2025-05-30T12:02:59,251 Created temporary directory: /tmp/pip-build-tracker-6li39yfo 2025-05-30T12:02:59,252 Initialized build tracking at /tmp/pip-build-tracker-6li39yfo 2025-05-30T12:02:59,253 Created build tracker: /tmp/pip-build-tracker-6li39yfo 2025-05-30T12:02:59,253 Entered build tracker: /tmp/pip-build-tracker-6li39yfo 2025-05-30T12:02:59,254 Created temporary directory: /tmp/pip-wheel-ogk9abeo 2025-05-30T12:02:59,258 Created temporary directory: /tmp/pip-ephem-wheel-cache-rai0hmk2 2025-05-30T12:02:59,309 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-05-30T12:02:59,311 2 location(s) to search for versions of kssdtree: 2025-05-30T12:02:59,311 * https://pypi.org/simple/kssdtree/ 2025-05-30T12:02:59,311 * https://www.piwheels.org/simple/kssdtree/ 2025-05-30T12:02:59,312 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2025-05-30T12:02:59,313 Getting page https://pypi.org/simple/kssdtree/ 2025-05-30T12:02:59,314 Found index url https://pypi.org/simple/ 2025-05-30T12:02:59,462 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2025-05-30T12:02:59,465 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 2025-05-30T12:02:59,465 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 2025-05-30T12:02:59,466 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 2025-05-30T12:02:59,467 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 2025-05-30T12:02:59,467 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 2025-05-30T12:02:59,468 Found link https://files.pythonhosted.org/packages/cd/4b/d886cbcc573ff0969da7d9c756049925b86141e60ee6708dfbbe0644d008/kssdtree-1.1.7.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.7 2025-05-30T12:02:59,469 Found link https://files.pythonhosted.org/packages/7e/8a/a62c8adc92df69ab8cb242827ee64a3e2b6d5c89b83425785dd00605af17/kssdtree-1.1.8.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.8 2025-05-30T12:02:59,469 Found link https://files.pythonhosted.org/packages/da/db/e458cca6427752c05428d2378ccdee631d32f760174fdaba65f73125e71b/kssdtree-1.1.9.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.9 2025-05-30T12:02:59,470 Found link https://files.pythonhosted.org/packages/9d/47/017180a30e73e421372377cbe6d01c5e51a5108ea2177f20ccd7d283f8d1/kssdtree-2.0.0.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.0 2025-05-30T12:02:59,471 Found link https://files.pythonhosted.org/packages/ba/39/d443cac955912a0371c93b797311cb9ec3a8d6ee0a5d7673376d826aa6b2/kssdtree-2.0.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.1 2025-05-30T12:02:59,472 Found link https://files.pythonhosted.org/packages/2e/32/e53c0e3735cbc913b2c96b4e0e1c1005fe816a4d71b38b80cdcfb5c67fa8/kssdtree-2.0.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.2 2025-05-30T12:02:59,472 Found link https://files.pythonhosted.org/packages/c0/0f/effc10c8e76dbe3b9a35a4b4d9e65a0a889ee805e10334541c3ca7ae3b94/kssdtree-2.0.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.3 2025-05-30T12:02:59,473 Found link https://files.pythonhosted.org/packages/fc/8d/d3790baa2f2f0a01c913005b94a82dc13ef601e7015e662ccff94bb1b458/kssdtree-2.0.4.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.4 2025-05-30T12:02:59,474 Found link https://files.pythonhosted.org/packages/b5/f8/19480a4c57704944f973ebf534f9582054949cca20170a33c6f874974440/kssdtree-2.0.5.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.5 2025-05-30T12:02:59,474 Found link https://files.pythonhosted.org/packages/46/ef/2d920d5d2fceded48c7add363e04f49ae85414bcd4360e1295d6fddc4a24/kssdtree-2.0.6.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.6 2025-05-30T12:02:59,475 Found link https://files.pythonhosted.org/packages/9c/1c/c6b3f05465d145856ac992328bd59e776286a59b120254620c1dbffcf67f/kssdtree-2.0.7.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.7 2025-05-30T12:02:59,476 Found link https://files.pythonhosted.org/packages/82/9b/dac2af6572f0c4421e5ba8341dcfddac466de30c62acfa019d9ef70b2670/kssdtree-2.0.8.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.8 2025-05-30T12:02:59,476 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2025-05-30T12:02:59,477 Getting page https://www.piwheels.org/simple/kssdtree/ 2025-05-30T12:02:59,478 Found index url https://www.piwheels.org/simple/ 2025-05-30T12:02:59,643 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kssdtree/ 2025-05-30T12:03:00,296 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kssdtree/ 2025-05-30T12:03:01,449 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kssdtree/ 2025-05-30T12:03:03,667 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kssdtree/ 2025-05-30T12:03:07,872 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kssdtree/ 2025-05-30T12:03:08,087 Could not fetch URL https://www.piwheels.org/simple/kssdtree/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/kssdtree/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-05-30T12:03:08,089 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2025-05-30T12:03:08,090 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2025-05-30T12:03:08,108 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2025-05-30T12:03:08,110 Collecting kssdtree==2.0.7 2025-05-30T12:03:08,112 Created temporary directory: /tmp/pip-unpack-jsxkyn47 2025-05-30T12:03:08,259 Downloading kssdtree-2.0.7.tar.gz (113 kB) 2025-05-30T12:03:08,481 Added kssdtree==2.0.7 from https://files.pythonhosted.org/packages/9c/1c/c6b3f05465d145856ac992328bd59e776286a59b120254620c1dbffcf67f/kssdtree-2.0.7.tar.gz to build tracker '/tmp/pip-build-tracker-6li39yfo' 2025-05-30T12:03:08,482 Running setup.py (path:/tmp/pip-wheel-ogk9abeo/kssdtree_bfaed8f53cdc4782b3b98ae1488ab726/setup.py) egg_info for package kssdtree 2025-05-30T12:03:08,483 Created temporary directory: /tmp/pip-pip-egg-info-_01uzz_4 2025-05-30T12:03:08,484 Preparing metadata (setup.py): started 2025-05-30T12:03:08,485 Running command python setup.py egg_info 2025-05-30T12:03:09,367 running egg_info 2025-05-30T12:03:09,394 creating /tmp/pip-pip-egg-info-_01uzz_4/kssdtree.egg-info 2025-05-30T12:03:09,394 writing /tmp/pip-pip-egg-info-_01uzz_4/kssdtree.egg-info/PKG-INFO 2025-05-30T12:03:09,398 writing dependency_links to /tmp/pip-pip-egg-info-_01uzz_4/kssdtree.egg-info/dependency_links.txt 2025-05-30T12:03:09,400 writing requirements to /tmp/pip-pip-egg-info-_01uzz_4/kssdtree.egg-info/requires.txt 2025-05-30T12:03:09,401 writing top-level names to /tmp/pip-pip-egg-info-_01uzz_4/kssdtree.egg-info/top_level.txt 2025-05-30T12:03:09,402 writing manifest file '/tmp/pip-pip-egg-info-_01uzz_4/kssdtree.egg-info/SOURCES.txt' 2025-05-30T12:03:09,510 reading manifest file '/tmp/pip-pip-egg-info-_01uzz_4/kssdtree.egg-info/SOURCES.txt' 2025-05-30T12:03:09,512 reading manifest template 'MANIFEST.in' 2025-05-30T12:03:09,530 writing manifest file '/tmp/pip-pip-egg-info-_01uzz_4/kssdtree.egg-info/SOURCES.txt' 2025-05-30T12:03:09,634 Preparing metadata (setup.py): finished with status 'done' 2025-05-30T12:03:09,637 Source in /tmp/pip-wheel-ogk9abeo/kssdtree_bfaed8f53cdc4782b3b98ae1488ab726 has version 2.0.7, which satisfies requirement kssdtree==2.0.7 from https://files.pythonhosted.org/packages/9c/1c/c6b3f05465d145856ac992328bd59e776286a59b120254620c1dbffcf67f/kssdtree-2.0.7.tar.gz 2025-05-30T12:03:09,638 Removed kssdtree==2.0.7 from https://files.pythonhosted.org/packages/9c/1c/c6b3f05465d145856ac992328bd59e776286a59b120254620c1dbffcf67f/kssdtree-2.0.7.tar.gz from build tracker '/tmp/pip-build-tracker-6li39yfo' 2025-05-30T12:03:09,643 Created temporary directory: /tmp/pip-unpack-g5mengoy 2025-05-30T12:03:09,644 Created temporary directory: /tmp/pip-unpack-wpr3c9wd 2025-05-30T12:03:09,645 Building wheels for collected packages: kssdtree 2025-05-30T12:03:09,649 Created temporary directory: /tmp/pip-wheel-wxatxkca 