2024-07-10T10:05:25,697 Created temporary directory: /tmp/pip-build-tracker-2k8_3vtu 2024-07-10T10:05:25,699 Initialized build tracking at /tmp/pip-build-tracker-2k8_3vtu 2024-07-10T10:05:25,699 Created build tracker: /tmp/pip-build-tracker-2k8_3vtu 2024-07-10T10:05:25,699 Entered build tracker: /tmp/pip-build-tracker-2k8_3vtu 2024-07-10T10:05:25,700 Created temporary directory: /tmp/pip-wheel-vi2qxesh 2024-07-10T10:05:25,704 Created temporary directory: /tmp/pip-ephem-wheel-cache-sbf2h8yh 2024-07-10T10:05:25,728 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-10T10:05:25,732 2 location(s) to search for versions of kssdtree: 2024-07-10T10:05:25,732 * https://pypi.org/simple/kssdtree/ 2024-07-10T10:05:25,732 * https://www.piwheels.org/simple/kssdtree/ 2024-07-10T10:05:25,732 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-07-10T10:05:25,733 Getting page https://pypi.org/simple/kssdtree/ 2024-07-10T10:05:25,734 Found index url https://pypi.org/simple/ 2024-07-10T10:05:25,785 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-07-10T10:05:25,787 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 2024-07-10T10:05:25,787 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 2024-07-10T10:05:25,788 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 2024-07-10T10:05:25,788 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 2024-07-10T10:05:25,788 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 2024-07-10T10:05:25,789 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-07-10T10:05:25,789 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-07-10T10:05:25,790 Found index url https://www.piwheels.org/simple/ 2024-07-10T10:05:25,865 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-07-10T10:05:25,873 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/) 2024-07-10T10:05:25,873 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/) 2024-07-10T10:05:25,874 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/) 2024-07-10T10:05:25,874 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/) 2024-07-10T10:05:25,874 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/) 2024-07-10T10:05:25,874 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/) 2024-07-10T10:05:25,875 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/) 2024-07-10T10:05:25,875 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/) 2024-07-10T10:05:25,875 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/) 2024-07-10T10:05:25,875 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/) 2024-07-10T10:05:25,875 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/) 2024-07-10T10:05:25,875 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/) 2024-07-10T10:05:25,876 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/) 2024-07-10T10:05:25,876 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/) 2024-07-10T10:05:25,876 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/) 2024-07-10T10:05:25,876 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/) 2024-07-10T10:05:25,876 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/) 2024-07-10T10:05:25,877 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/) 2024-07-10T10:05:25,877 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/) 2024-07-10T10:05:25,877 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/) 2024-07-10T10:05:25,877 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/) 2024-07-10T10:05:25,877 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/) 2024-07-10T10:05:25,878 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/) 2024-07-10T10:05:25,878 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/) 2024-07-10T10:05:25,878 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/) 2024-07-10T10:05:25,878 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/) 2024-07-10T10:05:25,878 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-07-10T10:05:25,879 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-07-10T10:05:25,897 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-07-10T10:05:25,913 Collecting kssdtree==1.1.6 2024-07-10T10:05:25,915 Created temporary directory: /tmp/pip-unpack-48voe6fy 2024-07-10T10:05:25,960 Downloading kssdtree-1.1.6.tar.gz (112 kB) 2024-07-10T10:05:26,155 Added kssdtree==1.1.6 from https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz to build tracker '/tmp/pip-build-tracker-2k8_3vtu' 2024-07-10T10:05:26,157 Running setup.py (path:/tmp/pip-wheel-vi2qxesh/kssdtree_935684a380a94d629b34b9fbe892681f/setup.py) egg_info for package kssdtree 2024-07-10T10:05:26,158 Created temporary directory: /tmp/pip-pip-egg-info-eaj52ji7 2024-07-10T10:05:26,158 Preparing metadata (setup.py): started 2024-07-10T10:05:26,159 Running command python setup.py egg_info 2024-07-10T10:05:27,261 running egg_info 2024-07-10T10:05:27,262 creating /tmp/pip-pip-egg-info-eaj52ji7/kssdtree.egg-info 2024-07-10T10:05:27,285 writing /tmp/pip-pip-egg-info-eaj52ji7/kssdtree.egg-info/PKG-INFO 2024-07-10T10:05:27,289 writing dependency_links to /tmp/pip-pip-egg-info-eaj52ji7/kssdtree.egg-info/dependency_links.txt 2024-07-10T10:05:27,291 writing requirements to /tmp/pip-pip-egg-info-eaj52ji7/kssdtree.egg-info/requires.txt 2024-07-10T10:05:27,292 writing top-level names to /tmp/pip-pip-egg-info-eaj52ji7/kssdtree.egg-info/top_level.txt 2024-07-10T10:05:27,293 writing manifest file '/tmp/pip-pip-egg-info-eaj52ji7/kssdtree.egg-info/SOURCES.txt' 2024-07-10T10:05:27,388 reading manifest file '/tmp/pip-pip-egg-info-eaj52ji7/kssdtree.egg-info/SOURCES.txt' 2024-07-10T10:05:27,390 reading manifest template 'MANIFEST.in' 2024-07-10T10:05:27,407 writing manifest file '/tmp/pip-pip-egg-info-eaj52ji7/kssdtree.egg-info/SOURCES.txt' 2024-07-10T10:05:27,504 Preparing metadata (setup.py): finished with status 'done' 2024-07-10T10:05:27,509 Source in /tmp/pip-wheel-vi2qxesh/kssdtree_935684a380a94d629b34b9fbe892681f has version 1.1.6, which satisfies requirement kssdtree==1.1.6 from https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz 2024-07-10T10:05:27,510 Removed kssdtree==1.1.6 from https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz from build tracker '/tmp/pip-build-tracker-2k8_3vtu' 2024-07-10T10:05:27,514 Created temporary directory: /tmp/pip-unpack-kg82fobo 2024-07-10T10:05:27,515 Created temporary directory: /tmp/pip-unpack-9m26sim3 2024-07-10T10:05:27,521 Building wheels for collected packages: kssdtree 2024-07-10T10:05:27,524 Created temporary directory: /tmp/pip-wheel-qzobj91w 2024-07-10T10:05:27,525 Building wheel for kssdtree (setup.py): started 2024-07-10T10:05:27,526 Destination directory: /tmp/pip-wheel-qzobj91w 2024-07-10T10:05:27,526 Running command python setup.py bdist_wheel 2024-07-10T10:05:28,604 running bdist_wheel 2024-07-10T10:05:28,698 running build 2024-07-10T10:05:28,698 running build_py 2024-07-10T10:05:28,724 creating build 2024-07-10T10:05:28,724 creating build/lib.linux-armv7l-cpython-39 2024-07-10T10:05:28,726 copying kssdtree.py -> build/lib.linux-armv7l-cpython-39 2024-07-10T10:05:28,729 copying toolutils.py -> build/lib.linux-armv7l-cpython-39 2024-07-10T10:05:28,731 running egg_info 2024-07-10T10:05:28,786 writing kssdtree.egg-info/PKG-INFO 2024-07-10T10:05:28,789 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-07-10T10:05:28,790 writing requirements to kssdtree.egg-info/requires.txt 2024-07-10T10:05:28,792 writing top-level names to kssdtree.egg-info/top_level.txt 2024-07-10T10:05:28,818 