2024-07-10T09:01:28,170 Created temporary directory: /tmp/pip-build-tracker-rykj1kwz 2024-07-10T09:01:28,171 Initialized build tracking at /tmp/pip-build-tracker-rykj1kwz 2024-07-10T09:01:28,172 Created build tracker: /tmp/pip-build-tracker-rykj1kwz 2024-07-10T09:01:28,172 Entered build tracker: /tmp/pip-build-tracker-rykj1kwz 2024-07-10T09:01:28,173 Created temporary directory: /tmp/pip-wheel-tr8lgac7 2024-07-10T09:01:28,176 Created temporary directory: /tmp/pip-ephem-wheel-cache-2pr5zkv7 2024-07-10T09:01:28,198 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-07-10T09:01:28,201 2 location(s) to search for versions of kssdtree: 2024-07-10T09:01:28,201 * https://pypi.org/simple/kssdtree/ 2024-07-10T09:01:28,201 * https://www.piwheels.org/simple/kssdtree/ 2024-07-10T09:01:28,202 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-07-10T09:01:28,203 Getting page https://pypi.org/simple/kssdtree/ 2024-07-10T09:01:28,204 Found index url https://pypi.org/simple/ 2024-07-10T09:01:28,415 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-07-10T09:01:28,417 Found link https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.1 2024-07-10T09:01:28,417 Found link https://files.pythonhosted.org/packages/9a/4c/6516f734f5860e4b30f9091aaac5811663bfae72c4de4ae6566c89192767/kssdtree-1.1.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.2 2024-07-10T09:01:28,418 Found link https://files.pythonhosted.org/packages/a4/cd/f2954686c636e853cc3fda197c459195377b78288874cf7d68218a8bdbf4/kssdtree-1.1.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.3 2024-07-10T09:01:28,419 Found link https://files.pythonhosted.org/packages/20/ea/b0301924e3f7d367cbb7b8da66837dba9af2a332bf56ed35e03a33faee76/kssdtree-1.1.4.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.4 2024-07-10T09:01:28,419 Found link https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.6 2024-07-10T09:01:28,420 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-07-10T09:01:28,421 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-07-10T09:01:28,422 Found index url https://www.piwheels.org/simple/ 2024-07-10T09:01:28,586 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-07-10T09:01:28,593 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp37-cp37m-linux_armv6l.whl#sha256=ffef4ae0f634dd977cc2ec6798b9f36f73d788aca27bb7199f552d5513c34413 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,594 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp37-cp37m-linux_armv7l.whl#sha256=ffef4ae0f634dd977cc2ec6798b9f36f73d788aca27bb7199f552d5513c34413 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,594 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp311-cp311-linux_armv6l.whl#sha256=64b685362c3f9027bfeafdffb6a5d58c349a76fd551eeb7b98de146827463e75 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,595 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp311-cp311-linux_armv7l.whl#sha256=64b685362c3f9027bfeafdffb6a5d58c349a76fd551eeb7b98de146827463e75 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,595 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp39-cp39-linux_armv6l.whl#sha256=34527068d84569095aefee41a353c5dfc0dfa55b68097890da9a1eca2ee9b726 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,596 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp39-cp39-linux_armv7l.whl#sha256=34527068d84569095aefee41a353c5dfc0dfa55b68097890da9a1eca2ee9b726 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,597 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp311-cp311-linux_armv6l.whl#sha256=6b76f3b3f532934ad49a829e7bf8176af580f4687f1491c49c3f571bf081f961 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,597 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp311-cp311-linux_armv7l.whl#sha256=6b76f3b3f532934ad49a829e7bf8176af580f4687f1491c49c3f571bf081f961 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,598 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp37-cp37m-linux_armv6l.whl#sha256=d179f6c6c0ad4e0f06950e1609118b065b3476c47446325f6614bdbef5ede0d0 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,598 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp37-cp37m-linux_armv7l.whl#sha256=d179f6c6c0ad4e0f06950e1609118b065b3476c47446325f6614bdbef5ede0d0 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,599 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp39-cp39-linux_armv6l.whl#sha256=6df2298fa80eefa823153fa0b9db67e35da72da7f88c5949f4f637872ff22c3b (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,599 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp39-cp39-linux_armv7l.whl#sha256=6df2298fa80eefa823153fa0b9db67e35da72da7f88c5949f4f637872ff22c3b (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,600 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv6l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,600 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv7l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,601 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv6l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,602 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv7l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,602 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp39-cp39-linux_armv6l.whl#sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,603 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp39-cp39-linux_armv7l.whl#sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,604 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv6l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,604 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv7l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,605 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv6l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,605 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv7l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,606 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv6l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,606 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv7l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2024-07-10T09:01:28,607 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-07-10T09:01:28,607 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-07-10T09:01:28,628 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-07-10T09:01:28,647 Collecting kssdtree==1.1.6 2024-07-10T09:01:28,649 Created temporary directory: /tmp/pip-unpack-vx5bv2bo 2024-07-10T09:01:28,861 Downloading kssdtree-1.1.6.tar.gz (112 kB) 2024-07-10T09:01:29,078 Added kssdtree==1.1.6 from https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz to build tracker '/tmp/pip-build-tracker-rykj1kwz' 2024-07-10T09:01:29,080 Running setup.py (path:/tmp/pip-wheel-tr8lgac7/kssdtree_38513facbe7d4b29a6d435572f7aa117/setup.py) egg_info for package kssdtree 2024-07-10T09:01:29,081 Created temporary directory: /tmp/pip-pip-egg-info-ylha_hxo 2024-07-10T09:01:29,082 Preparing metadata (setup.py): started 2024-07-10T09:01:29,083 Running command python setup.py egg_info 2024-07-10T09:01:30,242 running egg_info 2024-07-10T09:01:30,243 creating /tmp/pip-pip-egg-info-ylha_hxo/kssdtree.egg-info 2024-07-10T09:01:30,268 writing /tmp/pip-pip-egg-info-ylha_hxo/kssdtree.egg-info/PKG-INFO 2024-07-10T09:01:30,272 writing dependency_links to /tmp/pip-pip-egg-info-ylha_hxo/kssdtree.egg-info/dependency_links.txt 2024-07-10T09:01:30,274 writing requirements to /tmp/pip-pip-egg-info-ylha_hxo/kssdtree.egg-info/requires.txt 2024-07-10T09:01:30,275 writing top-level names to /tmp/pip-pip-egg-info-ylha_hxo/kssdtree.egg-info/top_level.txt 2024-07-10T09:01:30,276 writing manifest file '/tmp/pip-pip-egg-info-ylha_hxo/kssdtree.egg-info/SOURCES.txt' 2024-07-10T09:01:30,388 reading manifest file '/tmp/pip-pip-egg-info-ylha_hxo/kssdtree.egg-info/SOURCES.txt' 2024-07-10T09:01:30,389 reading manifest template 'MANIFEST.in' 2024-07-10T09:01:30,407 writing manifest file '/tmp/pip-pip-egg-info-ylha_hxo/kssdtree.egg-info/SOURCES.txt' 2024-07-10T09:01:30,525 Preparing metadata (setup.py): finished with status 'done' 2024-07-10T09:01:30,529 Source in /tmp/pip-wheel-tr8lgac7/kssdtree_38513facbe7d4b29a6d435572f7aa117 has version 1.1.6, which satisfies requirement kssdtree==1.1.6 from https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz 2024-07-10T09:01:30,530 Removed kssdtree==1.1.6 from