2025-05-30T12:03:09,650 DEPRECATION: Building 'kssdtree' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'kssdtree'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-05-30T12:03:09,651 Building wheel for kssdtree (setup.py): started 2025-05-30T12:03:09,652 Destination directory: /tmp/pip-wheel-wxatxkca 2025-05-30T12:03:09,653 Running command python setup.py bdist_wheel 2025-05-30T12:03:10,470 running bdist_wheel 2025-05-30T12:03:10,600 running build 2025-05-30T12:03:10,601 running build_py 2025-05-30T12:03:10,629 creating build/lib.linux-armv7l-cpython-311 2025-05-30T12:03:10,630 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2025-05-30T12:03:10,633 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2025-05-30T12:03:10,635 running egg_info 2025-05-30T12:03:10,662 writing kssdtree.egg-info/PKG-INFO 2025-05-30T12:03:10,665 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2025-05-30T12:03:10,667 writing requirements to kssdtree.egg-info/requires.txt 2025-05-30T12:03:10,668 writing top-level names to kssdtree.egg-info/top_level.txt 2025-05-30T12:03:10,697 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2025-05-30T12:03:10,703 reading manifest template 'MANIFEST.in' 2025-05-30T12:03:10,721 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2025-05-30T12:03:10,723 running build_ext 2025-05-30T12:03:11,185 building 'kssd' extension 2025-05-30T12:03:11,186 creating build/temp.linux-armv7l-cpython-311 2025-05-30T12:03:11,188 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 2025-05-30T12:03:11,366 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2025-05-30T12:03:11,367 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T12:03:11,368 109 | for (unsigned int i = 0; i < comp_num; i++) { 2025-05-30T12:03:11,368 | ^ 2025-05-30T12:03:11,371 co2mco.c: In function ‘co2unitllmco’: 2025-05-30T12:03:11,372 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T12:03:11,373 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2025-05-30T12:03:11,373 | ^ 2025-05-30T12:03:12,073 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 2025-05-30T12:03:12,451 command_composite.c: In function ‘get_species_abundance’: 2025-05-30T12:03:12,452 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2025-05-30T12:03:12,453 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2025-05-30T12:03:12,454 | ^~ 2025-05-30T12:03:12,455 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2025-05-30T12:03:12,456 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2025-05-30T12:03:12,457 | ^~ 2025-05-30T12:03:12,457 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:12,458 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-05-30T12:03:12,459 | ^ 2025-05-30T12:03:12,459 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:12,460 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-05-30T12:03:12,461 | ^~~~~~~~~~ 2025-05-30T12:03:12,462 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-05-30T12:03:12,462 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-05-30T12:03:12,463 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:12,464 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:12,464 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-05-30T12:03:12,465 | ^ 2025-05-30T12:03:12,466 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:12,466 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-05-30T12:03:12,467 | ^~~~~~~~~~ 2025-05-30T12:03:12,468 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-05-30T12:03:12,468 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-05-30T12:03:12,469 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:12,470 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:12,471 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-05-30T12:03:12,471 | ^ 2025-05-30T12:03:12,472 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:12,473 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-05-30T12:03:12,474 | ^~~~~~~~~~ 2025-05-30T12:03:12,474 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-05-30T12:03:12,475 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-05-30T12:03:12,475 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:12,476 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:12,476 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-05-30T12:03:12,477 | ^ 2025-05-30T12:03:12,477 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:12,478 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-05-30T12:03:12,479 | ^~~~~~~~~~ 2025-05-30T12:03:12,479 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-05-30T12:03:12,480 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-05-30T12:03:12,480 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:12,481 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:12,481 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-05-30T12:03:12,482 | ^ 2025-05-30T12:03:12,483 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:12,484 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-05-30T12:03:12,484 | ^~~~~~~~~~~~ 2025-05-30T12:03:12,485 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2025-05-30T12:03:12,485 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-05-30T12:03:12,486 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:12,708 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 2025-05-30T12:03:12,942 command_dist.c: In function ‘mco_cbd_co_dist’: 2025-05-30T12:03:12,943 command_dist.c:677:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T12:03:12,944 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T12:03:12,944 | ~~^ 2025-05-30T12:03:12,945 | | 2025-05-30T12:03:12,946 | long unsigned int 2025-05-30T12:03:12,946 | %u 2025-05-30T12:03:12,947 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T12:03:12,947 | ~~~~~~~ 2025-05-30T12:03:12,948 | | 2025-05-30T12:03:12,949 | size_t {aka unsigned int} 2025-05-30T12:03:12,950 command_dist.c:677:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T12:03:12,951 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T12:03:12,951 | ~~^ 2025-05-30T12:03:12,952 | | 2025-05-30T12:03:12,952 | long unsigned int 2025-05-30T12:03:12,953 | %u 2025-05-30T12:03:12,953 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T12:03:12,954 679 | maplength, (size_t) b * unitsz_distf_mapped); 2025-05-30T12:03:12,955 | ~~~~~~~~~ 2025-05-30T12:03:12,955 | | 2025-05-30T12:03:12,956 | size_t {aka unsigned int} 2025-05-30T12:03:12,956 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-05-30T12:03:12,957 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T12:03:12,957 | ~~^ 2025-05-30T12:03:12,958 | | 2025-05-30T12:03:12,958 | long unsigned int 2025-05-30T12:03:12,959 | %u 2025-05-30T12:03:12,960 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T12:03:12,961 679 | maplength, (size_t) b * unitsz_distf_mapped); 2025-05-30T12:03:12,961 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:12,962 | | 2025-05-30T12:03:12,963 | unsigned int 2025-05-30T12:03:12,963 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-05-30T12:03:12,964 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2025-05-30T12:03:12,965 | ^ 2025-05-30T12:03:12,965 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2025-05-30T12:03:12,966 command_dist.c:863:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T12:03:12,966 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-05-30T12:03:12,967 | ~~^ ~~~~~~~ 2025-05-30T12:03:12,967 | | | 2025-05-30T12:03:12,968 | long unsigned int size_t {aka unsigned int} 2025-05-30T12:03:12,969 | %u 2025-05-30T12:03:12,969 command_dist.c:863:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T12:03:12,970 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-05-30T12:03:12,971 | ~~^ 2025-05-30T12:03:12,971 | | 2025-05-30T12:03:12,972 | long unsigned int 2025-05-30T12:03:12,972 | %u 2025-05-30T12:03:12,973 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2025-05-30T12:03:12,973 | ~~~~~~~~~ 2025-05-30T12:03:12,974 | | 2025-05-30T12:03:12,974 | size_t {aka unsigned int} 2025-05-30T12:03:12,975 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-05-30T12:03:12,975 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-05-30T12:03:12,976 | ~~^ 2025-05-30T12:03:12,976 | | 2025-05-30T12:03:12,977 | long unsigned int 2025-05-30T12:03:12,978 | %u 2025-05-30T12:03:12,979 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2025-05-30T12:03:12,979 865 | (size_t) b * unitsz_distf_mapped); 2025-05-30T12:03:12,980 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:12,981 | | 2025-05-30T12:03:12,981 | unsigned int 2025-05-30T12:03:12,982 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2025-05-30T12:03:12,983 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2025-05-30T12:03:12,983 | ^~~~~~~ 2025-05-30T12:03:12,984 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2025-05-30T12:03:12,984 809 | struct stat cbd_fcode_stat; 2025-05-30T12:03:12,985 | ^~~~~~~~~~~~~~ 2025-05-30T12:03:12,985 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2025-05-30T12:03:12,986 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2025-05-30T12:03:12,986 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:12,987 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2025-05-30T12:03:12,988 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2025-05-30T12:03:12,988 | ^~~~~~~~~~~~~~~~~ 2025-05-30T12:03:12,989 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2025-05-30T12:03:12,990 command_dist.c:1018:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T12:03:12,991 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T12:03:12,992 | ~~^ 2025-05-30T12:03:12,992 | | 2025-05-30T12:03:12,993 | long unsigned int 2025-05-30T12:03:12,993 | %u 2025-05-30T12:03:12,994 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T12:03:12,994 | ~~~~~~~ 2025-05-30T12:03:12,995 | | 2025-05-30T12:03:12,995 | size_t {aka unsigned int} 2025-05-30T12:03:12,996 command_dist.c:1018:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T12:03:12,996 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T12:03:12,997 | ~~^ 2025-05-30T12:03:12,997 | | 2025-05-30T12:03:12,998 | long unsigned int 2025-05-30T12:03:12,998 | %u 2025-05-30T12:03:12,999 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T12:03:13,000 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2025-05-30T12:03:13,000 | ~~~~~~~~~ 2025-05-30T12:03:13,001 | | 2025-05-30T12:03:13,002 | size_t {aka unsigned int} 2025-05-30T12:03:13,002 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-05-30T12:03:13,003 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T12:03:13,004 | ~~^ 2025-05-30T12:03:13,005 | | 2025-05-30T12:03:13,005 | long unsigned int 2025-05-30T12:03:13,006 | %u 2025-05-30T12:03:13,007 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T12:03:13,007 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2025-05-30T12:03:13,008 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:13,009 | | 2025-05-30T12:03:13,009 | unsigned int 2025-05-30T12:03:13,010 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2025-05-30T12:03:13,011 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2025-05-30T12:03:13,011 | ^ 2025-05-30T12:03:13,012 command_dist.c: In function ‘mco_co_dist_core’: 2025-05-30T12:03:13,013 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-05-30T12:03:13,013 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2025-05-30T12:03:13,014 | ^ 2025-05-30T12:03:13,015 command_dist.c: In function ‘koc_dist_print_nobin’: 2025-05-30T12:03:13,016 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T12:03:13,016 1239 | for (int rid = 0; rid < ref_num; rid++) 2025-05-30T12:03:13,017 | ^ 2025-05-30T12:03:13,017 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T12:03:13,018 1245 | for (int rid = 0; rid < ref_num; rid++) { 2025-05-30T12:03:13,018 | ^ 2025-05-30T12:03:13,019 command_dist.c: In function ‘dist_print_nobin’: 2025-05-30T12:03:13,019 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T12:03:13,020 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2025-05-30T12:03:13,020 | ^ 2025-05-30T12:03:13,021 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T12:03:13,021 1356 | for (int rid = 0; rid < ref_num; rid++) { 2025-05-30T12:03:13,022 | ^ 2025-05-30T12:03:13,023 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T12:03:13,023 1382 | for (int rid = 0; rid < ref_num; rid++) 2025-05-30T12:03:13,024 | ^ 2025-05-30T12:03:13,383 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2025-05-30T12:03:13,384 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2025-05-30T12:03:13,385 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2025-05-30T12:03:13,385 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:13,386 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2025-05-30T12:03:13,387 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2025-05-30T12:03:13,388 | ^~~~~~~~~~~~ 2025-05-30T12:03:14,223 command_dist.c: In function ‘get_dim_shuffle’: 2025-05-30T12:03:14,224 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2025-05-30T12:03:14,225 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2025-05-30T12:03:14,226 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:14,226 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2025-05-30T12:03:14,227 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2025-05-30T12:03:14,228 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,126 command_dist.c: In function ‘mco_cbd_co_dist’: 2025-05-30T12:03:15,127 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:15,127 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T12:03:15,128 | ^~ ~~~~~~~~~ 2025-05-30T12:03:15,129 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-05-30T12:03:15,129 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T12:03:15,130 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,131 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T12:03:15,132 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T12:03:15,132 | ^~~~~~~~~~~~~~~ 2025-05-30T12:03:15,133 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-05-30T12:03:15,133 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T12:03:15,134 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,134 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T12:03:15,135 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T12:03:15,135 | ^~~~~~~~~~~ 2025-05-30T12:03:15,136 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:15,136 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T12:03:15,137 | ^~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,138 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2025-05-30T12:03:15,138 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T12:03:15,139 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,140 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T12:03:15,140 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T12:03:15,141 | ^~~~~ 2025-05-30T12:03:15,142 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:15,143 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T12:03:15,144 | ^~~~~~~~~~~ 2025-05-30T12:03:15,144 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-05-30T12:03:15,145 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T12:03:15,146 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,380 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2025-05-30T12:03:15,381 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:15,382 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T12:03:15,383 | ^~ ~~~~~~~~~ 2025-05-30T12:03:15,383 