2024-05-23T08:28:12,886 Created temporary directory: /tmp/pip-build-tracker-hrwdy_84 2024-05-23T08:28:12,888 Initialized build tracking at /tmp/pip-build-tracker-hrwdy_84 2024-05-23T08:28:12,888 Created build tracker: /tmp/pip-build-tracker-hrwdy_84 2024-05-23T08:28:12,889 Entered build tracker: /tmp/pip-build-tracker-hrwdy_84 2024-05-23T08:28:12,890 Created temporary directory: /tmp/pip-wheel-8pfq0xem 2024-05-23T08:28:12,893 Created temporary directory: /tmp/pip-ephem-wheel-cache-brvmj7dy 2024-05-23T08:28:12,916 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-05-23T08:28:12,920 2 location(s) to search for versions of kssdtree: 2024-05-23T08:28:12,920 * https://pypi.org/simple/kssdtree/ 2024-05-23T08:28:12,920 * https://www.piwheels.org/simple/kssdtree/ 2024-05-23T08:28:12,921 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-05-23T08:28:12,922 Getting page https://pypi.org/simple/kssdtree/ 2024-05-23T08:28:12,924 Found index url https://pypi.org/simple/ 2024-05-23T08:28:13,146 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-05-23T08:28:13,148 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 2024-05-23T08:28:13,149 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 2024-05-23T08:28:13,150 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 2024-05-23T08:28:13,150 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 2024-05-23T08:28:13,151 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-05-23T08:28:13,152 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-05-23T08:28:13,153 Found index url https://www.piwheels.org/simple/ 2024-05-23T08:28:13,524 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-05-23T08:28:13,533 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/) 2024-05-23T08:28:13,534 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/) 2024-05-23T08:28:13,534 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/) 2024-05-23T08:28:13,535 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/) 2024-05-23T08:28:13,536 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/) 2024-05-23T08:28:13,537 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/) 2024-05-23T08:28:13,537 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/) 2024-05-23T08:28:13,538 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/) 2024-05-23T08:28:13,539 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/) 2024-05-23T08:28:13,540 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/) 2024-05-23T08:28:13,540 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/) 2024-05-23T08:28:13,541 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/) 2024-05-23T08:28:13,542 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/) 2024-05-23T08:28:13,542 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/) 2024-05-23T08:28:13,543 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/) 2024-05-23T08:28:13,544 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/) 2024-05-23T08:28:13,544 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/) 2024-05-23T08:28:13,545 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/) 2024-05-23T08:28:13,546 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-05-23T08:28:13,547 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-05-23T08:28:13,574 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-05-23T08:28:13,600 Collecting kssdtree==1.1.4 2024-05-23T08:28:13,603 Created temporary directory: /tmp/pip-unpack-z8m59tvn 2024-05-23T08:28:13,840 Downloading kssdtree-1.1.4.tar.gz (113 kB) 2024-05-23T08:28:14,097 Added kssdtree==1.1.4 from https://files.pythonhosted.org/packages/20/ea/b0301924e3f7d367cbb7b8da66837dba9af2a332bf56ed35e03a33faee76/kssdtree-1.1.4.tar.gz to build tracker '/tmp/pip-build-tracker-hrwdy_84' 2024-05-23T08:28:14,098 Running setup.py (path:/tmp/pip-wheel-8pfq0xem/kssdtree_9f6f60e22fd142d9a6f423e0b7898715/setup.py) egg_info for package kssdtree 2024-05-23T08:28:14,099 Created temporary directory: /tmp/pip-pip-egg-info-43hp28fl 2024-05-23T08:28:14,100 Preparing metadata (setup.py): started 2024-05-23T08:28:14,102 Running command python setup.py egg_info 2024-05-23T08:28:15,212 running egg_info 2024-05-23T08:28:15,214 creating /tmp/pip-pip-egg-info-43hp28fl/kssdtree.egg-info 2024-05-23T08:28:15,239 writing /tmp/pip-pip-egg-info-43hp28fl/kssdtree.egg-info/PKG-INFO 2024-05-23T08:28:15,242 writing dependency_links to /tmp/pip-pip-egg-info-43hp28fl/kssdtree.egg-info/dependency_links.txt 2024-05-23T08:28:15,244 writing requirements to /tmp/pip-pip-egg-info-43hp28fl/kssdtree.egg-info/requires.txt 2024-05-23T08:28:15,246 writing top-level names to /tmp/pip-pip-egg-info-43hp28fl/kssdtree.egg-info/top_level.txt 2024-05-23T08:28:15,247 writing manifest file '/tmp/pip-pip-egg-info-43hp28fl/kssdtree.egg-info/SOURCES.txt' 2024-05-23T08:28:15,349 reading manifest file '/tmp/pip-pip-egg-info-43hp28fl/kssdtree.egg-info/SOURCES.txt' 2024-05-23T08:28:15,351 reading manifest template 'MANIFEST.in' 2024-05-23T08:28:15,367 writing manifest file '/tmp/pip-pip-egg-info-43hp28fl/kssdtree.egg-info/SOURCES.txt' 2024-05-23T08:28:15,485 Preparing metadata (setup.py): finished with status 'done' 2024-05-23T08:28:15,489 Source in /tmp/pip-wheel-8pfq0xem/kssdtree_9f6f60e22fd142d9a6f423e0b7898715 has version 1.1.4, which satisfies requirement kssdtree==1.1.4 from https://files.pythonhosted.org/packages/20/ea/b0301924e3f7d367cbb7b8da66837dba9af2a332bf56ed35e03a33faee76/kssdtree-1.1.4.tar.gz 2024-05-23T08:28:15,490 Removed kssdtree==1.1.4 from https://files.pythonhosted.org/packages/20/ea/b0301924e3f7d367cbb7b8da66837dba9af2a332bf56ed35e03a33faee76/kssdtree-1.1.4.tar.gz from build tracker '/tmp/pip-build-tracker-hrwdy_84' 2024-05-23T08:28:15,494 Created temporary directory: /tmp/pip-unpack-dhs7znz1 2024-05-23T08:28:15,495 Created temporary directory: /tmp/pip-unpack-m2hqc1ik 2024-05-23T08:28:15,500 Building wheels for collected packages: kssdtree 2024-05-23T08:28:15,504 Created temporary directory: /tmp/pip-wheel-g9iwuoht 2024-05-23T08:28:15,505 Building wheel for kssdtree (setup.py): started 2024-05-23T08:28:15,507 Destination directory: /tmp/pip-wheel-g9iwuoht 2024-05-23T08:28:15,507 Running command python setup.py bdist_wheel 2024-05-23T08:28:16,585 running bdist_wheel 2024-05-23T08:28:16,683 running build 2024-05-23T08:28:16,683 running build_py 2024-05-23T08:28:16,710 creating build 2024-05-23T08:28:16,711 creating build/lib.linux-armv7l-cpython-311 2024-05-23T08:28:16,712 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2024-05-23T08:28:16,715 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2024-05-23T08:28:16,718 running egg_info 2024-05-23T08:28:16,775 writing kssdtree.egg-info/PKG-INFO 2024-05-23T08:28:16,779 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-05-23T08:28:16,780 writing requirements to kssdtree.egg-info/requires.txt 2024-05-23T08:28:16,782 writing top-level names to kssdtree.egg-info/top_level.txt 2024-05-23T08:28:16,814 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-05-23T08:28:16,817 reading manifest template 'MANIFEST.in' 2024-05-23T08:28:16,834 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-05-23T08:28:16,836 running build_ext 2024-05-23T08:28:17,411 building 'kssd' extension 2024-05-23T08:28:17,412 creating build/temp.linux-armv7l-cpython-311 2024-05-23T08:28:17,413 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c co2mco.c -o build/temp.linux-armv7l-cpython-311/co2mco.o -fopenmp 2024-05-23T08:28:17,591 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-05-23T08:28:17,592 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-23T08:28:17,592 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-05-23T08:28:17,593 | ^ 2024-05-23T08:28:17,596 co2mco.c: In function ‘co2unitllmco’: 2024-05-23T08:28:17,597 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-23T08:28:17,597 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-05-23T08:28:17,598 | ^ 2024-05-23T08:28:18,308 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_composite.c -o build/temp.linux-armv7l-cpython-311/command_composite.o -fopenmp 2024-05-23T08:28:18,688 command_composite.c: In function ‘get_species_abundance’: 2024-05-23T08:28:18,689 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-05-23T08:28:18,689 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-05-23T08:28:18,690 | ^~ 2024-05-23T08:28:18,690 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-05-23T08:28:18,691 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-05-23T08:28:18,691 | ^~ 2024-05-23T08:28:18,692 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:18,692 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-05-23T08:28:18,693 | ^ 2024-05-23T08:28:18,694 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:18,694 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-05-23T08:28:18,695 | ^~~~~~~~~~ 2024-05-23T08:28:18,696 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-05-23T08:28:18,696 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-05-23T08:28:18,697 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:18,698 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:18,699 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-05-23T08:28:18,699 | ^ 2024-05-23T08:28:18,700 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:18,701 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-05-23T08:28:18,701 | ^~~~~~~~~~ 2024-05-23T08:28:18,702 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-05-23T08:28:18,702 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-05-23T08:28:18,703 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:18,704 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:18,705 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-05-23T08:28:18,705 | ^ 2024-05-23T08:28:18,706 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:18,707 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-05-23T08:28:18,707 | ^~~~~~~~~~ 2024-05-23T08:28:18,708 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-05-23T08:28:18,708 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-05-23T08:28:18,709 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:18,710 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:18,710 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-05-23T08:28:18,711 | ^ 2024-05-23T08:28:18,711 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:18,712 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-05-23T08:28:18,712 | ^~~~~~~~~~ 2024-05-23T08:28:18,713 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-05-23T08:28:18,713 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-05-23T08:28:18,714 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:18,714 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:18,715 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-05-23T08:28:18,715 | ^ 2024-05-23T08:28:18,716 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:18,717 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-05-23T08:28:18,718 | ^~~~~~~~~~~~ 2024-05-23T08:28:18,718 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2024-05-23T08:28:18,719 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-05-23T08:28:18,720 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:18,947 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist.c -o build/temp.linux-armv7l-cpython-311/command_dist.o -fopenmp 2024-05-23T08:28:19,187 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-05-23T08:28:19,189 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=] 2024-05-23T08:28:19,189 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-23T08:28:19,190 | ~~^ 2024-05-23T08:28:19,190 | | 2024-05-23T08:28:19,191 | long unsigned int 2024-05-23T08:28:19,191 | %u 2024-05-23T08:28:19,192 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-23T08:28:19,193 | ~~~~~~~ 2024-05-23T08:28:19,194 | | 2024-05-23T08:28:19,195 | size_t {aka unsigned int} 2024-05-23T08:28:19,195 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=] 2024-05-23T08:28:19,196 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-23T08:28:19,197 | ~~^ 2024-05-23T08:28:19,198 | | 2024-05-23T08:28:19,198 | long unsigned int 2024-05-23T08:28:19,199 | %u 2024-05-23T08:28:19,199 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-23T08:28:19,200 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-05-23T08:28:19,200 | ~~~~~~~~~ 2024-05-23T08:28:19,201 | | 2024-05-23T08:28:19,201 | size_t {aka unsigned int} 2024-05-23T08:28:19,201 command_dist.c:678:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-05-23T08:28:19,202 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-23T08:28:19,202 | ~~^ 2024-05-23T08:28:19,203 | | 2024-05-23T08:28:19,204 | long unsigned int 2024-05-23T08:28:19,204 | %u 2024-05-23T08:28:19,205 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-23T08:28:19,205 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-05-23T08:28:19,206 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:19,207 | | 2024-05-23T08:28:19,208 | unsigned int 2024-05-23T08:28:19,209 command_dist.c:716:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-05-23T08:28:19,210 716 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-05-23T08:28:19,211 | ^ 2024-05-23T08:28:19,214 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-05-23T08:28:19,216 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=] 2024-05-23T08:28:19,216 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-05-23T08:28:19,217 | ~~^ ~~~~~~~ 2024-05-23T08:28:19,218 | | | 2024-05-23T08:28:19,218 | long unsigned int size_t {aka unsigned int} 2024-05-23T08:28:19,219 | %u 2024-05-23T08:28:19,219 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=] 2024-05-23T08:28:19,220 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-05-23T08:28:19,221 | ~~^ 2024-05-23T08:28:19,222 | | 2024-05-23T08:28:19,222 | long unsigned int 2024-05-23T08:28:19,222 | %u 2024-05-23T08:28:19,223 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-05-23T08:28:19,223 | ~~~~~~~~~ 2024-05-23T08:28:19,224 | | 2024-05-23T08:28:19,224 | size_t {aka unsigned int} 2024-05-23T08:28:19,225 command_dist.c:864:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-05-23T08:28:19,225 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-05-23T08:28:19,226 | ~~^ 2024-05-23T08:28:19,226 | | 2024-05-23T08:28:19,227 | long unsigned int 2024-05-23T08:28:19,227 | %u 2024-05-23T08:28:19,228 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-05-23T08:28:19,229 866 | (size_t) b * unitsz_distf_mapped); 2024-05-23T08:28:19,229 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:19,230 | | 2024-05-23T08:28:19,231 | unsigned int 2024-05-23T08:28:19,232 command_dist.c:811:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-05-23T08:28:19,232 811 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-05-23T08:28:19,233 | ^~~~~~~ 2024-05-23T08:28:19,234 command_dist.c:810:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-05-23T08:28:19,234 810 | struct stat cbd_fcode_stat; 2024-05-23T08:28:19,235 | ^~~~~~~~~~~~~~ 2024-05-23T08:28:19,235 command_dist.c:809:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-05-23T08:28:19,236 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-05-23T08:28:19,236 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:19,237 command_dist.c:809:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-05-23T08:28:19,237 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-05-23T08:28:19,238 | ^~~~~~~~~~~~~~~~~ 2024-05-23T08:28:19,239 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-05-23T08:28:19,239 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=] 2024-05-23T08:28:19,240 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-23T08:28:19,241 | ~~^ 2024-05-23T08:28:19,242 | | 2024-05-23T08:28:19,242 | long unsigned int 2024-05-23T08:28:19,243 | %u 2024-05-23T08:28:19,243 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-23T08:28:19,244 | ~~~~~~~ 2024-05-23T08:28:19,244 | | 2024-05-23T08:28:19,245 | size_t {aka unsigned int} 2024-05-23T08:28:19,245 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=] 2024-05-23T08:28:19,246 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-23T08:28:19,246 | ~~^ 2024-05-23T08:28:19,247 | | 2024-05-23T08:28:19,247 | long unsigned int 2024-05-23T08:28:19,248 | %u 2024-05-23T08:28:19,248 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-23T08:28:19,249 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-05-23T08:28:19,250 | ~~~~~~~~~ 2024-05-23T08:28:19,250 | | 2024-05-23T08:28:19,251 | size_t {aka unsigned int} 2024-05-23T08:28:19,252 command_dist.c:1019:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-05-23T08:28:19,252 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-05-23T08:28:19,253 | ~~^ 2024-05-23T08:28:19,254 | | 2024-05-23T08:28:19,255 | long unsigned int 2024-05-23T08:28:19,255 | %u 2024-05-23T08:28:19,256 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-05-23T08:28:19,257 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-05-23T08:28:19,258 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:19,258 | | 2024-05-23T08:28:19,259 | unsigned int 2024-05-23T08:28:19,260 command_dist.c:1035:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-05-23T08:28:19,260 1035 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-05-23T08:28:19,261 | ^ 2024-05-23T08:28:19,262 command_dist.c: In function ‘mco_co_dist_core’: 2024-05-23T08:28:19,263 command_dist.c:1117:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-05-23T08:28:19,264 1117 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-05-23T08:28:19,265 | ^ 2024-05-23T08:28:19,265 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-05-23T08:28:19,266 command_dist.c:1240:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-23T08:28:19,267 1240 | for (int rid = 0; rid < ref_num; rid++) 2024-05-23T08:28:19,267 | ^ 2024-05-23T08:28:19,268 command_dist.c:1246:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-23T08:28:19,268 1246 | for (int rid = 0; rid < ref_num; rid++) { 2024-05-23T08:28:19,269 | ^ 2024-05-23T08:28:19,269 command_dist.c: In function ‘dist_print_nobin’: 2024-05-23T08:28:19,270 command_dist.c:1336:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-23T08:28:19,270 1336 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-05-23T08:28:19,270 | ^ 2024-05-23T08:28:19,271 command_dist.c:1357:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-23T08:28:19,272 1357 | for (int rid = 0; rid < ref_num; rid++) { 2024-05-23T08:28:19,273 | ^ 2024-05-23T08:28:19,273 command_dist.c:1383:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-23T08:28:19,274 1383 | for (int rid = 0; rid < ref_num; rid++) 2024-05-23T08:28:19,274 | ^ 2024-05-23T08:28:19,633 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-05-23T08:28:19,634 command_dist.c:404:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2024-05-23T08:28:19,634 404 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-05-23T08:28:19,635 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:19,636 command_dist.c:376:40: note: ‘com_abund_fp’ was declared here 2024-05-23T08:28:19,637 376 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-05-23T08:28:19,637 | ^~~~~~~~~~~~ 2024-05-23T08:28:20,467 command_dist.c: In function ‘get_dim_shuffle’: 2024-05-23T08:28:20,468 command_dist.c:268:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-05-23T08:28:20,469 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-05-23T08:28:20,470 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:20,471 command_dist.c:268:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-05-23T08:28:20,471 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-05-23T08:28:20,472 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,365 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-05-23T08:28:21,366 command_dist.c:597:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:21,367 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-23T08:28:21,367 | ^~ ~~~~~~~~~ 2024-05-23T08:28:21,368 command_dist.c:597:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-05-23T08:28:21,369 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-23T08:28:21,370 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,371 command_dist.c:626:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-23T08:28:21,372 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-23T08:28:21,373 | ^~~~~~~~~~~~~~~ 2024-05-23T08:28:21,373 command_dist.c:626:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-05-23T08:28:21,374 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-23T08:28:21,375 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,375 command_dist.c:682:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-23T08:28:21,376 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-05-23T08:28:21,376 | ^~~~~~~~~~~ 2024-05-23T08:28:21,377 command_dist.c:682:38: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:21,377 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-05-23T08:28:21,378 | ^~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,378 command_dist.c:682:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-05-23T08:28:21,379 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-05-23T08:28:21,379 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,380 command_dist.c:683:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-23T08:28:21,381 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-05-23T08:28:21,381 | ^~~~~ 2024-05-23T08:28:21,382 command_dist.c:683:32: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:21,383 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-05-23T08:28:21,383 | ^~~~~~~~~~~ 2024-05-23T08:28:21,384 command_dist.c:683:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-05-23T08:28:21,385 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-05-23T08:28:21,386 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,615 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-05-23T08:28:21,616 command_dist.c:764:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:21,617 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-23T08:28:21,618 | ^~ ~~~~~~~~~ 2024-05-23T08:28:21,619 command_dist.c:764:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-05-23T08:28:21,619 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-23T08:28:21,620 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,620 command_dist.c:791:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-23T08:28:21,621 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-23T08:28:21,622 | ^~~~~~~~~~~~~~~ 2024-05-23T08:28:21,622 command_dist.c:791:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-05-23T08:28:21,623 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-23T08:28:21,624 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,624 command_dist.c:824:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-23T08:28:21,625 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-05-23T08:28:21,626 | ^~~~~~~~~~~~~ 2024-05-23T08:28:21,626 command_dist.c:824:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-05-23T08:28:21,627 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-05-23T08:28:21,627 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,628 command_dist.c:850:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:21,628 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-05-23T08:28:21,629 | ^ 2024-05-23T08:28:21,629 command_dist.c:850:33: note: directive argument in the range [0, 536870912] 2024-05-23T08:28:21,630 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-05-23T08:28:21,630 | ^~~~~~~~~~ 2024-05-23T08:28:21,631 command_dist.c:850:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-05-23T08:28:21,632 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-05-23T08:28:21,632 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,633 command_dist.c:852:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:21,633 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-05-23T08:28:21,634 | ^ 2024-05-23T08:28:21,634 command_dist.c:852:28: note: directive argument in the range [0, 536870912] 2024-05-23T08:28:21,635 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-05-23T08:28:21,635 | ^~~~~~~~~~ 2024-05-23T08:28:21,636 command_dist.c:852:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-05-23T08:28:21,637 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-05-23T08:28:21,637 