2025-06-01T08:27:03,843 Created temporary directory: /tmp/pip-build-tracker-oxgxdj2h 2025-06-01T08:27:03,844 Initialized build tracking at /tmp/pip-build-tracker-oxgxdj2h 2025-06-01T08:27:03,844 Created build tracker: /tmp/pip-build-tracker-oxgxdj2h 2025-06-01T08:27:03,845 Entered build tracker: /tmp/pip-build-tracker-oxgxdj2h 2025-06-01T08:27:03,846 Created temporary directory: /tmp/pip-wheel-g3113c9n 2025-06-01T08:27:03,850 Created temporary directory: /tmp/pip-ephem-wheel-cache-4jpnzwue 2025-06-01T08:27:03,903 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-06-01T08:27:03,905 2 location(s) to search for versions of kssdtree: 2025-06-01T08:27:03,905 * https://pypi.org/simple/kssdtree/ 2025-06-01T08:27:03,905 * https://www.piwheels.org/simple/kssdtree/ 2025-06-01T08:27:03,906 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2025-06-01T08:27:03,907 Getting page https://pypi.org/simple/kssdtree/ 2025-06-01T08:27:03,908 Found index url https://pypi.org/simple/ 2025-06-01T08:27:04,138 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2025-06-01T08:27:04,144 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 2025-06-01T08:27:04,146 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 2025-06-01T08:27:04,147 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 2025-06-01T08:27:04,148 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 2025-06-01T08:27:04,149 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 2025-06-01T08:27:04,151 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 2025-06-01T08:27:04,152 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 2025-06-01T08:27:04,153 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 2025-06-01T08:27:04,154 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 2025-06-01T08:27:04,154 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 2025-06-01T08:27:04,155 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 2025-06-01T08:27:04,156 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 2025-06-01T08:27:04,156 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 2025-06-01T08:27:04,157 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 2025-06-01T08:27:04,158 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 2025-06-01T08:27:04,158 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 2025-06-01T08:27:04,159 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 2025-06-01T08:27:04,160 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2025-06-01T08:27:04,160 Getting page https://www.piwheels.org/simple/kssdtree/ 2025-06-01T08:27:04,162 Found index url https://www.piwheels.org/simple/ 2025-06-01T08:27:04,329 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/ 2025-06-01T08:27:04,998 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/ 2025-06-01T08:27:06,186 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/ 2025-06-01T08:27:08,362 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/ 2025-06-01T08:27:12,539 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/ 2025-06-01T08:27:12,727 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 2025-06-01T08:27:12,729 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2025-06-01T08:27:12,730 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2025-06-01T08:27:12,750 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2025-06-01T08:27:12,752 Collecting kssdtree==2.0.8 2025-06-01T08:27:12,754 Created temporary directory: /tmp/pip-unpack-fpq9x2st 2025-06-01T08:27:12,983 Downloading kssdtree-2.0.8.tar.gz (114 kB) 2025-06-01T08:27:13,222 Added kssdtree==2.0.8 from https://files.pythonhosted.org/packages/82/9b/dac2af6572f0c4421e5ba8341dcfddac466de30c62acfa019d9ef70b2670/kssdtree-2.0.8.tar.gz to build tracker '/tmp/pip-build-tracker-oxgxdj2h' 2025-06-01T08:27:13,224 Running setup.py (path:/tmp/pip-wheel-g3113c9n/kssdtree_ce1286783fbc46acb757a7822f0efe48/setup.py) egg_info for package kssdtree 2025-06-01T08:27:13,225 Created temporary directory: /tmp/pip-pip-egg-info-eyuclbuo 2025-06-01T08:27:13,226 Preparing metadata (setup.py): started 2025-06-01T08:27:13,227 Running command python setup.py egg_info 2025-06-01T08:27:14,136 running egg_info 2025-06-01T08:27:14,164 creating /tmp/pip-pip-egg-info-eyuclbuo/kssdtree.egg-info 2025-06-01T08:27:14,165 writing /tmp/pip-pip-egg-info-eyuclbuo/kssdtree.egg-info/PKG-INFO 2025-06-01T08:27:14,169 writing dependency_links to /tmp/pip-pip-egg-info-eyuclbuo/kssdtree.egg-info/dependency_links.txt 2025-06-01T08:27:14,171 writing requirements to /tmp/pip-pip-egg-info-eyuclbuo/kssdtree.egg-info/requires.txt 2025-06-01T08:27:14,172 writing top-level names to /tmp/pip-pip-egg-info-eyuclbuo/kssdtree.egg-info/top_level.txt 2025-06-01T08:27:14,173 writing manifest file '/tmp/pip-pip-egg-info-eyuclbuo/kssdtree.egg-info/SOURCES.txt' 2025-06-01T08:27:14,286 reading manifest file '/tmp/pip-pip-egg-info-eyuclbuo/kssdtree.egg-info/SOURCES.txt' 2025-06-01T08:27:14,288 reading manifest template 'MANIFEST.in' 2025-06-01T08:27:14,307 writing manifest file '/tmp/pip-pip-egg-info-eyuclbuo/kssdtree.egg-info/SOURCES.txt' 2025-06-01T08:27:14,415 Preparing metadata (setup.py): finished with status 'done' 2025-06-01T08:27:14,418 Source in /tmp/pip-wheel-g3113c9n/kssdtree_ce1286783fbc46acb757a7822f0efe48 