https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz from build tracker '/tmp/pip-build-tracker-rykj1kwz' 2024-07-10T09:01:30,534 Created temporary directory: /tmp/pip-unpack-zy8c0_pu 2024-07-10T09:01:30,535 Created temporary directory: /tmp/pip-unpack-mtagasg3 2024-07-10T09:01:30,540 Building wheels for collected packages: kssdtree 2024-07-10T09:01:30,544 Created temporary directory: /tmp/pip-wheel-ikn0x7z8 2024-07-10T09:01:30,545 Building wheel for kssdtree (setup.py): started 2024-07-10T09:01:30,546 Destination directory: /tmp/pip-wheel-ikn0x7z8 2024-07-10T09:01:30,547 Running command python setup.py bdist_wheel 2024-07-10T09:01:31,616 running bdist_wheel 2024-07-10T09:01:31,713 running build 2024-07-10T09:01:31,713 running build_py 2024-07-10T09:01:31,739 creating build 2024-07-10T09:01:31,740 creating build/lib.linux-armv7l-cpython-311 2024-07-10T09:01:31,741 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2024-07-10T09:01:31,744 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2024-07-10T09:01:31,746 running egg_info 2024-07-10T09:01:31,806 writing kssdtree.egg-info/PKG-INFO 2024-07-10T09:01:31,809 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-07-10T09:01:31,810 writing requirements to kssdtree.egg-info/requires.txt 2024-07-10T09:01:31,811 writing top-level names to kssdtree.egg-info/top_level.txt 2024-07-10T09:01:31,841 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-10T09:01:31,844 reading manifest template 'MANIFEST.in' 2024-07-10T09:01:31,860 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-07-10T09:01:31,862 running build_ext 2024-07-10T09:01:32,331 building 'kssd' extension 2024-07-10T09:01:32,332 creating build/temp.linux-armv7l-cpython-311 2024-07-10T09:01:32,333 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c co2mco.c -o build/temp.linux-armv7l-cpython-311/co2mco.o -fopenmp 2024-07-10T09:01:32,571 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-07-10T09:01:32,571 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T09:01:32,572 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-07-10T09:01:32,573 | ^ 2024-07-10T09:01:32,575 co2mco.c: In function ‘co2unitllmco’: 2024-07-10T09:01:32,576 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T09:01:32,577 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-07-10T09:01:32,577 | ^ 2024-07-10T09:01:33,277 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_composite.c -o build/temp.linux-armv7l-cpython-311/command_composite.o -fopenmp 2024-07-10T09:01:33,659 command_composite.c: In function ‘get_species_abundance’: 2024-07-10T09:01:33,660 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-10T09:01:33,661 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-07-10T09:01:33,661 | ^~ 2024-07-10T09:01:33,662 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-07-10T09:01:33,662 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-07-10T09:01:33,663 | ^~ 2024-07-10T09:01:33,664 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:33,664 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-10T09:01:33,665 | ^ 2024-07-10T09:01:33,666 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:33,666 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-10T09:01:33,667 | ^~~~~~~~~~ 2024-07-10T09:01:33,667 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-10T09:01:33,668 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-07-10T09:01:33,669 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:33,669 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:33,670 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-10T09:01:33,670 | ^ 2024-07-10T09:01:33,671 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:33,671 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-10T09:01:33,671 | ^~~~~~~~~~ 2024-07-10T09:01:33,672 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-10T09:01:33,673 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-07-10T09:01:33,673 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:33,674 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:33,674 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-10T09:01:33,675 | ^ 2024-07-10T09:01:33,675 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:33,676 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-10T09:01:33,676 | ^~~~~~~~~~ 2024-07-10T09:01:33,677 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-10T09:01:33,677 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-07-10T09:01:33,678 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:33,678 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:33,679 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-10T09:01:33,680 | ^ 2024-07-10T09:01:33,681 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:33,681 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-10T09:01:33,682 | ^~~~~~~~~~ 2024-07-10T09:01:33,682 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-07-10T09:01:33,683 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-07-10T09:01:33,684 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:33,684 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:33,685 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-10T09:01:33,686 | ^ 2024-07-10T09:01:33,686 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:33,687 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-10T09:01:33,688 | ^~~~~~~~~~~~ 2024-07-10T09:01:33,689 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2024-07-10T09:01:33,689 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-07-10T09:01:33,690 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:33,931 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist.c -o build/temp.linux-armv7l-cpython-311/command_dist.o -fopenmp 2024-07-10T09:01:34,164 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-10T09:01:34,166 command_dist.c:678:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T09:01:34,166 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T09:01:34,167 | ~~^ 2024-07-10T09:01:34,167 | | 2024-07-10T09:01:34,168 | long unsigned int 2024-07-10T09:01:34,168 | %u 2024-07-10T09:01:34,168 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T09:01:34,169 | ~~~~~~~ 2024-07-10T09:01:34,169 | | 2024-07-10T09:01:34,170 | size_t {aka unsigned int} 2024-07-10T09:01:34,171 command_dist.c:678:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T09:01:34,172 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T09:01:34,172 | ~~^ 2024-07-10T09:01:34,173 | | 2024-07-10T09:01:34,173 | long unsigned int 2024-07-10T09:01:34,174 | %u 2024-07-10T09:01:34,174 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T09:01:34,175 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T09:01:34,176 | ~~~~~~~~~ 2024-07-10T09:01:34,176 | | 2024-07-10T09:01:34,177 | size_t {aka unsigned int} 2024-07-10T09:01:34,177 command_dist.c:678:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-10T09:01:34,178 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T09:01:34,179 | ~~^ 2024-07-10T09:01:34,179 | | 2024-07-10T09:01:34,180 | long unsigned int 2024-07-10T09:01:34,181 | %u 2024-07-10T09:01:34,181 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T09:01:34,182 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T09:01:34,183 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:34,183 | | 2024-07-10T09:01:34,184 | unsigned int 2024-07-10T09:01:34,185 command_dist.c:716:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-10T09:01:34,186 716 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-07-10T09:01:34,186 | ^ 2024-07-10T09:01:34,194 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-10T09:01:34,197 command_dist.c:864:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T09:01:34,197 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-10T09:01:34,197 | ~~^ ~~~~~~~ 2024-07-10T09:01:34,198 | | | 2024-07-10T09:01:34,198 | long unsigned int size_t {aka unsigned int} 2024-07-10T09:01:34,199 | %u 2024-07-10T09:01:34,201 command_dist.c:864:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T09:01:34,201 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-10T09:01:34,202 | ~~^ 2024-07-10T09:01:34,202 | | 2024-07-10T09:01:34,203 | long unsigned int 2024-07-10T09:01:34,204 | %u 2024-07-10T09:01:34,204 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-10T09:01:34,205 | ~~~~~~~~~ 2024-07-10T09:01:34,206 | | 2024-07-10T09:01:34,206 | size_t {aka