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,894 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-05-23T08:28:21,895 command_dist.c:928:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:21,896 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-23T08:28:21,896 | ^~ ~~~~~~~~~ 2024-05-23T08:28:21,897 command_dist.c:928:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-05-23T08:28:21,898 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-05-23T08:28:21,898 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,899 command_dist.c:957:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-23T08:28:21,899 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-23T08:28:21,900 | ^~~~~~~~~~~~~~~ 2024-05-23T08:28:21,900 command_dist.c:957:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-05-23T08:28:21,901 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-05-23T08:28:21,902 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,902 command_dist.c:991:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-23T08:28:21,903 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-05-23T08:28:21,904 | ^~~~~~~~~~~~~ 2024-05-23T08:28:21,905 command_dist.c:991:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-05-23T08:28:21,905 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-05-23T08:28:21,906 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,906 command_dist.c:1023:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-23T08:28:21,906 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-05-23T08:28:21,907 | ^~~~~~~~~~~ 2024-05-23T08:28:21,907 command_dist.c:1023:38: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:21,908 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-05-23T08:28:21,908 | ^~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,908 command_dist.c:1023:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-05-23T08:28:21,909 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-05-23T08:28:21,910 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:21,910 command_dist.c:1024:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-05-23T08:28:21,911 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-05-23T08:28:21,911 | ^~~~~ 2024-05-23T08:28:21,912 command_dist.c:1024:32: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:21,912 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-05-23T08:28:21,913 | ^~~~~~~~~~~ 2024-05-23T08:28:21,914 command_dist.c:1024:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-05-23T08:28:21,915 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-05-23T08:28:21,915 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:22,183 command_dist.c: In function ‘combine_queries’: 2024-05-23T08:28:22,184 command_dist.c:1493:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-23T08:28:22,185 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-05-23T08:28:22,186 | ^ 2024-05-23T08:28:22,186 command_dist.c:1493:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-23T08:28:22,187 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-05-23T08:28:22,187 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:22,188 command_dist.c:1500:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-23T08:28:22,189 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-05-23T08:28:22,189 | ^ 2024-05-23T08:28:22,190 command_dist.c:1500:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-23T08:28:22,190 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-05-23T08:28:22,191 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:22,192 command_dist.c:1604:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:22,193 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-05-23T08:28:22,193 | ^~ ~~~~~~~~ 2024-05-23T08:28:22,194 command_dist.c:1604:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-05-23T08:28:22,195 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-05-23T08:28:22,196 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:22,686 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o -fopenmp 2024-05-23T08:28:22,862 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_set.c -o build/temp.linux-armv7l-cpython-311/command_set.o -fopenmp 2024-05-23T08:28:23,030 command_set.c: In function ‘sketch_operate’: 2024-05-23T08:28:23,030 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-05-23T08:28:23,031 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-05-23T08:28:23,031 | ^ 2024-05-23T08:28:23,043 command_set.c: In function ‘combin_subset_pans’: 2024-05-23T08:28:23,044 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-05-23T08:28:23,044 458 | free(co_dstat_fpath); 2024-05-23T08:28:23,045 | ^~~~~~~~~~~~~~ 2024-05-23T08:28:23,045 In file included from kssdheaders/global_basic.h:159, 2024-05-23T08:28:23,046 from command_set.c:15: 2024-05-23T08:28:23,047 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-05-23T08:28:23,048 568 | extern void free (void *__ptr) __THROW; 2024-05-23T08:28:23,048 | ~~~~~~^~~~~ 2024-05-23T08:28:23,050 command_set.c: In function ‘grouping_genomes’: 2024-05-23T08:28:23,051 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-05-23T08:28:23,052 563 | free(co_dstat_fpath); 2024-05-23T08:28:23,052 | ^~~~~~~~~~~~~~ 2024-05-23T08:28:23,053 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-05-23T08:28:23,054 568 | extern void free (void *__ptr) __THROW; 2024-05-23T08:28:23,055 | ~~~~~~^~~~~ 2024-05-23T08:28:23,218 command_set.c: In function ‘sketch_union’: 2024-05-23T08:28:23,219 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-23T08:28:23,220 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:23,220 | ^ 2024-05-23T08:28:23,221 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-23T08:28:23,222 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:23,222 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,223 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,224 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-05-23T08:28:23,224 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:23,225 command_set.c:83:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,225 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-05-23T08:28:23,226 | ^~~~~~~~~~ 2024-05-23T08:28:23,227 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-23T08:28:23,228 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-05-23T08:28:23,228 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,229 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,230 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-05-23T08:28:23,230 | ^~ ~~~~~~~~~~ 2024-05-23T08:28:23,231 command_set.c:93:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,231 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-05-23T08:28:23,232 | ^~~~~~~~~~ 2024-05-23T08:28:23,232 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-05-23T08:28:23,233 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-05-23T08:28:23,234 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,350 command_set.c: In function ‘sketch_operate’: 2024-05-23T08:28:23,350 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,351 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-05-23T08:28:23,351 | ^~ ~~~~~~~~~~ 2024-05-23T08:28:23,352 command_set.c:154:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,352 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-05-23T08:28:23,353 | ^~~~~~~~~~ 2024-05-23T08:28:23,354 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-05-23T08:28:23,354 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-05-23T08:28:23,355 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,356 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,356 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-05-23T08:28:23,357 | ^~ ~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,358 command_set.c:156:29: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,359 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-05-23T08:28:23,359 | ^~~~~~~~~~ 2024-05-23T08:28:23,360 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-05-23T08:28:23,361 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-05-23T08:28:23,361 