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-05-30T12:03:15,384 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T12:03:15,385 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,385 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T12:03:15,386 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T12:03:15,386 | ^~~~~~~~~~~~~~~ 2025-05-30T12:03:15,387 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-05-30T12:03:15,388 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T12:03:15,388 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,389 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T12:03:15,390 823 | sprintf(distf, "%s/distance.out", distout_dir); 2025-05-30T12:03:15,390 | ^~~~~~~~~~~~~ 2025-05-30T12:03:15,391 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-05-30T12:03:15,392 823 | sprintf(distf, "%s/distance.out", distout_dir); 2025-05-30T12:03:15,392 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,392 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:15,393 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-05-30T12:03:15,393 | ^ 2025-05-30T12:03:15,394 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2025-05-30T12:03:15,394 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-05-30T12:03:15,395 | ^~~~~~~~~~ 2025-05-30T12:03:15,396 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2025-05-30T12:03:15,396 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-05-30T12:03:15,397 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,397 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:15,398 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-05-30T12:03:15,398 | ^ 2025-05-30T12:03:15,399 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2025-05-30T12:03:15,400 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-05-30T12:03:15,401 | ^~~~~~~~~~ 2025-05-30T12:03:15,401 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2025-05-30T12:03:15,402 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-05-30T12:03:15,403 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,660 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2025-05-30T12:03:15,661 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:15,662 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T12:03:15,663 | ^~ ~~~~~~~~~ 2025-05-30T12:03:15,663 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-05-30T12:03:15,664 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T12:03:15,664 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,665 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T12:03:15,666 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T12:03:15,666 | ^~~~~~~~~~~~~~~ 2025-05-30T12:03:15,667 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-05-30T12:03:15,668 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T12:03:15,668 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,669 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T12:03:15,670 990 | sprintf(distf, "%s/distance.out", distout_dir); 2025-05-30T12:03:15,671 | ^~~~~~~~~~~~~ 2025-05-30T12:03:15,671 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-05-30T12:03:15,672 990 | sprintf(distf, "%s/distance.out", distout_dir); 2025-05-30T12:03:15,672 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,672 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T12:03:15,673 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T12:03:15,673 | ^~~~~~~~~~~ 2025-05-30T12:03:15,674 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:15,674 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T12:03:15,675 | ^~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,675 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2025-05-30T12:03:15,676 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T12:03:15,676 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,677 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T12:03:15,678 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T12:03:15,678 | ^~~~~ 2025-05-30T12:03:15,679 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:15,680 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T12:03:15,680 | ^~~~~~~~~~~ 2025-05-30T12:03:15,681 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-05-30T12:03:15,682 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T12:03:15,683 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,949 command_dist.c: In function ‘combine_queries’: 2025-05-30T12:03:15,950 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T12:03:15,951 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2025-05-30T12:03:15,952 | ^ 2025-05-30T12:03:15,953 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T12:03:15,953 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2025-05-30T12:03:15,954 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,954 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T12:03:15,955 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2025-05-30T12:03:15,955 | ^ 2025-05-30T12:03:15,956 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T12:03:15,957 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2025-05-30T12:03:15,957 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:15,958 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:15,959 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2025-05-30T12:03:15,960 | ^~ ~~~~~~~~ 2025-05-30T12:03:15,961 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-05-30T12:03:15,961 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2025-05-30T12:03:15,962 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:16,442 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 2025-05-30T12:03:16,613 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 2025-05-30T12:03:16,782 command_set.c: In function ‘sketch_operate’: 2025-05-30T12:03:16,783 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-05-30T12:03:16,783 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2025-05-30T12:03:16,784 | ^ 2025-05-30T12:03:16,797 command_set.c: In function ‘combin_subset_pans’: 2025-05-30T12:03:16,798 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2025-05-30T12:03:16,798 457 | free(co_dstat_fpath); 2025-05-30T12:03:16,799 | ^~~~~~~~~~~~~~ 2025-05-30T12:03:16,799 In file included from kssdheaders/global_basic.h:159, 2025-05-30T12:03:16,800 from command_set.c:15: 2025-05-30T12:03:16,801 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2025-05-30T12:03:16,801 568 | extern void free (void *__ptr) __THROW; 2025-05-30T12:03:16,802 | ~~~~~~^~~~~ 2025-05-30T12:03:16,807 command_set.c: In function ‘grouping_genomes’: 2025-05-30T12:03:16,808 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2025-05-30T12:03:16,809 562 | free(co_dstat_fpath); 2025-05-30T12:03:16,810 | ^~~~~~~~~~~~~~ 2025-05-30T12:03:16,811 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2025-05-30T12:03:16,811 568 | extern void free (void *__ptr) __THROW; 2025-05-30T12:03:16,812 | ~~~~~~^~~~~ 2025-05-30T12:03:16,978 command_set.c: In function ‘sketch_union’: 2025-05-30T12:03:16,979 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T12:03:16,979 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:16,980 | ^ 2025-05-30T12:03:16,980 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T12:03:16,981 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:16,982 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:16,982 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:16,983 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T12:03:16,984 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:16,984 command_set.c:82:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:16,985 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T12:03:16,986 | ^~~~~~~~~~ 