,110 | size_t {aka unsigned int} 2024-07-10T11:15:00,111 command_dist.c:864:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-10T11:15:00,111 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-10T11:15:00,112 | ~~^ 2024-07-10T11:15:00,112 | | 2024-07-10T11:15:00,113 | long unsigned int 2024-07-10T11:15:00,113 | %u 2024-07-10T11:15:00,114 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-10T11:15:00,114 866 | (size_t) b * unitsz_distf_mapped); 2024-07-10T11:15:00,115 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:00,115 | | 2024-07-10T11:15:00,116 | unsigned int 2024-07-10T11:15:00,116 command_dist.c:811:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-07-10T11:15:00,117 811 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-07-10T11:15:00,117 | ^~~~~~~ 2024-07-10T11:15:00,118 command_dist.c:810:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-07-10T11:15:00,118 810 | struct stat cbd_fcode_stat; 2024-07-10T11:15:00,119 | ^~~~~~~~~~~~~~ 2024-07-10T11:15:00,120 command_dist.c:809:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-07-10T11:15:00,120 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-10T11:15:00,121 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:00,121 command_dist.c:809:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-07-10T11:15:00,122 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-10T11:15:00,123 | ^~~~~~~~~~~~~~~~~ 2024-07-10T11:15:00,124 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-10T11:15:00,124 command_dist.c:1019:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T11:15:00,125 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T11:15:00,125 | ~~^ 2024-07-10T11:15:00,126 | | 2024-07-10T11:15:00,127 | long unsigned int 2024-07-10T11:15:00,127 | %u 2024-07-10T11:15:00,128 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T11:15:00,129 | ~~~~~~~ 2024-07-10T11:15:00,129 | | 2024-07-10T11:15:00,130 | size_t {aka unsigned int} 2024-07-10T11:15:00,131 command_dist.c:1019:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T11:15:00,131 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T11:15:00,132 | ~~^ 2024-07-10T11:15:00,133 | | 2024-07-10T11:15:00,133 | long unsigned int 2024-07-10T11:15:00,134 | %u 2024-07-10T11:15:00,134 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T11:15:00,135 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T11:15:00,135 | ~~~~~~~~~ 2024-07-10T11:15:00,136 | | 2024-07-10T11:15:00,136 | size_t {aka unsigned int} 2024-07-10T11:15:00,137 command_dist.c:1019:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-10T11:15:00,138 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T11:15:00,138 | ~~^ 2024-07-10T11:15:00,139 | | 2024-07-10T11:15:00,139 | long unsigned int 2024-07-10T11:15:00,140 | %u 2024-07-10T11:15:00,140 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T11:15:00,141 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T11:15:00,142 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:00,142 | | 2024-07-10T11:15:00,143 | unsigned int 2024-07-10T11:15:00,144 command_dist.c:1035:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-07-10T11:15:00,144 1035 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-07-10T11:15:00,145 | ^ 2024-07-10T11:15:00,146 command_dist.c: In function ‘mco_co_dist_core’: 2024-07-10T11:15:00,147 command_dist.c:1117:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-10T11:15:00,147 1117 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-07-10T11:15:00,148 | ^ 2024-07-10T11:15:00,148 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-07-10T11:15:00,149 command_dist.c:1240:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T11:15:00,150 1240 | for (int rid = 0; rid < ref_num; rid++) 2024-07-10T11:15:00,150 | ^ 2024-07-10T11:15:00,151 command_dist.c:1246:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T11:15:00,152 1246 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-10T11:15:00,152 | ^ 2024-07-10T11:15:00,153 command_dist.c: In function ‘dist_print_nobin’: 2024-07-10T11:15:00,154 command_dist.c:1336:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T11:15:00,154 1336 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-07-10T11:15:00,155 | ^ 2024-07-10T11:15:00,156 command_dist.c:1357:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T11:15:00,156 1357 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-10T11:15:00,157 | ^ 2024-07-10T11:15:00,157 command_dist.c:1383:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T11:15:00,158 1383 | for (int rid = 0; rid < ref_num; rid++) 2024-07-10T11:15:00,158 | ^ 2024-07-10T11:15:00,515 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-07-10T11:15:00,516 command_dist.c:404:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-10T11:15:00,516 404 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-07-10T11:15:00,517 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:00,518 command_dist.c:376:40: note: ‘com_abund_fp’ was declared here 2024-07-10T11:15:00,518 376 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-07-10T11:15:00,519 | ^~~~~~~~~~~~ 2024-07-10T11:15:01,355 command_dist.c: In function ‘get_dim_shuffle’: 2024-07-10T11:15:01,355 command_dist.c:268:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-07-10T11:15:01,356 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-10T11:15:01,357 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:01,357 command_dist.c:268:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-07-10T11:15:01,358 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-10T11:15:01,358 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,259 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-10T11:15:02,259 command_dist.c:597:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:02,260 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T11:15:02,261 | ^~ ~~~~~~~~~ 