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-10T10:05:28,822 reading manifest template 'MANIFEST.in' 2024-07-10T10:05:28,839 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-10T10:05:28,841 running build_ext 2024-07-10T10:05:29,344 building 'kssd' extension 2024-07-10T10:05:29,345 creating build/temp.linux-armv7l-cpython-39 2024-07-10T10:05:29,346 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c co2mco.c -o build/temp.linux-armv7l-cpython-39/co2mco.o -fopenmp 2024-07-10T10:05:29,508 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-07-10T10:05:29,508 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T10:05:29,508 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-07-10T10:05:29,508 | ^ 2024-07-10T10:05:29,510 co2mco.c: In function ‘co2unitllmco’: 2024-07-10T10:05:29,511 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T10:05:29,511 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-07-10T10:05:29,511 | ^ 2024-07-10T10:05:30,132 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_composite.c -o build/temp.linux-armv7l-cpython-39/command_composite.o -fopenmp 2024-07-10T10:05:30,429 command_composite.c: In function ‘get_species_abundance’: 2024-07-10T10:05:30,429 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-10T10:05:30,429 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-07-10T10:05:30,430 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,430 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-10T10:05:30,430 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-07-10T10:05:30,430 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,430 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:30,430 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-10T10:05:30,430 | ^ 2024-07-10T10:05:30,431 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-10T10:05:30,431 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-10T10:05:30,431 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,431 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:30,431 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-10T10:05:30,431 | ^ 2024-07-10T10:05:30,431 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-10T10:05:30,432 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-10T10:05:30,432 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,432 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:30,432 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-10T10:05:30,432 | ^ 2024-07-10T10:05:30,432 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-10T10:05:30,432 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-10T10:05:30,433 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,433 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:30,433 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-10T10:05:30,433 | ^ 2024-07-10T10:05:30,433 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-07-10T10:05:30,433 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-10T10:05:30,433 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,433 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:30,434 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-10T10:05:30,434 | ^ 2024-07-10T10:05:30,434 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-07-10T10:05:30,434 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-10T10:05:30,434 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,668 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist.c -o build/temp.linux-armv7l-cpython-39/command_dist.o -fopenmp 2024-07-10T10:05:30,880 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-10T10:05:30,881 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=] 2024-07-10T10:05:30,881 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T10:05:30,882 | ~~^ 2024-07-10T10:05:30,882 | | 2024-07-10T10:05:30,882 | long unsigned int 2024-07-10T10:05:30,882 | %u 2024-07-10T10:05:30,882 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T10:05:30,882 | ~~~~~~~ 2024-07-10T10:05:30,882 | | 2024-07-10T10:05:30,882 | size_t {aka unsigned int} 2024-07-10T10:05:30,883 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=] 2024-07-10T10:05:30,883 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T10:05:30,883 | ~~^ 2024-07-10T10:05:30,883 | | 2024-07-10T10:05:30,883 | long unsigned int 2024-07-10T10:05:30,883 | %u 2024-07-10T10:05:30,883 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T10:05:30,883 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T10:05:30,883 | ~~~~~~~~~ 2024-07-10T10:05:30,884 | | 2024-07-10T10:05:30,884 | size_t {aka unsigned int} 2024-07-10T10:05:30,884 command_dist.c:678:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-10T10:05:30,884 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T10:05:30,884 | ~~^ 2024-07-10T10:05:30,884 | | 2024-07-10T10:05:30,884 | long unsigned int 2024-07-10T10:05:30,885 | %u 2024-07-10T10:05:30,885 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T10:05:30,885 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T10:05:30,885 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,885 | | 2024-07-10T10:05:30,885 | unsigned int 2024-07-10T10:05:30,886 command_dist.c:716:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-10T10:05:30,886 716 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-07-10T10:05:30,886 | ^ 2024-07-10T10:05:30,892 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-10T10:05:30,893 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=] 2024-07-10T10:05:30,894 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-10T10:05:30,894 | ~~^ ~~~~~~~ 2024-07-10T10:05:30,894 | | | 2024-07-10T10:05:30,894 | long unsigned int size_t {aka unsigned int} 2024-07-10T10:05:30,894 | %u 2024-07-10T10:05:30,895 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=] 2024-07-10T10:05:30,895 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-10T10:05:30,895 | ~~^ 2024-07-10T10:05:30,895 | | 2024-07-10T10:05:30,895 | long unsigned int 2024-07-10T10:05:30,895 | %u 2024-07-10T10:05:30,896 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-10T10:05:30,896 | ~~~~~~~~~ 2024-07-10T10:05:30,896 | | 2024-07-10T10:05:30,896 | size_t {aka unsigned int} 2024-07-10T10:05:30,896 command_dist.c:864:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-10T10:05:30,896 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-10T10:05:30,897 | ~~^ 2024-07-10T10:05:30,897 | | 2024-07-10T10:05:30,897 | long unsigned int 2024-07-10T10:05:30,897 | %u 2024-07-10T10:05:30,897 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-10T10:05:30,897 866 | (size_t) b * unitsz_distf_mapped); 2024-07-10T10:05:30,897 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,897 | | 2024-07-10T10:05:30,898 | unsigned int 2024-07-10T10:05:30,898 command_dist.c:811:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-07-10T10:05:30,899 811 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-07-10T10:05:30,899 | ^~~~~~~ 2024-07-10T10:05:30,899 command_dist.c:810:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-07-10T10:05:30,899 810 | struct stat cbd_fcode_stat; 2024-07-10T10:05:30,899 | ^~~~~~~~~~~~~~ 2024-07-10T10:05:30,899 command_dist.c:809:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-07-10T10:05:30,900 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-10T10:05:30,900 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,900 command_dist.c:809:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-07-10T10:05:30,900 