has version 2.0.8, which satisfies requirement kssdtree==2.0.8 from https://files.pythonhosted.org/packages/82/9b/dac2af6572f0c4421e5ba8341dcfddac466de30c62acfa019d9ef70b2670/kssdtree-2.0.8.tar.gz 2025-06-01T08:27:14,419 Removed kssdtree==2.0.8 from https://files.pythonhosted.org/packages/82/9b/dac2af6572f0c4421e5ba8341dcfddac466de30c62acfa019d9ef70b2670/kssdtree-2.0.8.tar.gz from build tracker '/tmp/pip-build-tracker-oxgxdj2h' 2025-06-01T08:27:14,424 Created temporary directory: /tmp/pip-unpack-hqva3urk 2025-06-01T08:27:14,425 Created temporary directory: /tmp/pip-unpack-m9agy4ix 2025-06-01T08:27:14,425 Building wheels for collected packages: kssdtree 2025-06-01T08:27:14,429 Created temporary directory: /tmp/pip-wheel-24zd_2i2 2025-06-01T08:27:14,430 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 2025-06-01T08:27:14,432 Building wheel for kssdtree (setup.py): started 2025-06-01T08:27:14,433 Destination directory: /tmp/pip-wheel-24zd_2i2 2025-06-01T08:27:14,434 Running command python setup.py bdist_wheel 2025-06-01T08:27:15,280 running bdist_wheel 2025-06-01T08:27:15,412 running build 2025-06-01T08:27:15,413 running build_py 2025-06-01T08:27:15,442 creating build/lib.linux-armv7l-cpython-311 2025-06-01T08:27:15,444 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2025-06-01T08:27:15,447 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2025-06-01T08:27:15,449 running egg_info 2025-06-01T08:27:15,479 writing kssdtree.egg-info/PKG-INFO 2025-06-01T08:27:15,482 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2025-06-01T08:27:15,483 writing requirements to kssdtree.egg-info/requires.txt 2025-06-01T08:27:15,485 writing top-level names to kssdtree.egg-info/top_level.txt 2025-06-01T08:27:15,515 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2025-06-01T08:27:15,521 reading manifest template 'MANIFEST.in' 2025-06-01T08:27:15,539 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2025-06-01T08:27:15,541 running build_ext 2025-06-01T08:27:15,971 building 'kssd' extension 2025-06-01T08:27:15,973 creating build/temp.linux-armv7l-cpython-311 2025-06-01T08:27:15,975 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 2025-06-01T08:27:16,176 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2025-06-01T08:27:16,177 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-06-01T08:27:16,178 109 | for (unsigned int i = 0; i < comp_num; i++) { 2025-06-01T08:27:16,178 | ^ 2025-06-01T08:27:16,182 co2mco.c: In function ‘co2unitllmco’: 2025-06-01T08:27:16,183 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-06-01T08:27:16,184 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2025-06-01T08:27:16,184 | ^ 2025-06-01T08:27:16,941 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 2025-06-01T08:27:17,338 command_composite.c: In function ‘get_species_abundance’: 2025-06-01T08:27:17,339 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2025-06-01T08:27:17,340 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2025-06-01T08:27:17,341 | ^~ 2025-06-01T08:27:17,341 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2025-06-01T08:27:17,342 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2025-06-01T08:27:17,343 | ^~ 2025-06-01T08:27:17,344 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:17,345 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-06-01T08:27:17,346 | ^ 2025-06-01T08:27:17,347 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:17,348 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-06-01T08:27:17,349 | ^~~~~~~~~~ 2025-06-01T08:27:17,351 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-06-01T08:27:17,352 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-06-01T08:27:17,353 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:17,354 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:17,355 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-06-01T08:27:17,356 | ^ 2025-06-01T08:27:17,356 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:17,357 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-06-01T08:27:17,358 | ^~~~~~~~~~ 2025-06-01T08:27:17,358 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-06-01T08:27:17,359 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-06-01T08:27:17,360 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:17,360 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:17,361 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-06-01T08:27:17,362 | ^ 2025-06-01T08:27:17,363 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:17,363 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-06-01T08:27:17,364 | ^~~~~~~~~~ 2025-06-01T08:27:17,364 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-06-01T08:27:17,365 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-06-01T08:27:17,366 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:17,366 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:17,367 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-06-01T08:27:17,367 | ^ 2025-06-01T08:27:17,368 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:17,368 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-06-01T08:27:17,369 | ^~~~~~~~~~ 2025-06-01T08:27:17,369 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-06-01T08:27:17,370 