2024-07-10T11:15:02,261 command_dist.c:597:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-10T11:15:02,262 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T11:15:02,263 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,263 command_dist.c:626:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T11:15:02,264 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T11:15:02,264 | ^~~~~~~~~~~~~~~ 2024-07-10T11:15:02,265 command_dist.c:626:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-10T11:15:02,266 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T11:15:02,266 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,267 command_dist.c:682:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T11:15:02,268 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T11:15:02,268 | ^~~~~~~~~~~ 2024-07-10T11:15:02,269 command_dist.c:682:38: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:02,270 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T11:15:02,271 | ^~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,271 command_dist.c:682:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-10T11:15:02,272 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T11:15:02,273 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,273 command_dist.c:683:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T11:15:02,274 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T11:15:02,274 | ^~~~~ 2024-07-10T11:15:02,275 command_dist.c:683:32: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:02,275 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T11:15:02,276 | ^~~~~~~~~~~ 2024-07-10T11:15:02,277 command_dist.c:683:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T11:15:02,277 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T11:15:02,278 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,507 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-10T11:15:02,509 command_dist.c:764:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:02,509 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T11:15:02,510 | ^~ ~~~~~~~~~ 2024-07-10T11:15:02,510 command_dist.c:764:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-10T11:15:02,511 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T11:15:02,512 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,512 command_dist.c:791:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T11:15:02,513 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T11:15:02,514 | ^~~~~~~~~~~~~~~ 2024-07-10T11:15:02,515 command_dist.c:791:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-10T11:15:02,515 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T11:15:02,516 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,516 command_dist.c:824:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T11:15:02,517 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T11:15:02,517 | ^~~~~~~~~~~~~ 2024-07-10T11:15:02,518 command_dist.c:824:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-10T11:15:02,518 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T11:15:02,519 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,519 command_dist.c:850:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:02,520 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-10T11:15:02,521 | ^ 2024-07-10T11:15:02,522 command_dist.c:850:33: note: directive argument in the range [0, 536870912] 2024-07-10T11:15:02,523 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-10T11:15:02,523 | ^~~~~~~~~~ 2024-07-10T11:15:02,524 command_dist.c:850:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-10T11:15:02,524 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-10T11:15:02,525 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,525 command_dist.c:852:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:02,526 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-10T11:15:02,526 | ^ 2024-07-10T11:15:02,527 command_dist.c:852:28: note: directive argument in the range [0, 536870912] 2024-07-10T11:15:02,527 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-10T11:15:02,528 | ^~~~~~~~~~ 2024-07-10T11:15:02,528 command_dist.c:852:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-10T11:15:02,529 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-10T11:15:02,529 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,786 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-10T11:15:02,788 command_dist.c:928:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:02,788 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T11:15:02,789 | ^~ ~~~~~~~~~ 2024-07-10T11:15:02,789 command_dist.c:928:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-10T11:15:02,790 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T11:15:02,790 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,791 command_dist.c:957:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T11:15:02,791 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T11:15:02,792 | ^~~~~~~~~~~~~~~ 2024-07-10T11:15:02,793 command_dist.c:957:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-10T11:15:02,793 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T11:15:02,794 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,794 command_dist.c:991:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T11:15:02,795 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T11:15:02,795 | ^~~~~~~~~~~~~ 2024-07-10T11:15:02,796 command_dist.c:991:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-10T11:15:02,797 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T11:15:02,797 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,798 command_dist.c:1023:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T11:15:02,799 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T11:15:02,800 | ^~~~~~~~~~~ 2024-07-10T11:15:02,800 command_dist.c:1023:38: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:02,801 