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-10T10:05:30,900 | ^~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,905 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-10T10:05:30,907 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=] 2024-07-10T10:05:30,907 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T10:05:30,907 | ~~^ 2024-07-10T10:05:30,907 | | 2024-07-10T10:05:30,907 | long unsigned int 2024-07-10T10:05:30,908 | %u 2024-07-10T10:05:30,908 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T10:05:30,908 | ~~~~~~~ 2024-07-10T10:05:30,908 | | 2024-07-10T10:05:30,908 | size_t {aka unsigned int} 2024-07-10T10:05:30,909 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=] 2024-07-10T10:05:30,909 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T10:05:30,909 | ~~^ 2024-07-10T10:05:30,909 | | 2024-07-10T10:05:30,909 | long unsigned int 2024-07-10T10:05:30,909 | %u 2024-07-10T10:05:30,909 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T10:05:30,909 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T10:05:30,910 | ~~~~~~~~~ 2024-07-10T10:05:30,910 | | 2024-07-10T10:05:30,910 | size_t {aka unsigned int} 2024-07-10T10:05:30,910 command_dist.c:1019:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-10T10:05:30,910 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T10:05:30,911 | ~~^ 2024-07-10T10:05:30,911 | | 2024-07-10T10:05:30,911 | long unsigned int 2024-07-10T10:05:30,911 | %u 2024-07-10T10:05:30,911 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T10:05:30,911 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T10:05:30,911 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:30,911 | | 2024-07-10T10:05:30,912 | unsigned int 2024-07-10T10:05:30,912 command_dist.c:1035:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:30,912 1035 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-07-10T10:05:30,912 | ^ 2024-07-10T10:05:30,915 command_dist.c: In function ‘mco_co_dist_core’: 2024-07-10T10:05:30,916 command_dist.c:1117:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-10T10:05:30,916 1117 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-07-10T10:05:30,916 | ^ 2024-07-10T10:05:30,922 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-07-10T10:05:30,922 command_dist.c:1240:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:30,922 1240 | for (int rid = 0; rid < ref_num; rid++) 2024-07-10T10:05:30,923 | ^ 2024-07-10T10:05:30,924 command_dist.c:1246:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:30,924 1246 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-10T10:05:30,924 | ^ 2024-07-10T10:05:30,929 command_dist.c: In function ‘dist_print_nobin’: 2024-07-10T10:05:30,930 command_dist.c:1336:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:30,930 1336 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-07-10T10:05:30,930 | ^ 2024-07-10T10:05:30,932 command_dist.c:1357:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:30,932 1357 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-10T10:05:30,932 | ^ 2024-07-10T10:05:30,933 command_dist.c:1381:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:30,934 1381 | for (int rid = 0; rid < ref_num; rid++) 2024-07-10T10:05:30,934 | ^ 2024-07-10T10:05:30,934 command_dist.c:1383:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:30,934 1383 | for (int rid = 0; rid < ref_num; rid++) 2024-07-10T10:05:30,935 | ^ 2024-07-10T10:05:31,185 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-07-10T10:05:31,185 command_dist.c:404:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-07-10T10:05:31,185 404 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-07-10T10:05:31,185 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:31,186 command_dist.c:376:40: note: ‘com_abund_fp’ was declared here 2024-07-10T10:05:31,186 376 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-07-10T10:05:31,186 | ^~~~~~~~~~~~ 2024-07-10T10:05:31,907 command_dist.c: In function ‘get_dim_shuffle’: 2024-07-10T10:05:31,907 command_dist.c:268:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-07-10T10:05:31,907 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-10T10:05:31,907 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:31,907 command_dist.c:268:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-07-10T10:05:31,908 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-10T10:05:31,908 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:32,694 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-10T10:05:32,694 command_dist.c:597:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:32,694 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T10:05:32,694 | ^~ ~~~~~~~~~ 2024-07-10T10:05:32,695 command_dist.c:597:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-10T10:05:32,695 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T10:05:32,695 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:32,695 command_dist.c:626:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T10:05:32,695 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T10:05:32,695 | ^~~~~~~~~~~~~~~ 2024-07-10T10:05:32,696 command_dist.c:626:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-10T10:05:32,696 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T10:05:32,696 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:32,697 command_dist.c:682:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T10:05:32,697 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T10:05:32,697 | ^~~~~~~~~~~ 2024-07-10T10:05:32,697 command_dist.c:682:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-10T10:05:32,698 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T10:05:32,698 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:32,698 command_dist.c:683:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T10:05:32,698 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T10:05:32,698 | ^~~~~ 2024-07-10T10:05:32,698 command_dist.c:683:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T10:05:32,698 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T10:05:32,699 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:32,903 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-10T10:05:32,904 command_dist.c:764:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:32,904 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T10:05:32,904 | ^~ ~~~~~~~~~ 2024-07-10T10:05:32,905 command_dist.c:764:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-10T10:05:32,905 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T10:05:32,905 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:32,905 command_dist.c:791:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T10:05:32,905 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T10:05:32,906 | ^~~~~~~~~~~~~~~ 2024-07-10T10:05:32,906 command_dist.c:791:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-10T10:05:32,906 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T10:05:32,906 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:32,907 command_dist.c:824:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T10:05:32,907 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T10:05:32,907 | ^~~~~~~~~~~~~ 2024-07-10T10:05:32,907 command_dist.c:824:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-10T10:05:32,907 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T10:05:32,907 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:32,908 command_dist.c:850:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:32,908 