unsigned int} 2024-07-10T09:01:34,207 command_dist.c:864:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-10T09:01:34,208 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-07-10T09:01:34,208 | ~~^ 2024-07-10T09:01:34,209 | | 2024-07-10T09:01:34,209 | long unsigned int 2024-07-10T09:01:34,210 | %u 2024-07-10T09:01:34,211 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-07-10T09:01:34,211 866 | (size_t) b * unitsz_distf_mapped); 2024-07-10T09:01:34,212 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:34,213 | | 2024-07-10T09:01:34,214 | unsigned int 2024-07-10T09:01:34,214 command_dist.c:811:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-07-10T09:01:34,215 811 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-07-10T09:01:34,216 | ^~~~~~~ 2024-07-10T09:01:34,216 command_dist.c:810:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-07-10T09:01:34,217 810 | struct stat cbd_fcode_stat; 2024-07-10T09:01:34,218 | ^~~~~~~~~~~~~~ 2024-07-10T09:01:34,218 command_dist.c:809:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-07-10T09:01:34,219 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-10T09:01:34,219 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:34,220 command_dist.c:809:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-07-10T09:01:34,221 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-07-10T09:01:34,221 | ^~~~~~~~~~~~~~~~~ 2024-07-10T09:01:34,224 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-10T09:01:34,226 command_dist.c:1019:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T09:01:34,226 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T09:01:34,227 | ~~^ 2024-07-10T09:01:34,227 | | 2024-07-10T09:01:34,228 | long unsigned int 2024-07-10T09:01:34,228 | %u 2024-07-10T09:01:34,229 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T09:01:34,230 | ~~~~~~~ 2024-07-10T09:01:34,230 | | 2024-07-10T09:01:34,231 | size_t {aka unsigned int} 2024-07-10T09:01:34,232 command_dist.c:1019:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T09:01:34,233 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T09:01:34,233 | ~~^ 2024-07-10T09:01:34,234 | | 2024-07-10T09:01:34,235 | long unsigned int 2024-07-10T09:01:34,235 | %u 2024-07-10T09:01:34,236 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T09:01:34,237 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T09:01:34,237 | ~~~~~~~~~ 2024-07-10T09:01:34,238 | | 2024-07-10T09:01:34,239 | size_t {aka unsigned int} 2024-07-10T09:01:34,239 command_dist.c:1019:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-07-10T09:01:34,240 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-07-10T09:01:34,241 | ~~^ 2024-07-10T09:01:34,242 | | 2024-07-10T09:01:34,242 | long unsigned int 2024-07-10T09:01:34,243 | %u 2024-07-10T09:01:34,243 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-07-10T09:01:34,244 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-07-10T09:01:34,245 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:34,245 | | 2024-07-10T09:01:34,246 | unsigned int 2024-07-10T09:01:34,246 command_dist.c:1035:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-07-10T09:01:34,247 1035 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-07-10T09:01:34,247 | ^ 2024-07-10T09:01:34,248 command_dist.c: In function ‘mco_co_dist_core’: 2024-07-10T09:01:34,248 command_dist.c:1117:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-10T09:01:34,249 1117 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-07-10T09:01:34,249 | ^ 2024-07-10T09:01:34,250 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-07-10T09:01:34,250 command_dist.c:1240:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T09:01:34,251 1240 | for (int rid = 0; rid < ref_num; rid++) 2024-07-10T09:01:34,252 | ^ 2024-07-10T09:01:34,252 command_dist.c:1246:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T09:01:34,253 1246 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-10T09:01:34,254 | ^ 2024-07-10T09:01:34,258 command_dist.c: In function ‘dist_print_nobin’: 2024-07-10T09:01:34,259 command_dist.c:1336:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T09:01:34,260 1336 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-07-10T09:01:34,260 | ^ 2024-07-10T09:01:34,262 command_dist.c:1357:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T09:01:34,262 1357 | for (int rid = 0; rid < ref_num; rid++) { 2024-07-10T09:01:34,263 | ^ 2024-07-10T09:01:34,264 command_dist.c:1383:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T09:01:34,265 1383 | for (int rid = 0; rid < ref_num; rid++) 2024-07-10T09:01:34,266 | ^ 2024-07-10T09:01:34,626 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-07-10T09:01:34,627 command_dist.c:404:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2024-07-10T09:01:34,628 404 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-07-10T09:01:34,628 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:34,629 command_dist.c:376:40: note: ‘com_abund_fp’ was declared here 2024-07-10T09:01:34,630 376 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-07-10T09:01:34,630 | ^~~~~~~~~~~~ 2024-07-10T09:01:35,462 command_dist.c: In function ‘get_dim_shuffle’: 2024-07-10T09:01:35,462 command_dist.c:268:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-07-10T09:01:35,463 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-10T09:01:35,463 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:35,464 command_dist.c:268:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-07-10T09:01:35,464 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-07-10T09:01:35,465 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,362 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-07-10T09:01:36,363 command_dist.c:597:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:36,363 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T09:01:36,364 | ^~ ~~~~~~~~~ 2024-07-10T09:01:36,364 command_dist.c:597:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-10T09:01:36,365 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T09:01:36,365 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,366 command_dist.c:626:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T09:01:36,367 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T09:01:36,367 | ^~~~~~~~~~~~~~~ 2024-07-10T09:01:36,368 command_dist.c:626:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-10T09:01:36,368 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T09:01:36,369 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,370 command_dist.c:682:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T09:01:36,370 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T09:01:36,371 | ^~~~~~~~~~~ 2024-07-10T09:01:36,372 command_dist.c:682:38: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:36,372 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T09:01:36,373 | ^~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,374 command_dist.c:682:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-10T09:01:36,374 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T09:01:36,375 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,376 command_dist.c:683:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T09:01:36,376 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T09:01:36,377 | ^~~~~ 2024-07-10T09:01:36,378 command_dist.c:683:32: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:36,379 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T09:01:36,379 | ^~~~~~~~~~~ 2024-07-10T09:01:36,380 command_dist.c:683:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T09:01:36,381 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T09:01:36,381 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,614 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-07-10T09:01:36,615 command_dist.c:764:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:36,615 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T09:01:36,616 | ^~ ~~~~~~~~~ 2024-07-10T09:01:36,616 command_dist.c:764:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-10T09:01:36,617 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T09:01:36,617 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,618 command_dist.c:791:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T09:01:36,618 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T09:01:36,618 | ^~~~~~~~~~~~~~~ 2024-07-10T09:01:36,619 