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T11:15:02,802 | ^~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,802 command_dist.c:1023:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-10T11:15:02,803 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T11:15:02,803 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:02,804 command_dist.c:1024:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T11:15:02,804 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T11:15:02,805 | ^~~~~ 2024-07-10T11:15:02,806 command_dist.c:1024:32: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:02,806 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T11:15:02,807 | ^~~~~~~~~~~ 2024-07-10T11:15:02,807 command_dist.c:1024:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T11:15:02,808 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T11:15:02,809 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:03,080 command_dist.c: In function ‘combine_queries’: 2024-07-10T11:15:03,082 command_dist.c:1493:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T11:15:03,083 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-10T11:15:03,083 | ^ 2024-07-10T11:15:03,084 command_dist.c:1493:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T11:15:03,085 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-10T11:15:03,085 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:03,086 command_dist.c:1500:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T11:15:03,086 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-10T11:15:03,087 | ^ 2024-07-10T11:15:03,088 command_dist.c:1500:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T11:15:03,088 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-10T11:15:03,089 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:03,091 command_dist.c:1604:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:03,091 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-10T11:15:03,092 | ^~ ~~~~~~~~ 2024-07-10T11:15:03,092 command_dist.c:1604:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-10T11:15:03,093 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-10T11:15:03,094 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:03,570 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 2024-07-10T11:15:03,742 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 2024-07-10T11:15:03,910 command_set.c: In function ‘sketch_operate’: 2024-07-10T11:15:03,911 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-10T11:15:03,912 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-07-10T11:15:03,912 | ^ 2024-07-10T11:15:03,924 command_set.c: In function ‘combin_subset_pans’: 2024-07-10T11:15:03,925 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-10T11:15:03,926 458 | free(co_dstat_fpath); 2024-07-10T11:15:03,926 | ^~~~~~~~~~~~~~ 2024-07-10T11:15:03,927 In file included from kssdheaders/global_basic.h:159, 2024-07-10T11:15:03,927 from command_set.c:15: 2024-07-10T11:15:03,928 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-10T11:15:03,928 568 | extern void free (void *__ptr) __THROW; 2024-07-10T11:15:03,929 | ~~~~~~^~~~~ 2024-07-10T11:15:03,932 command_set.c: In function ‘grouping_genomes’: 2024-07-10T11:15:03,932 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-10T11:15:03,933 563 | free(co_dstat_fpath); 2024-07-10T11:15:03,933 | ^~~~~~~~~~~~~~ 2024-07-10T11:15:03,934 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-10T11:15:03,934 568 | extern void free (void *__ptr) __THROW; 2024-07-10T11:15:03,935 | ~~~~~~^~~~~ 2024-07-10T11:15:04,100 command_set.c: In function ‘sketch_union’: 2024-07-10T11:15:04,101 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T11:15:04,101 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:04,102 | ^ 2024-07-10T11:15:04,103 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T11:15:04,104 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:04,104 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,105 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,106 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T11:15:04,107 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:04,107 command_set.c:83:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,108 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T11:15:04,108 | ^~~~~~~~~~ 2024-07-10T11:15:04,109 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T11:15:04,110 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T11:15:04,111 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,111 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,112 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-10T11:15:04,113 | ^~ ~~~~~~~~~~ 2024-07-10T11:15:04,113 command_set.c:93:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,114 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-10T11:15:04,115 | ^~~~~~~~~~ 2024-07-10T11:15:04,116 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T11:15:04,116 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-10T11:15:04,117 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,234 command_set.c: In function ‘sketch_operate’: 2024-07-10T11:15:04,235 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,235 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-10T11:15:04,236 | ^~ ~~~~~~~~~~ 2024-07-10T11:15:04,236 command_set.c:154:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,236 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-10T11:15:04,237 | ^~~~~~~~~~ 2024-07-10T11:15:04,238 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T11:15:04,238 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-10T11:15:04,238 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,239 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,239 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-10T11:15:04,240 | ^~ ~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,241 command_set.c:156:29: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,242 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-10T11:15:04,242 | ^~~~~~~~~~ 2024-07-10T11:15:04,243 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-10T11:15:04,244 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-10T11:15:04,244 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,245 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,246 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T11:15:04,247 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:04,247 command_set.c:166:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,248 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T11:15:04,249 | ^~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,249 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T11:15:04,250 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T11:15:04,251 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,251 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,252 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T11:15:04,253 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:04,253 command_set.c:170:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,254 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T11:15:04,255 | ^~~~~~~~~~ 2024-07-10T11:15:04,256 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T11:15:04,256 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T11:15:04,256 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,257 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,257 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T11:15:04,258 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:04,258 command_set.c:175:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,259 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T11:15:04,259 | ^~~~~~~~~~ 2024-07-10T11:15:04,260 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T11:15:04,260 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T11:15:04,261 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,261 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,262 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T11:15:04,262 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:04,263 command_set.c:188:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,264 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T11:15:04,264 | ^~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,265 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T11:15:04,266 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T11:15:04,267 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,267 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T11:15:04,268 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:04,269 | ^ 2024-07-10T11:15:04,269 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T11:15:04,270 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:04,271 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,412 command_set.c: In function ‘uniq_sketch_union’: 2024-07-10T11:15:04,413 command_set.c:220:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T11:15:04,414 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-07-10T11:15:04,414 | ^ 2024-07-10T11:15:04,415 command_set.c:220:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2024-07-10T11:15:04,415 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-07-10T11:15:04,416 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,417 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T11:15:04,417 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:04,418 | ^ 2024-07-10T11:15:04,419 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T11:15:04,420 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:04,420 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,421 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,422 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T11:15:04,422 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:04,423 command_set.c:248:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,423 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T11:15:04,424 | ^~~~~~~~~~ 2024-07-10T11:15:04,424 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T11:15:04,425 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T11:15:04,425 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,426 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,426 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-10T11:15:04,427 | ^~ ~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,427 command_set.c:260:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,428 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-10T11:15:04,428 | ^~~~~~~~~~ 2024-07-10T11:15:04,429 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-10T11:15:04,429 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-10T11:15:04,430 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,558 command_set.c: In function ‘combin_pans’: 2024-07-10T11:15:04,559 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,559 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T11:15:04,560 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:04,561 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-07-10T11:15:04,562 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T11:15:04,562 | ^~~~~~~~~~ 2024-07-10T11:15:04,563 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-07-10T11:15:04,564 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T11:15:04,564 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,565 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,565 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T11:15:04,566 | ^~ ~~~~~~~~~~ 2024-07-10T11:15:04,567 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-07-10T11:15:04,567 