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-10T10:05:32,909 | ^ 2024-07-10T10:05:32,909 command_dist.c:850:33: note: directive argument in the range [0, 536870912] 2024-07-10T10:05:32,909 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-10T10:05:32,909 | ^~~~~~~~~~ 2024-07-10T10:05:32,909 command_dist.c:850:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-10T10:05:32,910 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-10T10:05:32,910 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:32,910 command_dist.c:852:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:32,910 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-10T10:05:32,910 | ^ 2024-07-10T10:05:32,911 command_dist.c:852:28: note: directive argument in the range [0, 536870912] 2024-07-10T10:05:32,911 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-10T10:05:32,911 | ^~~~~~~~~~ 2024-07-10T10:05:32,911 command_dist.c:852:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-10T10:05:32,911 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-10T10:05:32,911 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:33,151 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-10T10:05:33,152 command_dist.c:928:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:33,152 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T10:05:33,152 | ^~ ~~~~~~~~~ 2024-07-10T10:05:33,152 command_dist.c:928:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-10T10:05:33,153 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T10:05:33,153 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:33,153 command_dist.c:957:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T10:05:33,154 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T10:05:33,154 | ^~~~~~~~~~~~~~~ 2024-07-10T10:05:33,154 command_dist.c:957:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-10T10:05:33,154 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T10:05:33,154 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:33,155 command_dist.c:991:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T10:05:33,155 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T10:05:33,155 | ^~~~~~~~~~~~~ 2024-07-10T10:05:33,156 command_dist.c:991:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-10T10:05:33,156 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T10:05:33,156 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:33,157 command_dist.c:1023:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T10:05:33,157 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T10:05:33,157 | ^~~~~~~~~~~ 2024-07-10T10:05:33,158 command_dist.c:1023:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-10T10:05:33,158 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T10:05:33,158 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:33,159 command_dist.c:1024:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T10:05:33,159 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T10:05:33,159 | ^~~~~ 2024-07-10T10:05:33,159 command_dist.c:1024:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T10:05:33,159 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T10:05:33,159 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:33,410 command_dist.c: In function ‘combine_queries’: 2024-07-10T10:05:33,411 command_dist.c:1493:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T10:05:33,411 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-10T10:05:33,411 | ^ 2024-07-10T10:05:33,412 command_dist.c:1493:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T10:05:33,412 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-10T10:05:33,412 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:33,413 command_dist.c:1500:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T10:05:33,413 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-10T10:05:33,413 | ^ 2024-07-10T10:05:33,414 command_dist.c:1500:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T10:05:33,414 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-10T10:05:33,414 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:33,416 command_dist.c:1604:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:33,417 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-10T10:05:33,417 | ^~ ~~~~~~~~ 2024-07-10T10:05:33,417 command_dist.c:1604:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-10T10:05:33,418 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-10T10:05:33,418 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:33,894 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o -fopenmp 2024-07-10T10:05:34,060 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_set.c -o build/temp.linux-armv7l-cpython-39/command_set.o -fopenmp 2024-07-10T10:05:34,204 command_set.c: In function ‘sketch_operate’: 2024-07-10T10:05:34,204 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-10T10:05:34,204 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-07-10T10:05:34,205 | ^ 2024-07-10T10:05:34,214 command_set.c: In function ‘combin_subset_pans’: 2024-07-10T10:05:34,215 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-10T10:05:34,215 458 | free(co_dstat_fpath); 2024-07-10T10:05:34,215 | ^~~~~~~~~~~~~~ 2024-07-10T10:05:34,215 In file included from kssdheaders/global_basic.h:159, 2024-07-10T10:05:34,215 from command_set.c:15: 2024-07-10T10:05:34,215 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-10T10:05:34,216 565 | extern void free (void *__ptr) __THROW; 2024-07-10T10:05:34,216 | ~~~~~~^~~~~ 2024-07-10T10:05:34,220 command_set.c: In function ‘grouping_genomes’: 2024-07-10T10:05:34,220 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-10T10:05:34,220 563 | free(co_dstat_fpath); 2024-07-10T10:05:34,220 | ^~~~~~~~~~~~~~ 2024-07-10T10:05:34,220 In file included from kssdheaders/global_basic.h:159, 2024-07-10T10:05:34,220 from command_set.c:15: 2024-07-10T10:05:34,221 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-10T10:05:34,221 565 | extern void free (void *__ptr) __THROW; 2024-07-10T10:05:34,221 | ~~~~~~^~~~~ 2024-07-10T10:05:34,336 command_set.c: In function ‘sketch_union’: 2024-07-10T10:05:34,336 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T10:05:34,336 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:34,336 | ^ 2024-07-10T10:05:34,337 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T10:05:34,337 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:34,337 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,337 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,337 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T10:05:34,337 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:34,337 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T10:05:34,338 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T10:05:34,338 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,338 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,338 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-10T10:05:34,338 | ^~ ~~~~~~~~~~ 2024-07-10T10:05:34,338 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T10:05:34,338 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-10T10:05:34,338 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,449 command_set.c: In function ‘sketch_operate’: 2024-07-10T10:05:34,450 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,450 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-10T10:05:34,450 | ^~ ~~~~~~~~~~ 