2025-05-30T12:03:16,987 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T12:03:16,987 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T12:03:16,988 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:16,988 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:16,989 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-05-30T12:03:16,989 | ^~ ~~~~~~~~~~ 2025-05-30T12:03:16,990 command_set.c:92:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:16,990 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-05-30T12:03:16,991 | ^~~~~~~~~~ 2025-05-30T12:03:16,991 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-05-30T12:03:16,991 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-05-30T12:03:16,992 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,118 command_set.c: In function ‘sketch_operate’: 2025-05-30T12:03:17,119 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,119 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-05-30T12:03:17,120 | ^~ ~~~~~~~~~~ 2025-05-30T12:03:17,120 command_set.c:153:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,121 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-05-30T12:03:17,122 | ^~~~~~~~~~ 2025-05-30T12:03:17,122 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-05-30T12:03:17,123 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-05-30T12:03:17,124 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,125 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,125 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-05-30T12:03:17,126 | ^~ ~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,127 command_set.c:155:29: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,128 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-05-30T12:03:17,128 | ^~~~~~~~~~ 2025-05-30T12:03:17,129 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2025-05-30T12:03:17,130 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-05-30T12:03:17,130 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,131 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,131 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T12:03:17,132 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:17,133 command_set.c:165:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,134 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T12:03:17,134 | ^~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,135 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T12:03:17,136 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T12:03:17,136 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,137 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,137 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T12:03:17,138 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:17,138 command_set.c:169:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,139 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T12:03:17,139 | ^~~~~~~~~~ 2025-05-30T12:03:17,140 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T12:03:17,140 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T12:03:17,141 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,141 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,142 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T12:03:17,142 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:17,143 command_set.c:174:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,143 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T12:03:17,144 | ^~~~~~~~~~ 2025-05-30T12:03:17,145 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T12:03:17,146 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T12:03:17,146 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,147 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,148 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T12:03:17,149 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:17,149 command_set.c:187:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,150 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T12:03:17,151 | ^~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,151 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T12:03:17,152 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T12:03:17,153 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,153 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T12:03:17,154 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:17,155 | ^ 2025-05-30T12:03:17,155 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T12:03:17,156 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:17,157 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,293 command_set.c: In function ‘uniq_sketch_union’: 2025-05-30T12:03:17,294 command_set.c:219:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T12:03:17,295 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2025-05-30T12:03:17,295 | ^ 2025-05-30T12:03:17,295 command_set.c:219:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2025-05-30T12:03:17,296 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2025-05-30T12:03:17,296 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,297 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T12:03:17,297 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:17,298 | ^ 2025-05-30T12:03:17,298 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T12:03:17,299 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:17,300 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,300 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,301 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T12:03:17,301 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:17,302 command_set.c:247:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,302 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T12:03:17,303 | ^~~~~~~~~~ 2025-05-30T12:03:17,304 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T12:03:17,305 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T12:03:17,305 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,306 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,307 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-05-30T12:03:17,308 | ^~ ~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,308 command_set.c:259:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,309 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-05-30T12:03:17,310 | ^~~~~~~~~~ 2025-05-30T12:03:17,311 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2025-05-30T12:03:17,311 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-05-30T12:03:17,312 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,438 command_set.c: In function ‘combin_pans’: 2025-05-30T12:03:17,439 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,439 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T12:03:17,440 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:17,441 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2025-05-30T12:03:17,441 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T12:03:17,442 | ^~~~~~~~~~ 2025-05-30T12:03:17,443 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2025-05-30T12:03:17,444 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T12:03:17,444 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,445 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,446 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T12:03:17,446 | ^~ ~~~~~~~~~~ 2025-05-30T12:03:17,447 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2025-05-30T12:03:17,447 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T12:03:17,448 | ^~~~~~~~~~ 2025-05-30T12:03:17,448 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2025-05-30T12:03:17,449 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T12:03:17,449 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,450 