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T11:15:04,568 | ^~~~~~~~~~ 2024-07-10T11:15:04,569 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-07-10T11:15:04,570 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T11:15:04,571 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,572 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T11:15:04,573 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:04,574 | ^ 2024-07-10T11:15:04,575 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T11:15:04,576 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:04,576 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,775 command_set.c: In function ‘combin_subset_pans’: 2024-07-10T11:15:04,775 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,776 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T11:15:04,776 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:04,777 command_set.c:470:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,777 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T11:15:04,778 | ^~~~~~~~~~ 2024-07-10T11:15:04,778 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T11:15:04,778 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T11:15:04,779 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,779 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,780 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T11:15:04,780 | ^~ ~~~~~~~~~~ 2024-07-10T11:15:04,781 command_set.c:476:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,782 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T11:15:04,782 | ^~~~~~~~~~ 2024-07-10T11:15:04,783 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T11:15:04,784 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T11:15:04,784 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,785 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,786 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T11:15:04,786 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:04,787 command_set.c:482:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,788 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T11:15:04,788 | ^~~~~~~~~~ 2024-07-10T11:15:04,789 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T11:15:04,790 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T11:15:04,790 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,791 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:04,792 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T11:15:04,792 | ^~ ~~~~~~~~~~ 2024-07-10T11:15:04,793 command_set.c:513:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:04,794 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T11:15:04,794 | ^~~~~~~~~~ 2024-07-10T11:15:04,795 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T11:15:04,795 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T11:15:04,796 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:04,796 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T11:15:04,797 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:04,798 | ^ 2024-07-10T11:15:04,798 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T11:15:04,799 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:04,799 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:05,020 command_set.c: In function ‘grouping_genomes’: 2024-07-10T11:15:05,021 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:05,021 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T11:15:05,021 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:05,022 command_set.c:575:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:05,022 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T11:15:05,023 | ^~~~~~~~~~ 2024-07-10T11:15:05,024 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T11:15:05,024 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T11:15:05,025 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:05,026 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:05,026 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T11:15:05,027 | ^~ ~~~~~~~~~~ 2024-07-10T11:15:05,027 command_set.c:581:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:05,028 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T11:15:05,029 | ^~~~~~~~~~ 2024-07-10T11:15:05,029 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T11:15:05,030 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T11:15:05,030 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:05,031 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:05,031 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T11:15:05,032 | ^~ ~~~~~~~~~~~ 2024-07-10T11:15:05,033 command_set.c:613:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:05,033 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T11:15:05,034 | ^~~~~~~~~~ 2024-07-10T11:15:05,035 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T11:15:05,036 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T11:15:05,037 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:05,037 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T11:15:05,038 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T11:15:05,038 | ^~ ~~~~~~~~~~ 2024-07-10T11:15:05,039 command_set.c:635:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T11:15:05,039 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T11:15:05,040 | ^~~~~~~~~~ 2024-07-10T11:15:05,040 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T11:15:05,041 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T11:15:05,041 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:05,042 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T11:15:05,042 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:05,043 | ^ 2024-07-10T11:15:05,043 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T11:15:05,044 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T11:15:05,044 