2024-07-10T10:05:34,450 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T10:05:34,450 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-10T10:05:34,450 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,450 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,450 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-10T10:05:34,451 | ^~ ~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,451 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-10T10:05:34,451 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-10T10:05:34,451 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,451 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,451 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T10:05:34,451 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:34,451 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T10:05:34,452 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T10:05:34,452 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,452 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,452 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T10:05:34,452 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:34,452 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T10:05:34,452 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T10:05:34,452 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,453 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,453 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T10:05:34,453 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:34,453 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T10:05:34,453 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T10:05:34,453 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,453 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,453 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T10:05:34,454 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:34,454 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T10:05:34,454 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T10:05:34,454 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,454 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T10:05:34,454 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:34,454 | ^ 2024-07-10T10:05:34,455 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T10:05:34,455 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:34,455 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,602 command_set.c: In function ‘uniq_sketch_union’: 2024-07-10T10:05:34,603 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T10:05:34,603 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:34,603 | ^ 2024-07-10T10:05:34,603 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T10:05:34,603 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:34,603 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,604 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,604 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T10:05:34,604 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:34,604 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T10:05:34,604 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T10:05:34,604 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,604 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,605 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-10T10:05:34,605 | ^~ ~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,605 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-10T10:05:34,605 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-10T10:05:34,605 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,729 command_set.c: In function ‘combin_pans’: 2024-07-10T10:05:34,729 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,729 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T10:05:34,729 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:34,729 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-07-10T10:05:34,729 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T10:05:34,730 | ^~~~~~~~~~ 2024-07-10T10:05:34,730 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-07-10T10:05:34,730 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T10:05:34,730 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,730 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,730 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T10:05:34,730 | ^~ ~~~~~~~~~~ 2024-07-10T10:05:34,730 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-07-10T10:05:34,731 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T10:05:34,731 | ^~~~~~~~~~ 2024-07-10T10:05:34,731 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-07-10T10:05:34,731 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T10:05:34,731 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,731 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T10:05:34,731 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:34,731 | ^ 2024-07-10T10:05:34,732 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T10:05:34,732 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:34,732 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,914 command_set.c: In function ‘combin_subset_pans’: 2024-07-10T10:05:34,914 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,914 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T10:05:34,914 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:34,915 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T10:05:34,915 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T10:05:34,915 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,915 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,915 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T10:05:34,915 | ^~ ~~~~~~~~~~ 2024-07-10T10:05:34,915 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T10:05:34,916 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T10:05:34,916 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,916 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,916 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T10:05:34,916 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:34,916 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T10:05:34,917 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T10:05:34,917 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,918 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:34,918 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T10:05:34,918 | ^~ ~~~~~~~~~~ 2024-07-10T10:05:34,918 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T10:05:34,919 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T10:05:34,919 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:34,919 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T10:05:34,919 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:34,919 | ^ 2024-07-10T10:05:34,919 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T10:05:34,919 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:34,919 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:35,121 command_set.c: In function ‘grouping_genomes’: 2024-07-10T10:05:35,122 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:35,122 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T10:05:35,122 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:35,122 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T10:05:35,122 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T10:05:35,122 