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,362 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,362 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-05-23T08:28:23,363 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:23,364 command_set.c:166:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,364 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-05-23T08:28:23,365 | ^~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,366 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-23T08:28:23,367 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-05-23T08:28:23,367 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,368 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,368 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-05-23T08:28:23,369 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:23,369 command_set.c:170:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,370 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-05-23T08:28:23,370 | ^~~~~~~~~~ 2024-05-23T08:28:23,371 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-23T08:28:23,371 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-05-23T08:28:23,372 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,372 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,373 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-05-23T08:28:23,373 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:23,374 command_set.c:175:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,374 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-05-23T08:28:23,375 | ^~~~~~~~~~ 2024-05-23T08:28:23,376 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-23T08:28:23,376 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-05-23T08:28:23,377 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,377 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,378 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-05-23T08:28:23,378 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:23,379 command_set.c:188:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,380 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-05-23T08:28:23,380 | ^~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,381 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-23T08:28:23,382 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-05-23T08:28:23,382 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,383 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-23T08:28:23,383 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:23,384 | ^ 2024-05-23T08:28:23,385 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-23T08:28:23,385 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:23,386 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,524 command_set.c: In function ‘uniq_sketch_union’: 2024-05-23T08:28:23,525 command_set.c:220:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-23T08:28:23,525 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-05-23T08:28:23,526 | ^ 2024-05-23T08:28:23,527 command_set.c:220:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2024-05-23T08:28:23,527 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-05-23T08:28:23,528 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,528 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-23T08:28:23,529 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:23,529 | ^ 2024-05-23T08:28:23,530 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-23T08:28:23,530 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:23,531 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,531 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,532 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-05-23T08:28:23,532 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:23,533 command_set.c:248:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,533 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-05-23T08:28:23,534 | ^~~~~~~~~~ 2024-05-23T08:28:23,534 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-23T08:28:23,535 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-05-23T08:28:23,535 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,536 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,537 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-05-23T08:28:23,538 | ^~ ~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,538 command_set.c:260:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,539 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-05-23T08:28:23,540 | ^~~~~~~~~~ 2024-05-23T08:28:23,541 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-05-23T08:28:23,541 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-05-23T08:28:23,542 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,670 command_set.c: In function ‘combin_pans’: 2024-05-23T08:28:23,670 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,671 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-23T08:28:23,672 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:23,672 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-05-23T08:28:23,673 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-23T08:28:23,674 | ^~~~~~~~~~ 2024-05-23T08:28:23,674 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-05-23T08:28:23,675 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-23T08:28:23,675 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,676 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,677 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-23T08:28:23,678 | ^~ ~~~~~~~~~~ 2024-05-23T08:28:23,678 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-05-23T08:28:23,679 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-23T08:28:23,679 | ^~~~~~~~~~ 2024-05-23T08:28:23,680 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-05-23T08:28:23,680 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-23T08:28:23,681 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,681 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-23T08:28:23,682 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:23,682 | ^ 2024-05-23T08:28:23,683 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-23T08:28:23,684 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:23,684 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,887 command_set.c: In function ‘combin_subset_pans’: 2024-05-23T08:28:23,888 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,889 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-05-23T08:28:23,889 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:23,890 command_set.c:470:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,891 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-05-23T08:28:23,891 | ^~~~~~~~~~ 2024-05-23T08:28:23,892 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-23T08:28:23,893 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-05-23T08:28:23,894 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,894 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,895 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-05-23T08:28:23,896 | ^~ ~~~~~~~~~~ 2024-05-23T08:28:23,896 command_set.c:476:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,897 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-05-23T08:28:23,898 | ^~~~~~~~~~ 2024-05-23T08:28:23,899 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-23T08:28:23,899 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-05-23T08:28:23,900 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,901 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,901 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-23T08:28:23,902 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:23,903 command_set.c:482:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,904 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-23T08:28:23,904 | ^~~~~~~~~~ 2024-05-23T08:28:23,905 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-23T08:28:23,905 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-23T08:28:23,906 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,906 