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:05,315 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 2024-07-10T11:15:05,630 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 2024-07-10T11:15:05,812 global_basic.c: In function ‘organize_infile_list’: 2024-07-10T11:15:05,813 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-07-10T11:15:05,813 195 | while (isspace(*buf)) buf++; 2024-07-10T11:15:05,814 | ^~~~~~~ 2024-07-10T11:15:05,815 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2024-07-10T11:15:05,815 34 | #include 2024-07-10T11:15:05,816 +++ |+#include 2024-07-10T11:15:05,817 35 | 2024-07-10T11:15:05,817 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=] 2024-07-10T11:15:05,818 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-10T11:15:05,818 | ~~^ 2024-07-10T11:15:05,819 | | 2024-07-10T11:15:05,820 | long unsigned int 2024-07-10T11:15:05,820 | %u 2024-07-10T11:15:05,821 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-10T11:15:05,822 | ~~~~~~~~~~~ 2024-07-10T11:15:05,822 | | 2024-07-10T11:15:05,823 | size_t {aka unsigned int} 2024-07-10T11:15:05,824 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=] 2024-07-10T11:15:05,825 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-10T11:15:05,825 | ~~^ 2024-07-10T11:15:05,826 | | 2024-07-10T11:15:05,826 | long unsigned int 2024-07-10T11:15:05,826 | %u 2024-07-10T11:15:05,827 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-10T11:15:05,827 | ~~~~~~~~~~~ 2024-07-10T11:15:05,828 | | 2024-07-10T11:15:05,828 | size_t {aka unsigned int} 2024-07-10T11:15:06,609 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 2024-07-10T11:15:06,814 iseq2comem.c: In function ‘reads2mco’: 2024-07-10T11:15:06,817 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,818 156 | if (base > TL) { 2024-07-10T11:15:06,818 | ^ 2024-07-10T11:15:06,819 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,820 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T11:15:06,820 | ^~ 2024-07-10T11:15:06,821 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,822 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T11:15:06,823 | ^ 2024-07-10T11:15:06,825 iseq2comem.c: In function ‘fasta2co’: 2024-07-10T11:15:06,826 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,827 239 | if (base > TL) { 2024-07-10T11:15:06,829 | ^ 2024-07-10T11:15:06,830 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,830 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T11:15:06,831 | ^~ 2024-07-10T11:15:06,832 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,833 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T11:15:06,833 | ^ 2024-07-10T11:15:06,835 iseq2comem.c: In function ‘fastq2co’: 2024-07-10T11:15:06,835 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-07-10T11:15:06,836 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-07-10T11:15:06,837 | ^~ 2024-07-10T11:15:06,837 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,838 318 | if (base > TL) { 2024-07-10T11:15:06,838 | ^ 2024-07-10T11:15:06,839 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,839 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T11:15:06,840 | ^~ 2024-07-10T11:15:06,840 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,841 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T11:15:06,842 | ^ 2024-07-10T11:15:06,843 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,843 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-07-10T11:15:06,843 | ^ 2024-07-10T11:15:06,844 iseq2comem.c: In function ‘fastq2koc’: 2024-07-10T11:15:06,844 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,845 402 | if (base > TL) { 2024-07-10T11:15:06,846 | ^ 2024-07-10T11:15:06,846 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,847 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T11:15:06,847 | ^~ 2024-07-10T11:15:06,848 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,849 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T11:15:06,850 | ^ 2024-07-10T11:15:06,854 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-07-10T11:15:06,855 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,856 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T11:15:06,856 | ^~ 2024-07-10T11:15:06,857 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:06,857 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T11:15:06,858 | ^ 2024-07-10T11:15:08,202 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 2024-07-10T11:15:08,255 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 2024-07-10T11:15:08,380 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 2024-07-10T11:15:08,772 pykssd.c: In function ‘py_dist_dispatch’: 2024-07-10T11:15:08,772 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-07-10T11:15:08,773 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-07-10T11:15:08,773 | ^~~~~~ 2024-07-10T11:15:08,774 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-07-10T11:15:08,774 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-07-10T11:15:08,775 | ^~~~~~ 2024-07-10T11:15:08,776 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-07-10T11:15:08,776 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-07-10T11:15:08,777 | ^~~~~~ 2024-07-10T11:15:09,344 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 2024-07-10T11:15:09,490 building 'nj' extension 2024-07-10T11:15:09,490 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 2024-07-10T11:15:09,946 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 2024-07-10T11:15:10,093 buildtree.c: In function ‘UPGMA_buildtree’: 2024-07-10T11:15:10,093 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T11:15:10,094 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-10T11:15:10,095 | ^~ 2024-07-10T11:15:10,096 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T11:15:10,097 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-10T11:15:10,098 | ^~ 2024-07-10T11:15:10,755 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 2024-07-10T11:15:11,129 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 2024-07-10T11:15:11,264 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-07-10T11:15:11,265 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T11:15:11,266 226 | for( i=0; i < dest->size; i++) { 2024-07-10T11:15:11,267 | ^ 2024-07-10T11:15:11,267 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-07-10T11:15:11,269 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T11:15:11,269 260 | for( i=0; i < mat->size; i++) { 2024-07-10T11:15:11,270 | ^ 2024-07-10T11:15:11,270 distancemat.c: In function ‘print_DistanceMatrix’: 2024-07-10T11:15:11,270 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T11:15:11,271 349 | for(row=0; row < mat->size; row++) { 2024-07-10T11:15:11,272 | ^ 2024-07-10T11:15:11,273 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-07-10T11:15:11,273 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-07-10T11:15:11,274 410 | while(c = fgetc(handle)) { 2024-07-10T11:15:11,274 | ^ 2024-07-10T11:15:11,658 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 2024-07-10T11:15:12,094 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 2024-07-10T11:15:12,309 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 2024-07-10T11:15:13,119 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 2024-07-10T11:15:13,293 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 2024-07-10T11:15:13,400 building 'dnj' extension 2024-07-10T11:15:13,401 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 2024-07-10T11:15:13,456 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 2024-07-10T11:15:13,590 dnj.c: In function ‘minQpair’: 2024-07-10T11:15:13,591 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,592 70 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,592 | ^~~ 2024-07-10T11:15:13,593 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,594 126 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,594 | ^~~ 2024-07-10T11:15:13,595 dnj.c: In function ‘maxQpair’: 2024-07-10T11:15:13,596 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,596 157 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,598 | ^~~ 2024-07-10T11:15:13,598 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,598 213 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,599 | ^~~ 2024-07-10T11:15:13,599 dnj.c: In function ‘UPGMApair’: 2024-07-10T11:15:13,600 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,600 237 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,601 | ^~~ 2024-07-10T11:15:13,601 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,602 284 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,602 | ^~~ 2024-07-10T11:15:13,603 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,603 291 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,604 | ^~~ 2024-07-10T11:15:13,604 dnj.c: In function ‘minQrow’: 2024-07-10T11:15:13,605 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,605 374 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,606 | ^~~ 2024-07-10T11:15:13,606 dnj.c: In function ‘maxQrow’: 2024-07-10T11:15:13,607 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,607 435 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,608 | ^~~ 2024-07-10T11:15:13,608 dnj.c: In function ‘UPGMArow’: 2024-07-10T11:15:13,609 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,610 488 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,610 | ^~~ 2024-07-10T11:15:13,611 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,611 494 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,612 | ^~~ 2024-07-10T11:15:13,613 dnj.c: In function ‘minQ_thread’: 2024-07-10T11:15:13,613 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:13,614 553 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:13,615 | ^~~ 2024-07-10T11:15:14,958 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 2024-07-10T11:15:15,079 filebuff.c: In function ‘BuffgzFileBuff’: 2024-07-10T11:15:15,080 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:15,080 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-07-10T11:15:15,081 | ^~ 2024-07-10T11:15:15,406 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 2024-07-10T11:15:15,540 hclust.c: In function ‘minQ’: 2024-07-10T11:15:15,541 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T11:15:15,541 364 | while(++i < Q->n) { 2024-07-10T11:15:15,542 | ^ 2024-07-10T11:15:15,543 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:15,543 377 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:15,544 | ^~~ 2024-07-10T11:15:15,545 hclust.c: In function ‘maxQ’: 2024-07-10T11:15:15,545 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T11:15:15,546 394 | while(++i < Q->n) { 2024-07-10T11:15:15,546 | ^ 2024-07-10T11:15:15,547 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:15,547 407 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:15,547 | ^~~ 2024-07-10T11:15:17,927 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 2024-07-10T11:15:18,061 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-07-10T11:15:18,061 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T11:15:18,062 538 | if(pos != n) { 2024-07-10T11:15:18,062 | ^~ 2024-07-10T11:15:18,938 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 2024-07-10T11:15:18,991 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 2024-07-10T11:15:19,120 nj.c: In function ‘initQ’: 2024-07-10T11:15:19,121 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:19,122 243 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:19,123 | ^~~ 2024-07-10T11:15:19,123 nj.c: In function ‘initQ_MN’: 2024-07-10T11:15:19,124 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:19,125 358 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:19,125 | ^~~ 