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:35,123 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:35,123 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T10:05:35,123 | ^~ ~~~~~~~~~~ 2024-07-10T10:05:35,123 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T10:05:35,123 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T10:05:35,123 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:35,125 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:35,125 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T10:05:35,125 | ^~ ~~~~~~~~~~~ 2024-07-10T10:05:35,125 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T10:05:35,126 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T10:05:35,126 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:35,126 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T10:05:35,127 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T10:05:35,127 | ^~ ~~~~~~~~~~ 2024-07-10T10:05:35,127 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T10:05:35,127 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T10:05:35,127 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:35,128 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T10:05:35,128 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:35,128 | ^ 2024-07-10T10:05:35,128 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T10:05:35,128 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T10:05:35,128 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:35,397 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-39/command_shuffle.o -fopenmp 2024-07-10T10:05:35,677 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c global_basic.c -o build/temp.linux-armv7l-cpython-39/global_basic.o -fopenmp 2024-07-10T10:05:35,824 global_basic.c: In function ‘organize_infile_list’: 2024-07-10T10:05:35,825 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-07-10T10:05:35,825 195 | while (isspace(*buf)) buf++; 2024-07-10T10:05:35,825 | ^~~~~~~ 2024-07-10T10:05:35,825 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=] 2024-07-10T10:05:35,825 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-10T10:05:35,825 | ~~^ 2024-07-10T10:05:35,826 | | 2024-07-10T10:05:35,826 | long unsigned int 2024-07-10T10:05:35,826 | %u 2024-07-10T10:05:35,826 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-10T10:05:35,826 | ~~~~~~~~~~~ 2024-07-10T10:05:35,826 | | 2024-07-10T10:05:35,826 | size_t {aka unsigned int} 2024-07-10T10:05:35,827 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=] 2024-07-10T10:05:35,827 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-10T10:05:35,827 | ~~^ 2024-07-10T10:05:35,827 | | 2024-07-10T10:05:35,827 | long unsigned int 2024-07-10T10:05:35,827 | %u 2024-07-10T10:05:35,827 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-10T10:05:35,828 | ~~~~~~~~~~~ 2024-07-10T10:05:35,828 | | 2024-07-10T10:05:35,828 | size_t {aka unsigned int} 2024-07-10T10:05:36,498 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-39/iseq2comem.o -fopenmp 2024-07-10T10:05:36,649 iseq2comem.c: In function ‘reads2mco’: 2024-07-10T10:05:36,649 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,649 156 | if (base > TL) { 2024-07-10T10:05:36,649 | ^ 2024-07-10T10:05:36,649 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,650 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T10:05:36,650 | ^~ 2024-07-10T10:05:36,650 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,650 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T10:05:36,650 | ^ 2024-07-10T10:05:36,651 iseq2comem.c: In function ‘fasta2co’: 2024-07-10T10:05:36,651 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,651 239 | if (base > TL) { 2024-07-10T10:05:36,652 | ^ 2024-07-10T10:05:36,652 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,652 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T10:05:36,652 | ^~ 2024-07-10T10:05:36,652 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,652 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T10:05:36,653 | ^ 2024-07-10T10:05:36,653 iseq2comem.c: In function ‘fastq2co’: 2024-07-10T10:05:36,653 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-07-10T10:05:36,653 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-07-10T10:05:36,653 | ^~ 2024-07-10T10:05:36,654 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,654 318 | if (base > TL) { 2024-07-10T10:05:36,654 | ^ 2024-07-10T10:05:36,654 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,655 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T10:05:36,655 | ^~ 2024-07-10T10:05:36,655 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,655 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T10:05:36,655 | ^ 2024-07-10T10:05:36,655 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,655 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-07-10T10:05:36,656 | ^ 2024-07-10T10:05:36,657 iseq2comem.c: In function ‘fastq2koc’: 2024-07-10T10:05:36,657 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,657 402 | if (base > TL) { 2024-07-10T10:05:36,657 | ^ 2024-07-10T10:05:36,657 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,658 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T10:05:36,658 | ^~ 2024-07-10T10:05:36,658 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,658 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T10:05:36,658 | ^ 2024-07-10T10:05:36,663 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-07-10T10:05:36,663 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,663 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T10:05:36,664 | ^~ 2024-07-10T10:05:36,664 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:36,664 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T10:05:36,664 | ^ 2024-07-10T10:05:37,825 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-07-10T10:05:37,888 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mytime.c -o build/temp.linux-armv7l-cpython-39/mytime.o -fopenmp 2024-07-10T10:05:38,013 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c pykssd.c -o build/temp.linux-armv7l-cpython-39/pykssd.o -fopenmp 2024-07-10T10:05:38,321 pykssd.c: In function ‘py_dist_dispatch’: 2024-07-10T10:05:38,321 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-07-10T10:05:38,321 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-07-10T10:05:38,322 | ^~~~~~ 2024-07-10T10:05:38,322 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-07-10T10:05:38,322 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-07-10T10:05:38,322 | ^~~~~~ 2024-07-10T10:05:38,323 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-07-10T10:05:38,323 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-07-10T10:05:38,323 | ^~~~~~ 2024-07-10T10:05:38,461 pykssd.c: In function ‘rename_file’: 2024-07-10T10:05:38,461 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-07-10T10:05:38,461 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-07-10T10:05:38,461 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T10:05:38,461 pykssd.c:41:15: note: length computed here 2024-07-10T10:05:38,462 41 | int len = strlen(p1); 2024-07-10T10:05:38,462 | ^~~~~~~~~~ 2024-07-10T10:05:38,823 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/co2mco.o build/temp.linux-armv7l-cpython-39/command_composite.o build/temp.linux-armv7l-cpython-39/command_dist.o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o build/temp.linux-armv7l-cpython-39/command_set.o build/temp.linux-armv7l-cpython-39/command_shuffle.o build/temp.linux-armv7l-cpython-39/global_basic.o build/temp.linux-armv7l-cpython-39/iseq2comem.