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T12:03:17,451 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:17,451 | ^ 2025-05-30T12:03:17,452 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T12:03:17,452 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:17,453 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,655 command_set.c: In function ‘combin_subset_pans’: 2025-05-30T12:03:17,656 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,656 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T12:03:17,657 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:17,658 command_set.c:469:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,658 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T12:03:17,659 | ^~~~~~~~~~ 2025-05-30T12:03:17,660 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T12:03:17,660 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T12:03:17,661 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,662 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,662 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T12:03:17,663 | ^~ ~~~~~~~~~~ 2025-05-30T12:03:17,664 command_set.c:475:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,664 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T12:03:17,665 | ^~~~~~~~~~ 2025-05-30T12:03:17,665 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T12:03:17,666 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T12:03:17,667 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,668 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,669 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T12:03:17,669 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:17,670 command_set.c:481:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,671 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T12:03:17,671 | ^~~~~~~~~~ 2025-05-30T12:03:17,672 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T12:03:17,672 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T12:03:17,673 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,673 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,673 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T12:03:17,674 | ^~ ~~~~~~~~~~ 2025-05-30T12:03:17,674 command_set.c:512:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,675 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T12:03:17,676 | ^~~~~~~~~~ 2025-05-30T12:03:17,676 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T12:03:17,677 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T12:03:17,677 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,678 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T12:03:17,678 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:17,679 | ^ 2025-05-30T12:03:17,680 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T12:03:17,680 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:17,681 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,900 command_set.c: In function ‘grouping_genomes’: 2025-05-30T12:03:17,901 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,901 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T12:03:17,902 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:17,903 command_set.c:574:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,903 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T12:03:17,904 | ^~~~~~~~~~ 2025-05-30T12:03:17,905 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T12:03:17,905 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T12:03:17,906 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,907 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,907 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T12:03:17,908 | ^~ ~~~~~~~~~~ 2025-05-30T12:03:17,908 command_set.c:580:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,909 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T12:03:17,910 | ^~~~~~~~~~ 2025-05-30T12:03:17,910 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T12:03:17,911 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T12:03:17,912 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,913 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,913 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T12:03:17,914 | ^~ ~~~~~~~~~~~ 2025-05-30T12:03:17,914 command_set.c:612:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,915 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T12:03:17,915 | ^~~~~~~~~~ 2025-05-30T12:03:17,916 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T12:03:17,917 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T12:03:17,917 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,918 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T12:03:17,918 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T12:03:17,919 | ^~ ~~~~~~~~~~ 2025-05-30T12:03:17,920 command_set.c:634:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T12:03:17,920 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T12:03:17,921 | ^~~~~~~~~~ 2025-05-30T12:03:17,921 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T12:03:17,922 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T12:03:17,922 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:17,923 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T12:03:17,924 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:17,924 | ^ 2025-05-30T12:03:17,925 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T12:03:17,926 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T12:03:17,927 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:18,194 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 2025-05-30T12:03:18,506 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 2025-05-30T12:03:18,675 global_basic.c: In function ‘organize_infile_list’: 2025-05-30T12:03:18,676 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2025-05-30T12:03:18,677 195 | while (isspace(*buf)) buf++; 2025-05-30T12:03:18,677 | ^~~~~~~ 2025-05-30T12:03:18,678 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2025-05-30T12:03:18,679 34 | #include 2025-05-30T12:03:18,680 +++ |+#include 2025-05-30T12:03:18,680 35 | 2025-05-30T12:03:18,681 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=] 2025-05-30T12:03:18,682 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2025-05-30T12:03:18,683 | ~~^ 2025-05-30T12:03:18,683 | | 2025-05-30T12:03:18,684 | long unsigned int 2025-05-30T12:03:18,684 | %u 2025-05-30T12:03:18,685 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2025-05-30T12:03:18,685 | ~~~~~~~~~~~ 2025-05-30T12:03:18,686 | | 2025-05-30T12:03:18,687 | size_t {aka unsigned int} 2025-05-30T12:03:18,687 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=] 2025-05-30T12:03:18,689 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2025-05-30T12:03:18,689 | ~~^ 2025-05-30T12:03:18,690 | | 2025-05-30T12:03:18,690 | long unsigned int 2025-05-30T12:03:18,691 | %u 2025-05-30T12:03:18,691 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2025-05-30T12:03:18,692 | ~~~~~~~~~~~ 2025-05-30T12:03:18,693 | | 2025-05-30T12:03:18,694 | size_t {aka unsigned int} 2025-05-30T12:03:19,465 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 2025-05-30T12:03:19,641 iseq2comem.c: In function ‘reads2mco’: 2025-05-30T12:03:19,642 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,642 156 | if (base > TL) { 2025-05-30T12:03:19,643 | ^ 2025-05-30T12:03:19,644 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,645 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T12:03:19,645 | ^~ 2025-05-30T12:03:19,646 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,646 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T12:03:19,647 | ^ 2025-05-30T12:03:19,649 iseq2comem.c: In function ‘fasta2co’: 