2024-07-10T11:15:19,129 nj.c: In function ‘minD’: 2024-07-10T11:15:19,129 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:19,130 559 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:19,131 | ^~~ 2024-07-10T11:15:19,132 nj.c: In function ‘maxD’: 2024-07-10T11:15:19,132 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:19,133 642 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:19,134 | ^~~ 2024-07-10T11:15:19,137 nj.c: In function ‘minPair’: 2024-07-10T11:15:19,137 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T11:15:19,138 826 | pos <<= sizeof(unsigned) * 8; 2024-07-10T11:15:19,139 | ^~~ 2024-07-10T11:15:21,536 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 2024-07-10T11:15:22,073 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 2024-07-10T11:15:22,166 pherror.c: In function ‘cfread’: 2024-07-10T11:15:22,166 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T11:15:22,167 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-07-10T11:15:22,169 | ^~ 2024-07-10T11:15:22,260 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c phy.c -o build/temp.linux-armv7l-cpython-311/phy.o -fopenmp 2024-07-10T11:15:23,328 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 2024-07-10T11:15:23,705 In file included from pydnj.c:11: 2024-07-10T11:15:23,705 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-07-10T11:15:23,706 20 | #define _XOPEN_SOURCE 600 2024-07-10T11:15:23,706 | 2024-07-10T11:15:23,707 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-07-10T11:15:23,707 from /usr/include/stdlib.h:26, 2024-07-10T11:15:23,708 from /usr/include/python3.11/Python.h:23, 2024-07-10T11:15:23,708 from pydnj.c:1: 2024-07-10T11:15:23,709 /usr/include/features.h:214: note: this is the location of the previous definition 2024-07-10T11:15:23,709 214 | # define _XOPEN_SOURCE 700 2024-07-10T11:15:23,710 | 2024-07-10T11:15:23,729 pydnj.c: In function ‘py_build’: 2024-07-10T11:15:23,730 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-07-10T11:15:23,731 165 | p = omp_get_num_procs(); 2024-07-10T11:15:23,732 | ^~~~~~~~~~~~~~~~~ 2024-07-10T11:15:23,849 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2024-07-10T11:15:23,850 169 | free(file); 2024-07-10T11:15:23,851 | ^~~~~~~~~~ 2024-07-10T11:15:23,851 pydnj.c:125:12: note: returned from ‘fopen’ 2024-07-10T11:15:23,852 125 | file = fopen(inputfilename, "r"); 2024-07-10T11:15:23,853 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T11:15:23,924 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 2024-07-10T11:15:24,131 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 2024-07-10T11:15:24,239 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 2024-07-10T11:15:24,432 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 vector.c -o build/temp.linux-armv7l-cpython-311/vector.o -fopenmp 2024-07-10T11:15:24,623 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 2024-07-10T11:15:24,790 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-07-10T11:15:24,791 !! 2024-07-10T11:15:24,792 ******************************************************************************** 2024-07-10T11:15:24,792 Please avoid running ``setup.py`` directly. 2024-07-10T11:15:24,793 Instead, use pypa/build, pypa/installer or other 2024-07-10T11:15:24,793 standards-based tools. 2024-07-10T11:15:24,794 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-07-10T11:15:24,794 ******************************************************************************** 2024-07-10T11:15:24,795 !! 2024-07-10T11:15:24,796 self.initialize_options() 2024-07-10T11:15:24,816 installing to build/bdist.linux-armv7l/wheel 2024-07-10T11:15:24,817 running install 2024-07-10T11:15:24,841 running install_lib 2024-07-10T11:15:24,867 creating build/bdist.linux-armv7l 2024-07-10T11:15:24,868 creating build/bdist.linux-armv7l/wheel 2024-07-10T11:15:24,868 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-10T11:15:24,874 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-07-10T11:15:24,876 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-10T11:15:24,883 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-10T11:15:24,891 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-07-10T11:15:24,894 running install_egg_info 2024-07-10T11:15:24,926 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-1.1.7-py3.11.egg-info 2024-07-10T11:15:24,938 running install_scripts 2024-07-10T11:15:24,987 creating build/bdist.linux-armv7l/wheel/kssdtree-1.1.7.dist-info/WHEEL 2024-07-10T11:15:24,990 creating '/tmp/pip-wheel-zrz45_fx/kssdtree-1.1.7-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-07-10T11:15:25,055 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2024-07-10T11:15:25,139 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2024-07-10T11:15:25,143 adding 'kssdtree.py' 2024-07-10T11:15:25,164 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2024-07-10T11:15:25,167 adding 'toolutils.py' 2024-07-10T11:15:25,169 adding 'kssdtree-1.1.7.dist-info/METADATA' 2024-07-10T11:15:25,170 adding 'kssdtree-1.1.7.dist-info/WHEEL' 2024-07-10T11:15:25,171 adding 'kssdtree-1.1.7.dist-info/dependency_links.txt' 2024-07-10T11:15:25,172 adding 'kssdtree-1.1.7.dist-info/top_level.txt' 2024-07-10T11:15:25,173 adding 'kssdtree-1.1.7.dist-info/RECORD' 2024-07-10T11:15:25,179 removing build/bdist.linux-armv7l/wheel 2024-07-10T11:15:25,326 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-07-10T11:15:25,333 Created wheel for kssdtree: filename=kssdtree-1.1.7-cp311-cp311-linux_armv7l.whl size=379690 sha256=388a8dabd657ea83e6d22b52300337c74e9d84e506806cfd4d2a76eb98777e17 2024-07-10T11:15:25,334 Stored in directory: /tmp/pip-ephem-wheel-cache-3rzm72r3/wheels/12/d3/8b/46f5a5cfb2bb6ad1f00b99c14e905ef8261b79259c59ffafea 2024-07-10T11:15:25,343 Successfully built kssdtree 2024-07-10T11:15:25,356 Removed build tracker: '/tmp/pip-build-tracker-9hbkm2xf'