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/mytime.o build/temp.linux-armv7l-cpython-39/pykssd.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-07-10T10:05:38,973 building 'nj' extension 2024-07-10T10:05:38,974 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c align.c -o build/temp.linux-armv7l-cpython-39/align.o 2024-07-10T10:05:39,385 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c buildtree.c -o build/temp.linux-armv7l-cpython-39/buildtree.o 2024-07-10T10:05:39,511 buildtree.c: In function ‘UPGMA_buildtree’: 2024-07-10T10:05:39,512 buildtree.c:716:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:39,512 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-10T10:05:39,512 | ^~ 2024-07-10T10:05:39,513 buildtree.c:716:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:39,513 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-10T10:05:39,513 | ^~ 2024-07-10T10:05:40,076 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c cluster.c -o build/temp.linux-armv7l-cpython-39/cluster.o 2024-07-10T10:05:40,400 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c distancemat.c -o build/temp.linux-armv7l-cpython-39/distancemat.o 2024-07-10T10:05:40,518 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-07-10T10:05:40,518 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T10:05:40,519 226 | for( i=0; i < dest->size; i++) { 2024-07-10T10:05:40,519 | ^ 2024-07-10T10:05:40,519 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-07-10T10:05:40,519 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T10:05:40,519 260 | for( i=0; i < mat->size; i++) { 2024-07-10T10:05:40,519 | ^ 2024-07-10T10:05:40,519 distancemat.c: In function ‘print_DistanceMatrix’: 2024-07-10T10:05:40,520 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T10:05:40,520 349 | for(row=0; row < mat->size; row++) { 2024-07-10T10:05:40,520 | ^ 2024-07-10T10:05:40,520 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-07-10T10:05:40,520 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-07-10T10:05:40,521 410 | while(c = fgetc(handle)) { 2024-07-10T10:05:40,521 | ^ 2024-07-10T10:05:40,856 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c pynj.c -o build/temp.linux-armv7l-cpython-39/pynj.o 2024-07-10T10:05:41,225 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c sequence.c -o build/temp.linux-armv7l-cpython-39/sequence.o 2024-07-10T10:05:41,417 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c tree.c -o build/temp.linux-armv7l-cpython-39/tree.o 2024-07-10T10:05:42,147 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c util.c -o build/temp.linux-armv7l-cpython-39/util.o 2024-07-10T10:05:42,314 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/align.o build/temp.linux-armv7l-cpython-39/buildtree.o build/temp.linux-armv7l-cpython-39/cluster.o build/temp.linux-armv7l-cpython-39/distancemat.o build/temp.linux-armv7l-cpython-39/pynj.o build/temp.linux-armv7l-cpython-39/sequence.o build/temp.linux-armv7l-cpython-39/tree.o build/temp.linux-armv7l-cpython-39/util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so 2024-07-10T10:05:42,428 building 'dnj' extension 2024-07-10T10:05:42,429 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c bytescale.c -o build/temp.linux-armv7l-cpython-39/bytescale.o -fopenmp 2024-07-10T10:05:42,495 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c dnj.c -o build/temp.linux-armv7l-cpython-39/dnj.o -fopenmp 2024-07-10T10:05:42,615 dnj.c: In function ‘minQpair’: 2024-07-10T10:05:42,616 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,616 70 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,616 | ^~~ 2024-07-10T10:05:42,618 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,618 126 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,618 | ^~~ 2024-07-10T10:05:42,619 dnj.c: In function ‘maxQpair’: 2024-07-10T10:05:42,619 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,619 157 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,619 | ^~~ 2024-07-10T10:05:42,620 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,620 213 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,621 | ^~~ 2024-07-10T10:05:42,621 dnj.c: In function ‘UPGMApair’: 2024-07-10T10:05:42,622 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,622 237 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,622 | ^~~ 2024-07-10T10:05:42,623 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,623 284 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,623 | ^~~ 2024-07-10T10:05:42,624 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,624 291 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,624 | ^~~ 2024-07-10T10:05:42,625 dnj.c: In function ‘minQrow’: 2024-07-10T10:05:42,626 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,626 374 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,626 | ^~~ 2024-07-10T10:05:42,628 dnj.c: In function ‘maxQrow’: 2024-07-10T10:05:42,628 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,628 435 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,628 | ^~~ 2024-07-10T10:05:42,629 dnj.c: In function ‘UPGMArow’: 2024-07-10T10:05:42,630 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,630 488 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,630 | ^~~ 2024-07-10T10:05:42,631 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,631 494 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,631 | ^~~ 2024-07-10T10:05:42,632 dnj.c: In function ‘minQ_thread’: 2024-07-10T10:05:42,633 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:42,633 553 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:42,633 | ^~~ 2024-07-10T10:05:43,800 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c filebuff.c -o build/temp.linux-armv7l-cpython-39/filebuff.o -fopenmp 2024-07-10T10:05:43,906 filebuff.c: In function ‘BuffgzFileBuff’: 2024-07-10T10:05:43,906 filebuff.c:99:47: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:43,907 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-07-10T10:05:43,907 | ^~ 2024-07-10T10:05:44,190 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c hclust.c -o build/temp.linux-armv7l-cpython-39/hclust.o -fopenmp 2024-07-10T10:05:44,309 hclust.c: In function ‘minQ’: 2024-07-10T10:05:44,309 hclust.c:364:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:44,309 364 | while(++i < Q->n) { 2024-07-10T10:05:44,309 | ^ 2024-07-10T10:05:44,310 hclust.c:377:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:44,310 377 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:44,310 | ^~~ 2024-07-10T10:05:44,310 hclust.c: In function ‘maxQ’: 2024-07-10T10:05:44,311 hclust.c:394:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T10:05:44,311 394 | while(++i < Q->n) { 2024-07-10T10:05:44,311 | ^ 2024-07-10T10:05:44,312 hclust.c:407:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:44,312 407 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:44,312 | ^~~ 2024-07-10T10:05:46,351 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c matrix.c -o build/temp.linux-armv7l-cpython-39/matrix.o -fopenmp 2024-07-10T10:05:46,468 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-07-10T10:05:46,469 matrix.c:538:9: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T10:05:46,469 538 | if(pos != n) { 2024-07-10T10:05:46,469 | ^~ 2024-07-10T10:05:47,246 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-07-10T10:05:47,308 