command_dist.c:791:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-10T09:01:36,619 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T09:01:36,620 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,620 command_dist.c:824:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T09:01:36,621 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T09:01:36,621 | ^~~~~~~~~~~~~ 2024-07-10T09:01:36,622 command_dist.c:824:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-10T09:01:36,623 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T09:01:36,623 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,624 command_dist.c:850:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:36,625 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-10T09:01:36,625 | ^ 2024-07-10T09:01:36,626 command_dist.c:850:33: note: directive argument in the range [0, 536870912] 2024-07-10T09:01:36,626 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-10T09:01:36,627 | ^~~~~~~~~~ 2024-07-10T09:01:36,628 command_dist.c:850:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-10T09:01:36,628 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-07-10T09:01:36,629 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,630 command_dist.c:852:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:36,630 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-10T09:01:36,631 | ^ 2024-07-10T09:01:36,632 command_dist.c:852:28: note: directive argument in the range [0, 536870912] 2024-07-10T09:01:36,632 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-10T09:01:36,633 | ^~~~~~~~~~ 2024-07-10T09:01:36,634 command_dist.c:852:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-07-10T09:01:36,635 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-07-10T09:01:36,635 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,898 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-07-10T09:01:36,899 command_dist.c:928:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:36,900 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T09:01:36,900 | ^~ ~~~~~~~~~ 2024-07-10T09:01:36,901 command_dist.c:928:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-07-10T09:01:36,901 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-07-10T09:01:36,901 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,902 command_dist.c:957:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T09:01:36,902 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T09:01:36,903 | ^~~~~~~~~~~~~~~ 2024-07-10T09:01:36,903 command_dist.c:957:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-07-10T09:01:36,904 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-07-10T09:01:36,904 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,905 command_dist.c:991:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T09:01:36,905 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T09:01:36,906 | ^~~~~~~~~~~~~ 2024-07-10T09:01:36,907 command_dist.c:991:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-10T09:01:36,907 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-07-10T09:01:36,908 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,909 command_dist.c:1023:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T09:01:36,909 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T09:01:36,910 | ^~~~~~~~~~~ 2024-07-10T09:01:36,910 command_dist.c:1023:38: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:36,911 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T09:01:36,912 | ^~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,912 command_dist.c:1023:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-07-10T09:01:36,913 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-07-10T09:01:36,913 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:36,914 command_dist.c:1024:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-07-10T09:01:36,915 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T09:01:36,915 | ^~~~~ 2024-07-10T09:01:36,916 command_dist.c:1024:32: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:36,917 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T09:01:36,917 | ^~~~~~~~~~~ 2024-07-10T09:01:36,918 command_dist.c:1024:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T09:01:36,919 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-07-10T09:01:36,920 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:37,188 command_dist.c: In function ‘combine_queries’: 2024-07-10T09:01:37,190 command_dist.c:1493:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T09:01:37,190 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-10T09:01:37,190 | ^ 2024-07-10T09:01:37,191 command_dist.c:1493:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T09:01:37,192 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-07-10T09:01:37,192 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:37,193 command_dist.c:1500:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T09:01:37,193 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-10T09:01:37,194 | ^ 2024-07-10T09:01:37,194 command_dist.c:1500:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T09:01:37,195 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-07-10T09:01:37,196 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:37,197 command_dist.c:1604:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:37,198 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-10T09:01:37,198 | ^~ ~~~~~~~~ 2024-07-10T09:01:37,199 command_dist.c:1604:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-07-10T09:01:37,200 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-07-10T09:01:37,201 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:37,679 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o -fopenmp 2024-07-10T09:01:37,853 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_set.c -o build/temp.linux-armv7l-cpython-311/command_set.o -fopenmp 2024-07-10T09:01:38,023 command_set.c: In function ‘sketch_operate’: 2024-07-10T09:01:38,023 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-07-10T09:01:38,024 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-07-10T09:01:38,025 | ^ 2024-07-10T09:01:38,036 command_set.c: In function ‘combin_subset_pans’: 2024-07-10T09:01:38,037 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-10T09:01:38,038 458 | free(co_dstat_fpath); 2024-07-10T09:01:38,038 | ^~~~~~~~~~~~~~ 2024-07-10T09:01:38,039 In file included from kssdheaders/global_basic.h:159, 2024-07-10T09:01:38,040 from command_set.c:15: 2024-07-10T09:01:38,041 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-10T09:01:38,041 568 | extern void free (void *__ptr) __THROW; 2024-07-10T09:01:38,042 | ~~~~~~^~~~~ 2024-07-10T09:01:38,044 command_set.c: In function ‘grouping_genomes’: 2024-07-10T09:01:38,044 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-07-10T09:01:38,045 563 | free(co_dstat_fpath); 2024-07-10T09:01:38,046 | ^~~~~~~~~~~~~~ 2024-07-10T09:01:38,046 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-07-10T09:01:38,047 568 | extern void free (void *__ptr) __THROW; 2024-07-10T09:01:38,047 | ~~~~~~^~~~~ 2024-07-10T09:01:38,249 command_set.c: In function ‘sketch_union’: 2024-07-10T09:01:38,250 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T09:01:38,251 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:38,251 | ^ 2024-07-10T09:01:38,252 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T09:01:38,252 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:38,253 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,253 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,254 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T09:01:38,254 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:38,255 command_set.c:83:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,256 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T09:01:38,256 | ^~~~~~~~~~ 2024-07-10T09:01:38,257 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T09:01:38,258 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T09:01:38,258 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,259 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,260 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-10T09:01:38,261 | ^~ ~~~~~~~~~~ 2024-07-10T09:01:38,261 command_set.c:93:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,262 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-10T09:01:38,263 | ^~~~~~~~~~ 2024-07-10T09:01:38,263 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T09:01:38,264 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-07-10T09:01:38,265 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,382 command_set.c: In function ‘sketch_operate’: 2024-07-10T09:01:38,382 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,383 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-10T09:01:38,383 | ^~ ~~~~~~~~~~ 2024-07-10T09:01:38,384 command_set.c:154:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,385 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-10T09:01:38,385 | ^~~~~~~~~~ 2024-07-10T09:01:38,386 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-07-10T09:01:38,386 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-07-10T09:01:38,387 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,388 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,389 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-10T09:01:38,389 | ^~ ~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,390 command_set.c:156:29: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,390 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-10T09:01:38,391 | ^~~~~~~~~~ 2024-07-10T09:01:38,391 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-10T09:01:38,392 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-07-10T09:01:38,393 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,393 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,394 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T09:01:38,394 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:38,395 command_set.c:166:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,395 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T09:01:38,396 | ^~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,397 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T09:01:38,397 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T09:01:38,398 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,398 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,399 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T09:01:38,399 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:38,400 command_set.c:170:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,401 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T09:01:38,401 | ^~~~~~~~~~ 2024-07-10T09:01:38,402 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T09:01:38,402 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-07-10T09:01:38,403 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,404 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,404 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T09:01:38,405 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:38,405 command_set.c:175:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,406 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T09:01:38,406 | ^~~~~~~~~~ 2024-07-10T09:01:38,407 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T09:01:38,408 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T09:01:38,409 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,410 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,410 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T09:01:38,411 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:38,411 command_set.c:188:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,412 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T09:01:38,412 | ^~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,413 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T09:01:38,413 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-07-10T09:01:38,414 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,414 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T09:01:38,415 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:38,415 | ^ 2024-07-10T09:01:38,416 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T09:01:38,417 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:38,417 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,556 command_set.c: In function ‘uniq_sketch_union’: 2024-07-10T09:01:38,557 command_set.c:220:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T09:01:38,558 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-07-10T09:01:38,558 | ^ 2024-07-10T09:01:38,559 command_set.c:220:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2024-07-10T09:01:38,560 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-07-10T09:01:38,560 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,561 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T09:01:38,562 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:38,562 | ^ 2024-07-10T09:01:38,563 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T09:01:38,564 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:38,565 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,565 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,566 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T09:01:38,567 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:38,567 command_set.c:248:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,568 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T09:01:38,569 | ^~~~~~~~~~ 2024-07-10T09:01:38,569 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T09:01:38,570 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-07-10T09:01:38,571 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,571 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,572 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-10T09:01:38,573 | ^~ ~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,574 command_set.c:260:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,574 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-10T09:01:38,574 | ^~~~~~~~~~ 2024-07-10T09:01:38,575 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-07-10T09:01:38,575 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-07-10T09:01:38,576 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,702 command_set.c: In function ‘combin_pans’: 2024-07-10T09:01:38,703 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,703 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T09:01:38,704 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:38,704 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-07-10T09:01:38,705 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T09:01:38,705 | ^~~~~~~~~~ 2024-07-10T09:01:38,706 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-07-10T09:01:38,706 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T09:01:38,707 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,707 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,708 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T09:01:38,709 | ^~ ~~~~~~~~~~ 2024-07-10T09:01:38,710 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-07-10T09:01:38,710 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T09:01:38,711 | ^~~~~~~~~~ 2024-07-10T09:01:38,712 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-07-10T09:01:38,713 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T09:01:38,713 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,714 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T09:01:38,715 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:38,715 | ^ 2024-07-10T09:01:38,716 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T09:01:38,717 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:38,718 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,919 command_set.c: In function ‘combin_subset_pans’: 2024-07-10T09:01:38,920 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,921 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T09:01:38,921 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:38,922 command_set.c:470:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,923 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T09:01:38,923 | ^~~~~~~~~~ 2024-07-10T09:01:38,924 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T09:01:38,925 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T09:01:38,925 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,926 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,926 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T09:01:38,927 | ^~ ~~~~~~~~~~ 2024-07-10T09:01:38,927 command_set.c:476:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,928 