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:23,907 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-23T08:28:23,907 | ^~ ~~~~~~~~~~ 2024-05-23T08:28:23,908 command_set.c:513:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:23,908 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-23T08:28:23,909 | ^~~~~~~~~~ 2024-05-23T08:28:23,910 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-23T08:28:23,910 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-23T08:28:23,911 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:23,911 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-23T08:28:23,912 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:23,912 | ^ 2024-05-23T08:28:23,913 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-23T08:28:23,914 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:23,914 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:24,134 command_set.c: In function ‘grouping_genomes’: 2024-05-23T08:28:24,134 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:24,135 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-05-23T08:28:24,136 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:24,136 command_set.c:575:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:24,137 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-05-23T08:28:24,138 | ^~~~~~~~~~ 2024-05-23T08:28:24,138 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-23T08:28:24,139 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-05-23T08:28:24,139 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:24,140 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:24,141 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-05-23T08:28:24,141 | ^~ ~~~~~~~~~~ 2024-05-23T08:28:24,142 command_set.c:581:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:24,142 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-05-23T08:28:24,143 | ^~~~~~~~~~ 2024-05-23T08:28:24,143 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-23T08:28:24,144 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-05-23T08:28:24,145 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:24,145 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:24,146 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-23T08:28:24,147 | ^~ ~~~~~~~~~~~ 2024-05-23T08:28:24,147 command_set.c:613:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:24,148 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-23T08:28:24,148 | ^~~~~~~~~~ 2024-05-23T08:28:24,149 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-05-23T08:28:24,149 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-05-23T08:28:24,150 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:24,150 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-05-23T08:28:24,151 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-23T08:28:24,151 | ^~ ~~~~~~~~~~ 2024-05-23T08:28:24,152 command_set.c:635:25: note: directive argument in the range [-2147483644, 2147483646] 2024-05-23T08:28:24,152 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-23T08:28:24,153 | ^~~~~~~~~~ 2024-05-23T08:28:24,154 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-05-23T08:28:24,154 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-05-23T08:28:24,155 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:24,155 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-05-23T08:28:24,156 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:24,157 | ^ 2024-05-23T08:28:24,157 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-05-23T08:28:24,158 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-05-23T08:28:24,159 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:24,433 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-311/command_shuffle.o -fopenmp 2024-05-23T08:28:24,747 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c global_basic.c -o build/temp.linux-armv7l-cpython-311/global_basic.o -fopenmp 2024-05-23T08:28:24,926 global_basic.c: In function ‘organize_infile_list’: 2024-05-23T08:28:24,926 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-05-23T08:28:24,927 195 | while (isspace(*buf)) buf++; 2024-05-23T08:28:24,928 | ^~~~~~~ 2024-05-23T08:28:24,928 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2024-05-23T08:28:24,929 34 | #include 2024-05-23T08:28:24,930 +++ |+#include 2024-05-23T08:28:24,930 35 | 2024-05-23T08:28:24,931 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=] 2024-05-23T08:28:24,932 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-05-23T08:28:24,933 | ~~^ 2024-05-23T08:28:24,934 | | 2024-05-23T08:28:24,934 | long unsigned int 2024-05-23T08:28:24,934 | %u 2024-05-23T08:28:24,935 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-05-23T08:28:24,935 | ~~~~~~~~~~~ 2024-05-23T08:28:24,936 | | 2024-05-23T08:28:24,936 | size_t {aka unsigned int} 2024-05-23T08:28:24,937 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=] 2024-05-23T08:28:24,937 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-05-23T08:28:24,938 | ~~^ 2024-05-23T08:28:24,938 | | 2024-05-23T08:28:24,939 | long unsigned int 2024-05-23T08:28:24,939 | %u 2024-05-23T08:28:24,940 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-05-23T08:28:24,940 | ~~~~~~~~~~~ 2024-05-23T08:28:24,941 | | 2024-05-23T08:28:24,942 | size_t {aka unsigned int} 2024-05-23T08:28:25,696 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-311/iseq2comem.o -fopenmp 2024-05-23T08:28:25,873 iseq2comem.c: In function ‘reads2mco’: 2024-05-23T08:28:25,874 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,874 156 | if (base > TL) { 2024-05-23T08:28:25,875 | ^ 2024-05-23T08:28:25,876 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,876 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-23T08:28:25,877 | ^~ 2024-05-23T08:28:25,878 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,878 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-23T08:28:25,879 | ^ 2024-05-23T08:28:25,881 iseq2comem.c: In function ‘fasta2co’: 2024-05-23T08:28:25,882 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,882 239 | if (base > TL) { 2024-05-23T08:28:25,883 | ^ 2024-05-23T08:28:25,883 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,884 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-23T08:28:25,885 | ^~ 2024-05-23T08:28:25,886 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,886 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-23T08:28:25,887 | ^ 2024-05-23T08:28:25,887 iseq2comem.c: In function ‘fastq2co’: 2024-05-23T08:28:25,888 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-05-23T08:28:25,888 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-05-23T08:28:25,889 | ^~ 2024-05-23T08:28:25,891 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,891 318 | if (base > TL) { 2024-05-23T08:28:25,892 | ^ 2024-05-23T08:28:25,892 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,893 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-23T08:28:25,893 | ^~ 2024-05-23T08:28:25,894 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,894 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-23T08:28:25,895 | ^ 2024-05-23T08:28:25,898 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,898 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-05-23T08:28:25,899 | ^ 2024-05-23T08:28:25,901 iseq2comem.c: In function ‘fastq2koc’: 2024-05-23T08:28:25,902 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,903 402 | if (base > TL) { 2024-05-23T08:28:25,903 | ^ 2024-05-23T08:28:25,904 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,905 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-23T08:28:25,905 | ^~ 2024-05-23T08:28:25,906 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,907 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-23T08:28:25,907 | ^ 2024-05-23T08:28:25,914 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-05-23T08:28:25,915 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,915 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-23T08:28:25,916 | ^~ 2024-05-23T08:28:25,917 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:25,917 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-05-23T08:28:25,918 | ^ 2024-05-23T08:28:27,263 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2024-05-23T08:28:27,316 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mytime.c -o build/temp.linux-armv7l-cpython-311/mytime.o -fopenmp 2024-05-23T08:28:27,441 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c pykssd.c -o build/temp.linux-armv7l-cpython-311/pykssd.o -fopenmp 2024-05-23T08:28:27,840 pykssd.c: In function ‘py_dist_dispatch’: 2024-05-23T08:28:27,840 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-05-23T08:28:27,841 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-05-23T08:28:27,841 | ^~~~~~ 2024-05-23T08:28:27,842 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-05-23T08:28:27,842 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-05-23T08:28:27,843 | ^~~~~~ 2024-05-23T08:28:27,844 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-05-23T08:28:27,844 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-05-23T08:28:27,845 | ^~~~~~ 2024-05-23T08:28:28,405 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/co2mco.o build/temp.linux-armv7l-cpython-311/command_composite.o build/temp.linux-armv7l-cpython-311/command_dist.o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o build/temp.linux-armv7l-cpython-311/command_set.o build/temp.linux-armv7l-cpython-311/command_shuffle.o build/temp.linux-armv7l-cpython-311/global_basic.o build/temp.linux-armv7l-cpython-311/iseq2comem.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/mytime.o build/temp.linux-armv7l-cpython-311/pykssd.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -fopenmp 2024-05-23T08:28:28,558 building 'nj' extension 2024-05-23T08:28:28,559 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c align.c -o build/temp.linux-armv7l-cpython-311/align.o 2024-05-23T08:28:29,019 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c buildtree.c -o build/temp.linux-armv7l-cpython-311/buildtree.o 2024-05-23T08:28:29,165 buildtree.c: In function ‘UPGMA_buildtree’: 2024-05-23T08:28:29,166 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-23T08:28:29,167 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-05-23T08:28:29,167 | ^~ 2024-05-23T08:28:29,168 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-23T08:28:29,169 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-05-23T08:28:29,170 | ^~ 2024-05-23T08:28:29,859 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c cluster.c -o build/temp.linux-armv7l-cpython-311/cluster.o 2024-05-23T08:28:30,229 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c distancemat.c -o build/temp.linux-armv7l-cpython-311/distancemat.o 2024-05-23T08:28:30,365 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-05-23T08:28:30,366 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-23T08:28:30,366 226 | for( i=0; i < dest->size; i++) { 2024-05-23T08:28:30,367 | ^ 2024-05-23T08:28:30,367 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-05-23T08:28:30,368 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-23T08:28:30,369 260 | for( i=0; i < mat->size; i++) { 2024-05-23T08:28:30,369 | ^ 2024-05-23T08:28:30,370 distancemat.c: In function ‘print_DistanceMatrix’: 2024-05-23T08:28:30,370 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-23T08:28:30,371 349 | for(row=0; row < mat->size; row++) { 2024-05-23T08:28:30,371 | ^ 2024-05-23T08:28:30,372 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-05-23T08:28:30,373 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-05-23T08:28:30,374 410 | while(c = fgetc(handle)) { 2024-05-23T08:28:30,374 | ^ 2024-05-23T08:28:30,759 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c pynj.c -o build/temp.linux-armv7l-cpython-311/pynj.o 2024-05-23T08:28:31,201 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c sequence.c -o build/temp.linux-armv7l-cpython-311/sequence.o 2024-05-23T08:28:31,416 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c tree.c -o build/temp.linux-armv7l-cpython-311/tree.o 2024-05-23T08:28:32,256 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c util.c -o build/temp.linux-armv7l-cpython-311/util.o 2024-05-23T08:28:32,440 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/align.o build/temp.linux-armv7l-cpython-311/buildtree.o build/temp.linux-armv7l-cpython-311/cluster.o build/temp.linux-armv7l-cpython-311/distancemat.o build/temp.linux-armv7l-cpython-311/pynj.o build/temp.linux-armv7l-cpython-311/sequence.o build/temp.linux-armv7l-cpython-311/tree.o build/temp.linux-armv7l-cpython-311/util.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so 2024-05-23T08:28:32,551 building 'dnj' extension 2024-05-23T08:28:32,552 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c bytescale.c -o build/temp.linux-armv7l-cpython-311/bytescale.o -fopenmp 2024-05-23T08:28:32,609 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c dnj.c -o build/temp.linux-armv7l-cpython-311/dnj.o -fopenmp 2024-05-23T08:28:32,747 dnj.c: In function ‘minQpair’: 2024-05-23T08:28:32,748 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,749 70 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,750 | ^~~ 2024-05-23T08:28:32,750 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,751 126 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,751 | ^~~ 2024-05-23T08:28:32,752 dnj.c: In function ‘maxQpair’: 2024-05-23T08:28:32,752 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,753 157 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,753 | ^~~ 2024-05-23T08:28:32,754 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,754 213 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,755 | ^~~ 2024-05-23T08:28:32,755 dnj.c: In function ‘UPGMApair’: 2024-05-23T08:28:32,756 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,757 237 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,757 | ^~~ 2024-05-23T08:28:32,758 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,758 284 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,759 | ^~~ 2024-05-23T08:28:32,759 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,760 291 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,760 | ^~~ 2024-05-23T08:28:32,761 dnj.c: In function ‘minQrow’: 2024-05-23T08:28:32,762 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,763 374 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,763 | ^~~ 2024-05-23T08:28:32,764 dnj.c: In function ‘maxQrow’: 2024-05-23T08:28:32,765 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,766 435 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,767 | ^~~ 2024-05-23T08:28:32,767 dnj.c: In function ‘UPGMArow’: 2024-05-23T08:28:32,768 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,769 488 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,769 | ^~~ 2024-05-23T08:28:32,770 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,771 494 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,771 | ^~~ 2024-05-23T08:28:32,772 dnj.c: In function ‘minQ_thread’: 2024-05-23T08:28:32,773 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:32,773 553 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:32,774 | ^~~ 2024-05-23T08:28:34,131 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c filebuff.c -o build/temp.linux-armv7l-cpython-311/filebuff.o -fopenmp 2024-05-23T08:28:34,249 filebuff.c: In function ‘BuffgzFileBuff’: 2024-05-23T08:28:34,250 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:34,250 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-05-23T08:28:34,251 | ^~ 2024-05-23T08:28:34,575 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c hclust.c -o build/temp.linux-armv7l-cpython-311/hclust.o -fopenmp 2024-05-23T08:28:34,708 hclust.c: In function ‘minQ’: 2024-05-23T08:28:34,709 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-23T08:28:34,709 364 | while(++i < Q->n) { 2024-05-23T08:28:34,710 | ^ 2024-05-23T08:28:34,710 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:34,711 377 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:34,711 | ^~~ 2024-05-23T08:28:34,712 hclust.c: In function ‘maxQ’: 2024-05-23T08:28:34,712 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-05-23T08:28:34,713 394 | while(++i < Q->n) { 2024-05-23T08:28:34,714 | ^ 2024-05-23T08:28:34,714 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:34,715 407 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:34,715 | ^~~ 2024-05-23T08:28:37,089 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c matrix.c -o build/temp.linux-armv7l-cpython-311/matrix.o -fopenmp 2024-05-23T08:28:37,220 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-05-23T08:28:37,221 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-05-23T08:28:37,221 538 | if(pos != n) { 2024-05-23T08:28:37,222 | ^~ 2024-05-23T08:28:38,097 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2024-05-23T08:28:38,151 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nj.c -o build/temp.linux-armv7l-cpython-311/nj.o -fopenmp 2024-05-23T08:28:38,283 nj.c: In function ‘initQ’: 2024-05-23T08:28:38,284 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:38,285 243 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:38,286 | ^~~ 2024-05-23T08:28:38,286 nj.c: In function ‘initQ_MN’: 2024-05-23T08:28:38,287 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:38,287 358 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:38,288 | ^~~ 2024-05-23T08:28:38,291 nj.c: In function ‘minD’: 2024-05-23T08:28:38,292 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:38,293 559 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:38,293 | ^~~ 2024-05-23T08:28:38,294 nj.c: In function ‘maxD’: 2024-05-23T08:28:38,294 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:38,295 642 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:38,296 | ^~~ 2024-05-23T08:28:38,299 nj.c: In function ‘minPair’: 2024-05-23T08:28:38,299 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-05-23T08:28:38,300 826 | pos <<= sizeof(unsigned) * 8; 2024-05-23T08:28:38,301 | ^~~ 2024-05-23T08:28:40,669 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nwck.c -o build/temp.linux-armv7l-cpython-311/nwck.o -fopenmp 2024-05-23T08:28:41,208 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pherror.c -o build/temp.linux-armv7l-cpython-311/pherror.o -fopenmp 2024-05-23T08:28:41,302 pherror.c: In function ‘cfread’: 2024-05-23T08:28:41,303 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-05-23T08:28:41,303 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-05-23T08:28:41,304 | ^~ 2024-05-23T08:28:41,396 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c phy.c -o build/temp.linux-armv7l-cpython-311/phy.o -fopenmp 2024-05-23T08:28:42,498 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pydnj.c -o build/temp.linux-armv7l-cpython-311/pydnj.o -fopenmp 2024-05-23T08:28:42,869 In file included from pydnj.c:11: 2024-05-23T08:28:42,870 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-05-23T08:28:42,870 20 | #define _XOPEN_SOURCE 600 2024-05-23T08:28:42,871 | 2024-05-23T08:28:42,871 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-05-23T08:28:42,872 from /usr/include/stdlib.h:26, 2024-05-23T08:28:42,872 from /usr/include/python3.11/Python.h:23, 2024-05-23T08:28:42,873 from pydnj.c:1: 2024-05-23T08:28:42,874 /usr/include/features.h:214: note: this is the location of the previous definition 2024-05-23T08:28:42,874 214 | # define _XOPEN_SOURCE 700 2024-05-23T08:28:42,875 | 2024-05-23T08:28:42,895 pydnj.c: In function ‘py_build’: 2024-05-23T08:28:42,895 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-05-23T08:28:42,896 165 | p = omp_get_num_procs(); 2024-05-23T08:28:42,897 | ^~~~~~~~~~~~~~~~~ 2024-05-23T08:28:43,019 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2024-05-23T08:28:43,020 169 | free(file); 2024-05-23T08:28:43,021 | ^~~~~~~~~~ 2024-05-23T08:28:43,021 pydnj.c:125:12: note: returned from ‘fopen’ 2024-05-23T08:28:43,022 125 | file = fopen(inputfilename, "r"); 2024-05-23T08:28:43,022 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-05-23T08:28:43,097 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c qseqs.c -o build/temp.linux-armv7l-cpython-311/qseqs.o -fopenmp 2024-05-23T08:28:43,307 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c str.c -o build/temp.linux-armv7l-cpython-311/str.o -fopenmp 2024-05-23T08:28:43,420 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c tmp.c -o build/temp.linux-armv7l-cpython-311/tmp.o -fopenmp 2024-05-23T08:28:43,614 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c vector.c -o build/temp.linux-armv7l-cpython-311/vector.o -fopenmp 2024-05-23T08:28:43,775 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/bytescale.o build/temp.linux-armv7l-cpython-311/dnj.o build/temp.linux-armv7l-cpython-311/filebuff.o build/temp.linux-armv7l-cpython-311/hclust.o build/temp.linux-armv7l-cpython-311/matrix.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/nj.o build/temp.linux-armv7l-cpython-311/nwck.o build/temp.linux-armv7l-cpython-311/pherror.o build/temp.linux-armv7l-cpython-311/phy.o build/temp.linux-armv7l-cpython-311/pydnj.o build/temp.linux-armv7l-cpython-311/qseqs.o build/temp.linux-armv7l-cpython-311/str.o build/temp.linux-armv7l-cpython-311/tmp.o build/temp.linux-armv7l-cpython-311/vector.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -fopenmp 2024-05-23T08:28:43,966 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-05-23T08:28:43,967 !! 2024-05-23T08:28:43,968 ******************************************************************************** 2024-05-23T08:28:43,968 Please avoid running ``setup.py`` directly. 2024-05-23T08:28:43,969 Instead, use pypa/build, pypa/installer or other 2024-05-23T08:28:43,969 standards-based tools. 2024-05-23T08:28:43,970 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-05-23T08:28:43,971 ******************************************************************************** 2024-05-23T08:28:43,972 !! 2024-05-23T08:28:43,972 self.initialize_options() 2024-05-23T08:28:43,995 installing to build/bdist.linux-armv7l/wheel 2024-05-23T08:28:43,995 running install 2024-05-23T08:28:44,020 running install_lib 2024-05-23T08:28:44,046 creating build/bdist.linux-armv7l 2024-05-23T08:28:44,047 creating build/bdist.linux-armv7l/wheel 2024-05-23T08:28:44,048 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-05-23T08:28:44,063 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-05-23T08:28:44,068 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-05-23T08:28:44,071 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-05-23T08:28:44,084 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-05-23T08:28:44,087 running install_egg_info 2024-05-23T08:28:44,121 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-1.1.4-py3.11.egg-info 2024-05-23T08:28:44,134 running install_scripts 2024-05-23T08:28:44,184 creating build/bdist.linux-armv7l/wheel/kssdtree-1.1.4.dist-info/WHEEL 2024-05-23T08:28:44,187 creating '/tmp/pip-wheel-g9iwuoht/kssdtree-1.1.4-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-05-23T08:28:44,253 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2024-05-23T08:28:44,339 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2024-05-23T08:28:44,344 adding 'kssdtree.py' 2024-05-23T08:28:44,365 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2024-05-23T08:28:44,368 adding 'toolutils.py' 2024-05-23T08:28:44,371 adding 'kssdtree-1.1.4.dist-info/METADATA' 2024-05-23T08:28:44,373 adding 'kssdtree-1.1.4.dist-info/WHEEL' 2024-05-23T08:28:44,375 adding 'kssdtree-1.1.4.dist-info/dependency_links.txt' 2024-05-23T08:28:44,377 adding 'kssdtree-1.1.4.dist-info/top_level.txt' 2024-05-23T08:28:44,378 adding 'kssdtree-1.1.4.dist-info/RECORD' 2024-05-23T08:28:44,395 removing build/bdist.linux-armv7l/wheel 2024-05-23T08:28:44,552 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-05-23T08:28:44,558 Created wheel for kssdtree: filename=kssdtree-1.1.4-cp311-cp311-linux_armv7l.whl size=379683 sha256=64b685362c3f9027bfeafdffb6a5d58c349a76fd551eeb7b98de146827463e75 2024-05-23T08:28:44,560 Stored in directory: /tmp/pip-ephem-wheel-cache-brvmj7dy/wheels/bf/a3/c7/424045f819618dff398174994012f3ccb595fe076c5643be84 2024-05-23T08:28:44,569 Successfully built kssdtree 2024-05-23T08:28:44,582 Removed build tracker: '/tmp/pip-build-tracker-hrwdy_84'