2025-05-30T12:03:19,650 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,651 239 | if (base > TL) { 2025-05-30T12:03:19,651 | ^ 2025-05-30T12:03:19,652 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,653 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T12:03:19,654 | ^~ 2025-05-30T12:03:19,654 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,655 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T12:03:19,655 | ^ 2025-05-30T12:03:19,656 iseq2comem.c: In function ‘fastq2co’: 2025-05-30T12:03:19,656 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2025-05-30T12:03:19,657 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2025-05-30T12:03:19,657 | ^~ 2025-05-30T12:03:19,659 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,660 318 | if (base > TL) { 2025-05-30T12:03:19,660 | ^ 2025-05-30T12:03:19,661 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,661 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T12:03:19,662 | ^~ 2025-05-30T12:03:19,663 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,663 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T12:03:19,664 | ^ 2025-05-30T12:03:19,665 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,665 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2025-05-30T12:03:19,666 | ^ 2025-05-30T12:03:19,667 iseq2comem.c: In function ‘fastq2koc’: 2025-05-30T12:03:19,668 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,668 402 | if (base > TL) { 2025-05-30T12:03:19,669 | ^ 2025-05-30T12:03:19,670 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,671 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T12:03:19,672 | ^~ 2025-05-30T12:03:19,672 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,673 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T12:03:19,674 | ^ 2025-05-30T12:03:19,676 iseq2comem.c: In function ‘mt_shortreads2koc’: 2025-05-30T12:03:19,677 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,677 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T12:03:19,678 | ^~ 2025-05-30T12:03:19,679 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:19,681 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T12:03:19,682 | ^ 2025-05-30T12:03:21,021 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 2025-05-30T12:03:21,074 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 2025-05-30T12:03:21,195 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 2025-05-30T12:03:21,595 pykssd.c: In function ‘py_dist_dispatch’: 2025-05-30T12:03:21,596 pykssd.c:334:13: warning: unused variable ‘state1’ [-Wunused-variable] 2025-05-30T12:03:21,596 334 | int state1 = dist_dispatch(&dist_opt_val1); 2025-05-30T12:03:21,597 | ^~~~~~ 2025-05-30T12:03:21,597 pykssd.c:396:13: warning: unused variable ‘state2’ [-Wunused-variable] 2025-05-30T12:03:21,598 396 | int state2 = dist_dispatch(&dist_opt_val2); 2025-05-30T12:03:21,598 | ^~~~~~ 2025-05-30T12:03:21,599 pykssd.c:530:13: warning: unused variable ‘state4’ [-Wunused-variable] 2025-05-30T12:03:21,600 530 | int state4 = dist_dispatch(&dist_opt_val4); 2025-05-30T12:03:21,600 | ^~~~~~ 2025-05-30T12:03:22,246 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 2025-05-30T12:03:22,444 building 'nj' extension 2025-05-30T12:03:22,444 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 2025-05-30T12:03:22,901 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 2025-05-30T12:03:23,050 buildtree.c: In function ‘UPGMA_buildtree’: 2025-05-30T12:03:23,050 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T12:03:23,051 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2025-05-30T12:03:23,051 | ^~ 2025-05-30T12:03:23,053 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T12:03:23,053 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2025-05-30T12:03:23,054 | ^~ 2025-05-30T12:03:23,714 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 2025-05-30T12:03:24,082 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 2025-05-30T12:03:24,216 distancemat.c: In function ‘clone_DistanceMatrix’: 2025-05-30T12:03:24,216 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T12:03:24,217 226 | for( i=0; i < dest->size; i++) { 2025-05-30T12:03:24,217 | ^ 2025-05-30T12:03:24,218 distancemat.c: In function ‘empty_DistanceMatrix’: 2025-05-30T12:03:24,219 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T12:03:24,219 260 | for( i=0; i < mat->size; i++) { 2025-05-30T12:03:24,220 | ^ 2025-05-30T12:03:24,221 distancemat.c: In function ‘print_DistanceMatrix’: 2025-05-30T12:03:24,221 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T12:03:24,222 349 | for(row=0; row < mat->size; row++) { 2025-05-30T12:03:24,222 | ^ 2025-05-30T12:03:24,224 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2025-05-30T12:03:24,224 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2025-05-30T12:03:24,225 410 | while(c = fgetc(handle)) { 2025-05-30T12:03:24,225 | ^ 2025-05-30T12:03:24,612 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 2025-05-30T12:03:25,048 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 2025-05-30T12:03:25,261 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 2025-05-30T12:03:26,067 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 2025-05-30T12:03:26,240 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 2025-05-30T12:03:26,349 building 'dnj' extension 2025-05-30T12:03:26,350 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 2025-05-30T12:03:26,405 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 2025-05-30T12:03:26,540 dnj.c: In function ‘minQpair’: 2025-05-30T12:03:26,541 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,541 70 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,542 | ^~~ 2025-05-30T12:03:26,542 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,543 126 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,543 | ^~~ 2025-05-30T12:03:26,544 dnj.c: In function ‘maxQpair’: 2025-05-30T12:03:26,545 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,545 157 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,546 | ^~~ 2025-05-30T12:03:26,546 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,546 213 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,547 | ^~~ 2025-05-30T12:03:26,547 dnj.c: In function ‘UPGMApair’: 2025-05-30T12:03:26,548 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,548 237 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,549 | ^~~ 2025-05-30T12:03:26,549 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,550 284 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,550 | ^~~ 2025-05-30T12:03:26,551 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,552 291 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,552 | ^~~ 2025-05-30T12:03:26,553 dnj.c: In function ‘minQrow’: 2025-05-30T12:03:26,554 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,554 374 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,555 | ^~~ 2025-05-30T12:03:26,555 dnj.c: In function ‘maxQrow’: 2025-05-30T12:03:26,556 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,557 435 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,557 | ^~~ 2025-05-30T12:03:26,558 dnj.c: In function ‘UPGMArow’: 2025-05-30T12:03:26,558 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,559 488 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,559 | ^~~ 2025-05-30T12:03:26,560 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,560 494 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,561 | ^~~ 2025-05-30T12:03:26,562 dnj.c: In function ‘minQ_thread’: 2025-05-30T12:03:26,562 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:26,563 553 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:26,563 | ^~~ 2025-05-30T12:03:27,917 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 2025-05-30T12:03:28,036 