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T09:01:38,928 | ^~~~~~~~~~ 2024-07-10T09:01:38,929 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T09:01:38,929 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T09:01:38,930 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,930 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,931 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T09:01:38,931 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:38,932 command_set.c:482:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,933 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T09:01:38,933 | ^~~~~~~~~~ 2024-07-10T09:01:38,934 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T09:01:38,935 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T09:01:38,935 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,936 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:38,937 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T09:01:38,937 | ^~ ~~~~~~~~~~ 2024-07-10T09:01:38,938 command_set.c:513:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:38,938 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T09:01:38,939 | ^~~~~~~~~~ 2024-07-10T09:01:38,940 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T09:01:38,940 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T09:01:38,941 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:38,941 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T09:01:38,942 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:38,943 | ^ 2024-07-10T09:01:38,943 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T09:01:38,944 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:38,945 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:39,165 command_set.c: In function ‘grouping_genomes’: 2024-07-10T09:01:39,166 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:39,167 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T09:01:39,168 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:39,169 command_set.c:575:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:39,169 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T09:01:39,169 | ^~~~~~~~~~ 2024-07-10T09:01:39,170 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T09:01:39,170 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-07-10T09:01:39,171 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:39,171 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:39,171 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T09:01:39,172 | ^~ ~~~~~~~~~~ 2024-07-10T09:01:39,172 command_set.c:581:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:39,173 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T09:01:39,173 | ^~~~~~~~~~ 2024-07-10T09:01:39,174 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T09:01:39,174 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-07-10T09:01:39,175 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:39,176 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:39,176 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T09:01:39,177 | ^~ ~~~~~~~~~~~ 2024-07-10T09:01:39,178 command_set.c:613:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:39,178 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T09:01:39,179 | ^~~~~~~~~~ 2024-07-10T09:01:39,180 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-07-10T09:01:39,181 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-07-10T09:01:39,181 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:39,182 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-07-10T09:01:39,183 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T09:01:39,183 | ^~ ~~~~~~~~~~ 2024-07-10T09:01:39,184 command_set.c:635:25: note: directive argument in the range [-2147483644, 2147483646] 2024-07-10T09:01:39,185 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T09:01:39,185 | ^~~~~~~~~~ 2024-07-10T09:01:39,186 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-07-10T09:01:39,187 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-07-10T09:01:39,187 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:39,188 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-07-10T09:01:39,189 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:39,189 | ^ 2024-07-10T09:01:39,190 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-07-10T09:01:39,191 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-07-10T09:01:39,191 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:39,468 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-311/command_shuffle.o -fopenmp 2024-07-10T09:01:39,805 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c global_basic.c -o build/temp.linux-armv7l-cpython-311/global_basic.o -fopenmp 2024-07-10T09:01:39,975 global_basic.c: In function ‘organize_infile_list’: 2024-07-10T09:01:39,975 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-07-10T09:01:39,976 195 | while (isspace(*buf)) buf++; 2024-07-10T09:01:39,977 | ^~~~~~~ 2024-07-10T09:01:39,977 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2024-07-10T09:01:39,978 34 | #include 2024-07-10T09:01:39,978 +++ |+#include 2024-07-10T09:01:39,979 35 | 2024-07-10T09:01:39,979 global_basic.c:201:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T09:01:39,980 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-10T09:01:39,981 | ~~^ 2024-07-10T09:01:39,981 | | 2024-07-10T09:01:39,982 | long unsigned int 2024-07-10T09:01:39,983 | %u 2024-07-10T09:01:39,983 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-10T09:01:39,984 | ~~~~~~~~~~~ 2024-07-10T09:01:39,985 | | 2024-07-10T09:01:39,986 | size_t {aka unsigned int} 2024-07-10T09:01:39,987 global_basic.c:233:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-07-10T09:01:39,988 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-07-10T09:01:39,989 | ~~^ 2024-07-10T09:01:39,989 | | 2024-07-10T09:01:39,990 | long unsigned int 2024-07-10T09:01:39,990 | %u 2024-07-10T09:01:39,991 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-07-10T09:01:39,992 | ~~~~~~~~~~~ 2024-07-10T09:01:39,993 | | 2024-07-10T09:01:39,993 | size_t {aka unsigned int} 2024-07-10T09:01:40,740 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-311/iseq2comem.o -fopenmp 2024-07-10T09:01:40,917 iseq2comem.c: In function ‘reads2mco’: 2024-07-10T09:01:40,917 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,918 156 | if (base > TL) { 2024-07-10T09:01:40,918 | ^ 2024-07-10T09:01:40,919 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,919 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T09:01:40,920 | ^~ 2024-07-10T09:01:40,921 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,921 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T09:01:40,922 | ^ 2024-07-10T09:01:40,922 iseq2comem.c: In function ‘fasta2co’: 2024-07-10T09:01:40,923 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,923 239 | if (base > TL) { 2024-07-10T09:01:40,924 | ^ 2024-07-10T09:01:40,924 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,925 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T09:01:40,925 | ^~ 2024-07-10T09:01:40,926 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,927 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T09:01:40,927 | ^ 2024-07-10T09:01:40,928 iseq2comem.c: In function ‘fastq2co’: 2024-07-10T09:01:40,929 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-07-10T09:01:40,930 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-07-10T09:01:40,930 | ^~ 2024-07-10T09:01:40,931 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,932 318 | if (base > TL) { 2024-07-10T09:01:40,932 | ^ 2024-07-10T09:01:40,933 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,934 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T09:01:40,935 | ^~ 2024-07-10T09:01:40,936 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,937 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T09:01:40,937 | ^ 2024-07-10T09:01:40,938 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,939 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-07-10T09:01:40,940 | ^ 2024-07-10T09:01:40,941 iseq2comem.c: In function ‘fastq2koc’: 2024-07-10T09:01:40,941 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,942 402 | if (base > TL) { 2024-07-10T09:01:40,942 | ^ 2024-07-10T09:01:40,943 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,943 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T09:01:40,944 | ^~ 2024-07-10T09:01:40,944 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,945 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T09:01:40,945 | ^ 2024-07-10T09:01:40,947 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-07-10T09:01:40,947 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,948 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T09:01:40,949 | ^~ 2024-07-10T09:01:40,949 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:40,950 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-07-10T09:01:40,951 | ^ 2024-07-10T09:01:42,291 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2024-07-10T09:01:42,346 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mytime.c -o build/temp.linux-armv7l-cpython-311/mytime.o -fopenmp 2024-07-10T09:01:42,469 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c pykssd.c -o build/temp.linux-armv7l-cpython-311/pykssd.o -fopenmp 2024-07-10T09:01:42,858 pykssd.c: In function ‘py_dist_dispatch’: 2024-07-10T09:01:42,858 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-07-10T09:01:42,859 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-07-10T09:01:42,859 | ^~~~~~ 2024-07-10T09:01:42,860 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-07-10T09:01:42,861 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-07-10T09:01:42,862 | ^~~~~~ 2024-07-10T09:01:42,863 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-07-10T09:01:42,864 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-07-10T09:01:42,865 | ^~~~~~ 2024-07-10T09:01:43,430 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/co2mco.o build/temp.linux-armv7l-cpython-311/command_composite.o build/temp.linux-armv7l-cpython-311/command_dist.o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o build/temp.linux-armv7l-cpython-311/command_set.o build/temp.linux-armv7l-cpython-311/command_shuffle.o build/temp.linux-armv7l-cpython-311/global_basic.o build/temp.linux-armv7l-cpython-311/iseq2comem.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/mytime.o build/temp.linux-armv7l-cpython-311/pykssd.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -fopenmp 2024-07-10T09:01:43,578 building 'nj' extension 2024-07-10T09:01:43,579 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c align.c -o build/temp.linux-armv7l-cpython-311/align.o 2024-07-10T09:01:44,068 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c buildtree.c -o build/temp.linux-armv7l-cpython-311/buildtree.o 2024-07-10T09:01:44,216 buildtree.c: In function ‘UPGMA_buildtree’: 2024-07-10T09:01:44,217 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T09:01:44,217 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-10T09:01:44,218 | ^~ 2024-07-10T09:01:44,219 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T09:01:44,220 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-07-10T09:01:44,220 | ^~ 2024-07-10T09:01:44,875 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c cluster.c -o build/temp.linux-armv7l-cpython-311/cluster.o 2024-07-10T09:01:45,242 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c distancemat.c -o build/temp.linux-armv7l-cpython-311/distancemat.o 2024-07-10T09:01:45,379 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-07-10T09:01:45,380 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T09:01:45,381 226 | for( i=0; i < dest->size; i++) { 2024-07-10T09:01:45,382 | ^ 2024-07-10T09:01:45,382 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-07-10T09:01:45,383 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T09:01:45,384 260 | for( i=0; i < mat->size; i++) { 2024-07-10T09:01:45,385 | ^ 2024-07-10T09:01:45,386 distancemat.c: In function ‘print_DistanceMatrix’: 2024-07-10T09:01:45,387 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T09:01:45,387 349 | for(row=0; row < mat->size; row++) { 2024-07-10T09:01:45,388 | ^ 2024-07-10T09:01:45,389 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-07-10T09:01:45,389 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-07-10T09:01:45,390 410 | while(c = fgetc(handle)) { 2024-07-10T09:01:45,391 | ^ 2024-07-10T09:01:45,780 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c pynj.c -o build/temp.linux-armv7l-cpython-311/pynj.o 2024-07-10T09:01:46,248 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c sequence.c -o build/temp.linux-armv7l-cpython-311/sequence.o 2024-07-10T09:01:46,464 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c tree.c -o build/temp.linux-armv7l-cpython-311/tree.o 2024-07-10T09:01:47,311 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c util.c -o build/temp.linux-armv7l-cpython-311/util.o 2024-07-10T09:01:47,486 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/align.o build/temp.linux-armv7l-cpython-311/buildtree.o build/temp.linux-armv7l-cpython-311/cluster.o build/temp.linux-armv7l-cpython-311/distancemat.o build/temp.linux-armv7l-cpython-311/pynj.o build/temp.linux-armv7l-cpython-311/sequence.o build/temp.linux-armv7l-cpython-311/tree.o build/temp.linux-armv7l-cpython-311/util.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so 2024-07-10T09:01:47,595 building 'dnj' extension 2024-07-10T09:01:47,595 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c bytescale.c -o build/temp.linux-armv7l-cpython-311/bytescale.o -fopenmp 2024-07-10T09:01:47,651 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c dnj.c -o build/temp.linux-armv7l-cpython-311/dnj.o -fopenmp 2024-07-10T09:01:47,821 dnj.c: In function ‘minQpair’: 2024-07-10T09:01:47,822 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,822 70 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,823 | ^~~ 2024-07-10T09:01:47,824 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,825 126 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,826 | ^~~ 2024-07-10T09:01:47,826 dnj.c: In function ‘maxQpair’: 2024-07-10T09:01:47,827 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,828 157 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,829 | ^~~ 2024-07-10T09:01:47,830 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,830 213 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,831 | ^~~ 2024-07-10T09:01:47,831 dnj.c: In function ‘UPGMApair’: 2024-07-10T09:01:47,832 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,833 237 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,833 | ^~~ 2024-07-10T09:01:47,834 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,835 284 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,835 | ^~~ 2024-07-10T09:01:47,836 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,837 291 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,837 | ^~~ 2024-07-10T09:01:47,838 dnj.c: In function ‘minQrow’: 2024-07-10T09:01:47,839 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,840 374 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,841 | ^~~ 2024-07-10T09:01:47,842 dnj.c: In function ‘maxQrow’: 2024-07-10T09:01:47,842 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,843 435 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,843 | ^~~ 2024-07-10T09:01:47,844 dnj.c: In function ‘UPGMArow’: 2024-07-10T09:01:47,845 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,845 488 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,845 | ^~~ 2024-07-10T09:01:47,846 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,846 494 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,847 | ^~~ 2024-07-10T09:01:47,847 dnj.c: In function ‘minQ_thread’: 2024-07-10T09:01:47,848 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:47,848 553 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:47,849 | ^~~ 2024-07-10T09:01:49,246 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c filebuff.c -o build/temp.linux-armv7l-cpython-311/filebuff.o -fopenmp 2024-07-10T09:01:49,363 filebuff.c: In function ‘BuffgzFileBuff’: 2024-07-10T09:01:49,364 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:49,365 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-07-10T09:01:49,365 | ^~ 2024-07-10T09:01:49,689 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c hclust.c -o build/temp.linux-armv7l-cpython-311/hclust.o -fopenmp 2024-07-10T09:01:49,830 hclust.c: In function ‘minQ’: 2024-07-10T09:01:49,831 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T09:01:49,831 364 | while(++i < Q->n) { 2024-07-10T09:01:49,832 | ^ 2024-07-10T09:01:49,833 