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c nj.c -o build/temp.linux-armv7l-cpython-39/nj.o -fopenmp 2024-07-10T10:05:47,423 nj.c: In function ‘initQ’: 2024-07-10T10:05:47,424 nj.c:243:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:47,424 243 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:47,424 | ^~~ 2024-07-10T10:05:47,425 nj.c: In function ‘initQ_MN’: 2024-07-10T10:05:47,425 nj.c:358:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:47,425 358 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:47,426 | ^~~ 2024-07-10T10:05:47,429 nj.c: In function ‘minD’: 2024-07-10T10:05:47,429 nj.c:559:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:47,429 559 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:47,429 | ^~~ 2024-07-10T10:05:47,431 nj.c: In function ‘maxD’: 2024-07-10T10:05:47,431 nj.c:642:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:47,431 642 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:47,431 | ^~~ 2024-07-10T10:05:47,434 nj.c: In function ‘minPair’: 2024-07-10T10:05:47,434 nj.c:826:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T10:05:47,435 826 | pos <<= sizeof(unsigned) * 8; 2024-07-10T10:05:47,435 | ^~~ 2024-07-10T10:05:49,447 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c nwck.c -o build/temp.linux-armv7l-cpython-39/nwck.o -fopenmp 2024-07-10T10:05:49,916 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pherror.c -o build/temp.linux-armv7l-cpython-39/pherror.o -fopenmp 2024-07-10T10:05:50,005 pherror.c: In function ‘cfread’: 2024-07-10T10:05:50,005 pherror.c:58:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T10:05:50,005 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-07-10T10:05:50,005 | ^~ 2024-07-10T10:05:50,097 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c phy.c -o build/temp.linux-armv7l-cpython-39/phy.o -fopenmp 2024-07-10T10:05:51,017 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pydnj.c -o build/temp.linux-armv7l-cpython-39/pydnj.o -fopenmp 2024-07-10T10:05:51,319 In file included from pydnj.c:11: 2024-07-10T10:05:51,319 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-07-10T10:05:51,319 20 | #define _XOPEN_SOURCE 600 2024-07-10T10:05:51,319 | 2024-07-10T10:05:51,320 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-07-10T10:05:51,320 from /usr/include/limits.h:26, 2024-07-10T10:05:51,320 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:195, 2024-07-10T10:05:51,320 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/syslimits.h:7, 2024-07-10T10:05:51,320 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:34, 2024-07-10T10:05:51,320 from /usr/include/python3.9/Python.h:11, 2024-07-10T10:05:51,321 from pydnj.c:1: 2024-07-10T10:05:51,321 /usr/include/features.h:207: note: this is the location of the previous definition 2024-07-10T10:05:51,321 207 | # define _XOPEN_SOURCE 700 2024-07-10T10:05:51,321 | 2024-07-10T10:05:51,335 pydnj.c: In function ‘py_build’: 2024-07-10T10:05:51,336 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-07-10T10:05:51,336 165 | p = omp_get_num_procs(); 2024-07-10T10:05:51,336 | ^~~~~~~~~~~~~~~~~ 2024-07-10T10:05:51,519 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c qseqs.c -o build/temp.linux-armv7l-cpython-39/qseqs.o -fopenmp 2024-07-10T10:05:51,706 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c str.c -o build/temp.linux-armv7l-cpython-39/str.o -fopenmp 2024-07-10T10:05:51,816 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c tmp.c -o build/temp.linux-armv7l-cpython-39/tmp.o -fopenmp 2024-07-10T10:05:52,000 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c vector.c -o build/temp.linux-armv7l-cpython-39/vector.o -fopenmp 2024-07-10T10:05:52,155 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/bytescale.o build/temp.linux-armv7l-cpython-39/dnj.o build/temp.linux-armv7l-cpython-39/filebuff.o build/temp.linux-armv7l-cpython-39/hclust.o build/temp.linux-armv7l-cpython-39/matrix.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/nj.o build/temp.linux-armv7l-cpython-39/nwck.o build/temp.linux-armv7l-cpython-39/pherror.o build/temp.linux-armv7l-cpython-39/phy.o build/temp.linux-armv7l-cpython-39/pydnj.o build/temp.linux-armv7l-cpython-39/qseqs.o build/temp.linux-armv7l-cpython-39/str.o build/temp.linux-armv7l-cpython-39/tmp.o build/temp.linux-armv7l-cpython-39/vector.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-07-10T10:05:52,328 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-07-10T10:05:52,329 !! 2024-07-10T10:05:52,329 ******************************************************************************** 2024-07-10T10:05:52,329 Please avoid running ``setup.py`` directly. 2024-07-10T10:05:52,329 Instead, use pypa/build, pypa/installer or other 2024-07-10T10:05:52,329 standards-based tools. 2024-07-10T10:05:52,329 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-07-10T10:05:52,330 ******************************************************************************** 2024-07-10T10:05:52,330 !! 2024-07-10T10:05:52,330 self.initialize_options() 2024-07-10T10:05:52,352 installing to build/bdist.linux-armv7l/wheel 2024-07-10T10:05:52,352 running install 2024-07-10T10:05:52,378 running install_lib 2024-07-10T10:05:52,402 creating build/bdist.linux-armv7l 2024-07-10T10:05:52,403 creating build/bdist.linux-armv7l/wheel 2024-07-10T10:05:52,404 copying build/lib.linux-armv7l-cpython-39/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-07-10T10:05:52,406 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-10T10:05:52,414 copying build/lib.linux-armv7l-cpython-39/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-07-10T10:05:52,417 copying build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-10T10:05:52,424 copying build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-10T10:05:52,428 running install_egg_info 2024-07-10T10:05:52,457 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-1.1.6-py3.9.egg-info 2024-07-10T10:05:52,468 running install_scripts 2024-07-10T10:05:52,488 creating build/bdist.linux-armv7l/wheel/kssdtree-1.1.6.dist-info/WHEEL 2024-07-10T10:05:52,491 creating '/tmp/pip-wheel-qzobj91w/kssdtree-1.1.6-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-07-10T10:05:52,596 adding 'dnj.cpython-39-arm-linux-gnueabihf.so' 2024-07-10T10:05:52,692 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2024-07-10T10:05:52,697 adding 'kssdtree.py' 2024-07-10T10:05:52,719 adding 'nj.cpython-39-arm-linux-gnueabihf.so' 2024-07-10T10:05:52,722 adding 'toolutils.py' 2024-07-10T10:05:52,724 adding 'kssdtree-1.1.6.dist-info/METADATA' 2024-07-10T10:05:52,725 adding 'kssdtree-1.1.6.dist-info/WHEEL' 2024-07-10T10:05:52,726 adding 'kssdtree-1.1.6.dist-info/dependency_links.txt' 2024-07-10T10:05:52,727 adding 'kssdtree-1.1.6.dist-info/top_level.txt' 2024-07-10T10:05:52,728 adding 'kssdtree-1.1.6.dist-info/RECORD' 2024-07-10T10:05:52,734 removing build/bdist.linux-armv7l/wheel 2024-07-10T10:05:52,873 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-07-10T10:05:52,880 Created wheel for kssdtree: filename=kssdtree-1.1.6-cp39-cp39-linux_armv7l.whl size=375684 sha256=9defb70b5162efc2c0eb6e415a7e37c604aa9b248a006af86af8f59a3bce5d2b 2024-07-10T10:05:52,881 Stored in directory: /tmp/pip-ephem-wheel-cache-sbf2h8yh/wheels/97/18/a8/b13948d17ba0cb10cec968616a36e8856760187c532c24b762 2024-07-10T10:05:52,891 Successfully built kssdtree 2024-07-10T10:05:52,903 Removed build tracker: '/tmp/pip-build-tracker-2k8_3vtu'