filebuff.c: In function ‘BuffgzFileBuff’: 2025-05-30T12:03:28,037 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:28,038 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2025-05-30T12:03:28,039 | ^~ 2025-05-30T12:03:28,367 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 2025-05-30T12:03:28,501 hclust.c: In function ‘minQ’: 2025-05-30T12:03:28,501 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T12:03:28,502 364 | while(++i < Q->n) { 2025-05-30T12:03:28,502 | ^ 2025-05-30T12:03:28,503 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:28,503 377 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:28,504 | ^~~ 2025-05-30T12:03:28,505 hclust.c: In function ‘maxQ’: 2025-05-30T12:03:28,505 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T12:03:28,506 394 | while(++i < Q->n) { 2025-05-30T12:03:28,506 | ^ 2025-05-30T12:03:28,507 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:28,507 407 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:28,508 | ^~~ 2025-05-30T12:03:30,898 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 2025-05-30T12:03:31,024 matrix.c: In function ‘ltdMatrix_popArrange’: 2025-05-30T12:03:31,025 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T12:03:31,025 538 | if(pos != n) { 2025-05-30T12:03:31,026 | ^~ 2025-05-30T12:03:31,903 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 2025-05-30T12:03:31,956 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 2025-05-30T12:03:32,083 nj.c: In function ‘initQ’: 2025-05-30T12:03:32,084 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:32,084 243 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:32,085 | ^~~ 2025-05-30T12:03:32,086 nj.c: In function ‘initQ_MN’: 2025-05-30T12:03:32,086 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:32,087 358 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:32,087 | ^~~ 2025-05-30T12:03:32,091 nj.c: In function ‘minD’: 2025-05-30T12:03:32,091 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:32,092 559 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:32,093 | ^~~ 2025-05-30T12:03:32,093 nj.c: In function ‘maxD’: 2025-05-30T12:03:32,094 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:32,095 642 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:32,096 | ^~~ 2025-05-30T12:03:32,098 nj.c: In function ‘minPair’: 2025-05-30T12:03:32,099 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T12:03:32,100 826 | pos <<= sizeof(unsigned) * 8; 2025-05-30T12:03:32,101 | ^~~ 2025-05-30T12:03:34,529 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 2025-05-30T12:03:35,072 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 2025-05-30T12:03:35,163 pherror.c: In function ‘cfread’: 2025-05-30T12:03:35,164 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T12:03:35,164 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2025-05-30T12:03:35,165 | ^~ 2025-05-30T12:03:35,256 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 2025-05-30T12:03:36,319 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 2025-05-30T12:03:36,687 In file included from pydnj.c:11: 2025-05-30T12:03:36,688 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2025-05-30T12:03:36,689 20 | #define _XOPEN_SOURCE 600 2025-05-30T12:03:36,689 | 2025-05-30T12:03:36,690 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2025-05-30T12:03:36,690 from /usr/include/stdlib.h:26, 2025-05-30T12:03:36,691 from /usr/include/python3.11/Python.h:23, 2025-05-30T12:03:36,692 from pydnj.c:1: 2025-05-30T12:03:36,692 /usr/include/features.h:214: note: this is the location of the previous definition 2025-05-30T12:03:36,693 214 | # define _XOPEN_SOURCE 700 2025-05-30T12:03:36,694 | 2025-05-30T12:03:36,715 pydnj.c: In function ‘py_build’: 2025-05-30T12:03:36,715 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2025-05-30T12:03:36,716 165 | p = omp_get_num_procs(); 2025-05-30T12:03:36,718 | ^~~~~~~~~~~~~~~~~ 2025-05-30T12:03:36,837 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2025-05-30T12:03:36,838 169 | free(file); 2025-05-30T12:03:36,839 | ^~~~~~~~~~ 2025-05-30T12:03:36,839 pydnj.c:125:12: note: returned from ‘fopen’ 2025-05-30T12:03:36,840 125 | file = fopen(inputfilename, "r"); 2025-05-30T12:03:36,841 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T12:03:36,912 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 2025-05-30T12:03:37,117 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 2025-05-30T12:03:37,224 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 2025-05-30T12:03:37,426 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 2025-05-30T12:03:37,603 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 2025-05-30T12:03:37,784 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-05-30T12:03:37,785 !! 2025-05-30T12:03:37,786 ******************************************************************************** 2025-05-30T12:03:37,786 Please avoid running ``setup.py`` directly. 2025-05-30T12:03:37,787 Instead, use pypa/build, pypa/installer or other 2025-05-30T12:03:37,787 standards-based tools. 2025-05-30T12:03:37,789 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-05-30T12:03:37,789 or your builds will no longer be supported. 2025-05-30T12:03:37,791 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-05-30T12:03:37,791 ******************************************************************************** 2025-05-30T12:03:37,792 !! 2025-05-30T12:03:37,793 self.initialize_options() 2025-05-30T12:03:37,815 installing to build/bdist.linux-armv7l/wheel 2025-05-30T12:03:37,816 running install 2025-05-30T12:03:37,841 running install_lib 2025-05-30T12:03:37,868 creating build/bdist.linux-armv7l/wheel 2025-05-30T12:03:37,870 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel/. 2025-05-30T12:03:37,872 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-05-30T12:03:37,880 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel/. 2025-05-30T12:03:37,883 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-05-30T12:03:37,888 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-05-30T12:03:37,897 running install_egg_info 2025-05-30T12:03:37,930 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/./kssdtree-2.0.7-py3.11.egg-info 2025-05-30T12:03:37,941 running install_scripts 2025-05-30T12:03:37,990 creating build/bdist.linux-armv7l/wheel/kssdtree-2.0.7.dist-info/WHEEL 2025-05-30T12:03:37,992 creating '/tmp/pip-wheel-wxatxkca/kssdtree-2.0.7-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-05-30T12:03:38,058 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2025-05-30T12:03:38,143 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2025-05-30T12:03:38,148 adding 'kssdtree.py' 2025-05-30T12:03:38,169 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2025-05-30T12:03:38,172 adding 'toolutils.py' 2025-05-30T12:03:38,174 adding 'kssdtree-2.0.7.dist-info/METADATA' 2025-05-30T12:03:38,176 adding 'kssdtree-2.0.7.dist-info/WHEEL' 2025-05-30T12:03:38,177 adding 'kssdtree-2.0.7.dist-info/dependency_links.txt' 2025-05-30T12:03:38,178 adding 'kssdtree-2.0.7.dist-info/top_level.txt' 2025-05-30T12:03:38,180 adding 'kssdtree-2.0.7.dist-info/RECORD' 2025-05-30T12:03:38,186 removing build/bdist.linux-armv7l/wheel 2025-05-30T12:03:38,321 Building wheel for kssdtree (setup.py): finished with status 'done' 2025-05-30T12:03:38,331 Created wheel for kssdtree: filename=kssdtree-2.0.7-cp311-cp311-linux_armv7l.whl size=381934 sha256=f267901a8f679be9a77fc090fb1c15f5144a295e5158a4ff2e62e2ba29fec967 2025-05-30T12:03:38,332 Stored in directory: /tmp/pip-ephem-wheel-cache-rai0hmk2/wheels/58/c8/07/d4cbe011c4cce2dd650de58be656027b7c506ae7247b8334d9 2025-05-30T12:03:38,341 Successfully built kssdtree 2025-05-30T12:03:38,350 Removed build tracker: '/tmp/pip-build-tracker-6li39yfo'