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:49,834 377 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:49,834 | ^~~ 2024-07-10T09:01:49,835 hclust.c: In function ‘maxQ’: 2024-07-10T09:01:49,836 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-07-10T09:01:49,836 394 | while(++i < Q->n) { 2024-07-10T09:01:49,837 | ^ 2024-07-10T09:01:49,837 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:49,838 407 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:49,839 | ^~~ 2024-07-10T09:01:52,218 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c matrix.c -o build/temp.linux-armv7l-cpython-311/matrix.o -fopenmp 2024-07-10T09:01:52,346 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-07-10T09:01:52,346 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-07-10T09:01:52,347 538 | if(pos != n) { 2024-07-10T09:01:52,348 | ^~ 2024-07-10T09:01:53,221 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2024-07-10T09:01:53,274 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nj.c -o build/temp.linux-armv7l-cpython-311/nj.o -fopenmp 2024-07-10T09:01:53,403 nj.c: In function ‘initQ’: 2024-07-10T09:01:53,404 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:53,405 243 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:53,405 | ^~~ 2024-07-10T09:01:53,406 nj.c: In function ‘initQ_MN’: 2024-07-10T09:01:53,407 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:53,407 358 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:53,408 | ^~~ 2024-07-10T09:01:53,411 nj.c: In function ‘minD’: 2024-07-10T09:01:53,412 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:53,413 559 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:53,413 | ^~~ 2024-07-10T09:01:53,414 nj.c: In function ‘maxD’: 2024-07-10T09:01:53,414 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:53,415 642 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:53,415 | ^~~ 2024-07-10T09:01:53,419 nj.c: In function ‘minPair’: 2024-07-10T09:01:53,419 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-07-10T09:01:53,420 826 | pos <<= sizeof(unsigned) * 8; 2024-07-10T09:01:53,421 | ^~~ 2024-07-10T09:01:55,787 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nwck.c -o build/temp.linux-armv7l-cpython-311/nwck.o -fopenmp 2024-07-10T09:01:56,331 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pherror.c -o build/temp.linux-armv7l-cpython-311/pherror.o -fopenmp 2024-07-10T09:01:56,425 pherror.c: In function ‘cfread’: 2024-07-10T09:01:56,426 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-07-10T09:01:56,426 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-07-10T09:01:56,427 | ^~ 2024-07-10T09:01:56,519 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c phy.c -o build/temp.linux-armv7l-cpython-311/phy.o -fopenmp 2024-07-10T09:01:57,587 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pydnj.c -o build/temp.linux-armv7l-cpython-311/pydnj.o -fopenmp 2024-07-10T09:01:57,955 In file included from pydnj.c:11: 2024-07-10T09:01:57,956 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-07-10T09:01:57,956 20 | #define _XOPEN_SOURCE 600 2024-07-10T09:01:57,957 | 2024-07-10T09:01:57,958 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-07-10T09:01:57,958 from /usr/include/stdlib.h:26, 2024-07-10T09:01:57,959 from /usr/include/python3.11/Python.h:23, 2024-07-10T09:01:57,960 from pydnj.c:1: 2024-07-10T09:01:57,961 /usr/include/features.h:214: note: this is the location of the previous definition 2024-07-10T09:01:57,961 214 | # define _XOPEN_SOURCE 700 2024-07-10T09:01:57,962 | 2024-07-10T09:01:57,981 pydnj.c: In function ‘py_build’: 2024-07-10T09:01:57,981 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-07-10T09:01:57,982 165 | p = omp_get_num_procs(); 2024-07-10T09:01:57,983 | ^~~~~~~~~~~~~~~~~ 2024-07-10T09:01:58,101 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2024-07-10T09:01:58,102 169 | free(file); 2024-07-10T09:01:58,102 | ^~~~~~~~~~ 2024-07-10T09:01:58,103 pydnj.c:125:12: note: returned from ‘fopen’ 2024-07-10T09:01:58,103 125 | file = fopen(inputfilename, "r"); 2024-07-10T09:01:58,104 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-07-10T09:01:58,178 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c qseqs.c -o build/temp.linux-armv7l-cpython-311/qseqs.o -fopenmp 2024-07-10T09:01:58,385 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c str.c -o build/temp.linux-armv7l-cpython-311/str.o -fopenmp 2024-07-10T09:01:58,495 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c tmp.c -o build/temp.linux-armv7l-cpython-311/tmp.o -fopenmp 2024-07-10T09:01:58,694 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c vector.c -o build/temp.linux-armv7l-cpython-311/vector.o -fopenmp 2024-07-10T09:01:58,855 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/bytescale.o build/temp.linux-armv7l-cpython-311/dnj.o build/temp.linux-armv7l-cpython-311/filebuff.o build/temp.linux-armv7l-cpython-311/hclust.o build/temp.linux-armv7l-cpython-311/matrix.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/nj.o build/temp.linux-armv7l-cpython-311/nwck.o build/temp.linux-armv7l-cpython-311/pherror.o build/temp.linux-armv7l-cpython-311/phy.o build/temp.linux-armv7l-cpython-311/pydnj.o build/temp.linux-armv7l-cpython-311/qseqs.o build/temp.linux-armv7l-cpython-311/str.o build/temp.linux-armv7l-cpython-311/tmp.o build/temp.linux-armv7l-cpython-311/vector.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -fopenmp 2024-07-10T09:01:59,017 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-07-10T09:01:59,018 !! 2024-07-10T09:01:59,019 ******************************************************************************** 2024-07-10T09:01:59,020 Please avoid running ``setup.py`` directly. 2024-07-10T09:01:59,021 Instead, use pypa/build, pypa/installer or other 2024-07-10T09:01:59,021 standards-based tools. 2024-07-10T09:01:59,022 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-07-10T09:01:59,023 ******************************************************************************** 2024-07-10T09:01:59,024 !! 2024-07-10T09:01:59,025 self.initialize_options() 2024-07-10T09:01:59,042 installing to build/bdist.linux-armv7l/wheel 2024-07-10T09:01:59,043 running install 2024-07-10T09:01:59,067 running install_lib 2024-07-10T09:01:59,092 creating build/bdist.linux-armv7l 2024-07-10T09:01:59,093 creating build/bdist.linux-armv7l/wheel 2024-07-10T09:01:59,094 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-10T09:01:59,101 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-10T09:01:59,109 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-07-10T09:01:59,113 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-07-10T09:01:59,115 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-07-10T09:01:59,117 running install_egg_info 2024-07-10T09:01:59,148 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-1.1.6-py3.11.egg-info 2024-07-10T09:01:59,160 running install_scripts 2024-07-10T09:01:59,235 creating build/bdist.linux-armv7l/wheel/kssdtree-1.1.6.dist-info/WHEEL 2024-07-10T09:01:59,238 creating '/tmp/pip-wheel-ikn0x7z8/kssdtree-1.1.6-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-07-10T09:01:59,313 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2024-07-10T09:01:59,397 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2024-07-10T09:01:59,402 adding 'kssdtree.py' 2024-07-10T09:01:59,422 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2024-07-10T09:01:59,425 adding 'toolutils.py' 2024-07-10T09:01:59,427 adding 'kssdtree-1.1.6.dist-info/METADATA' 2024-07-10T09:01:59,428 adding 'kssdtree-1.1.6.dist-info/WHEEL' 2024-07-10T09:01:59,429 adding 'kssdtree-1.1.6.dist-info/dependency_links.txt' 2024-07-10T09:01:59,430 adding 'kssdtree-1.1.6.dist-info/top_level.txt' 2024-07-10T09:01:59,431 adding 'kssdtree-1.1.6.dist-info/RECORD' 2024-07-10T09:01:59,441 removing build/bdist.linux-armv7l/wheel 2024-07-10T09:01:59,598 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-07-10T09:01:59,604 Created wheel for kssdtree: filename=kssdtree-1.1.6-cp311-cp311-linux_armv7l.whl size=379695 sha256=0901b6cf3efb240d5d32b1e88a8863f28e2986a2c0749886421c643b98a4aec2 2024-07-10T09:01:59,605 Stored in directory: /tmp/pip-ephem-wheel-cache-2pr5zkv7/wheels/66/a4/f7/b85aee3028e74279d77e98a5ed3242075ef64bc52081b30bf1 2024-07-10T09:01:59,614 Successfully built kssdtree 2024-07-10T09:01:59,629 Removed build tracker: '/tmp/pip-build-tracker-rykj1kwz'