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-06-01T08:27:17,370 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:17,371 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:17,372 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-06-01T08:27:17,372 | ^ 2025-06-01T08:27:17,373 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:17,374 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-06-01T08:27:17,375 | ^~~~~~~~~~~~ 2025-06-01T08:27:17,376 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2025-06-01T08:27:17,376 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-06-01T08:27:17,377 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:17,601 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 2025-06-01T08:27:17,854 command_dist.c: In function ‘mco_cbd_co_dist’: 2025-06-01T08:27:17,856 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=] 2025-06-01T08:27:17,856 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-06-01T08:27:17,857 | ~~^ 2025-06-01T08:27:17,857 | | 2025-06-01T08:27:17,858 | long unsigned int 2025-06-01T08:27:17,859 | %u 2025-06-01T08:27:17,859 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-06-01T08:27:17,860 | ~~~~~~~ 2025-06-01T08:27:17,860 | | 2025-06-01T08:27:17,861 | size_t {aka unsigned int} 2025-06-01T08:27:17,862 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=] 2025-06-01T08:27:17,863 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-06-01T08:27:17,863 | ~~^ 2025-06-01T08:27:17,864 | | 2025-06-01T08:27:17,864 | long unsigned int 2025-06-01T08:27:17,865 | %u 2025-06-01T08:27:17,865 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-06-01T08:27:17,866 679 | maplength, (size_t) b * unitsz_distf_mapped); 2025-06-01T08:27:17,866 | ~~~~~~~~~ 2025-06-01T08:27:17,867 | | 2025-06-01T08:27:17,867 | size_t {aka unsigned int} 2025-06-01T08:27:17,868 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-06-01T08:27:17,868 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-06-01T08:27:17,869 | ~~^ 2025-06-01T08:27:17,870 | | 2025-06-01T08:27:17,870 | long unsigned int 2025-06-01T08:27:17,871 | %u 2025-06-01T08:27:17,871 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-06-01T08:27:17,872 679 | maplength, (size_t) b * unitsz_distf_mapped); 2025-06-01T08:27:17,872 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:17,873 | | 2025-06-01T08:27:17,873 | unsigned int 2025-06-01T08:27:17,874 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-06-01T08:27:17,875 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2025-06-01T08:27:17,875 | ^ 2025-06-01T08:27:17,878 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2025-06-01T08:27:17,880 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=] 2025-06-01T08:27:17,881 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-06-01T08:27:17,881 | ~~^ ~~~~~~~ 2025-06-01T08:27:17,882 | | | 2025-06-01T08:27:17,882 | long unsigned int size_t {aka unsigned int} 2025-06-01T08:27:17,883 | %u 2025-06-01T08:27:17,883 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=] 2025-06-01T08:27:17,884 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-06-01T08:27:17,885 | ~~^ 2025-06-01T08:27:17,886 | | 2025-06-01T08:27:17,886 | long unsigned int 2025-06-01T08:27:17,887 | %u 2025-06-01T08:27:17,887 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2025-06-01T08:27:17,888 | ~~~~~~~~~ 2025-06-01T08:27:17,888 | | 2025-06-01T08:27:17,888 | size_t {aka unsigned int} 2025-06-01T08:27:17,889 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-06-01T08:27:17,889 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-06-01T08:27:17,891 | ~~^ 2025-06-01T08:27:17,891 | | 2025-06-01T08:27:17,892 | long unsigned int 2025-06-01T08:27:17,893 | %u 2025-06-01T08:27:17,893 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2025-06-01T08:27:17,894 865 | (size_t) b * unitsz_distf_mapped); 2025-06-01T08:27:17,895 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:17,896 | | 2025-06-01T08:27:17,896 | unsigned int 2025-06-01T08:27:17,897 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2025-06-01T08:27:17,898 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2025-06-01T08:27:17,899 | ^~~~~~~ 2025-06-01T08:27:17,899 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2025-06-01T08:27:17,900 809 | struct stat cbd_fcode_stat; 2025-06-01T08:27:17,900 | ^~~~~~~~~~~~~~ 2025-06-01T08:27:17,901 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2025-06-01T08:27:17,901 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2025-06-01T08:27:17,902 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:17,902 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2025-06-01T08:27:17,903 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2025-06-01T08:27:17,903 | ^~~~~~~~~~~~~~~~~ 2025-06-01T08:27:17,904 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2025-06-01T08:27:17,905 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=] 2025-06-01T08:27:17,905 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-06-01T08:27:17,906 | ~~^ 2025-06-01T08:27:17,907 | | 2025-06-01T08:27:17,907 | long unsigned int 2025-06-01T08:27:17,907 | %u 2025-06-01T08:27:17,908 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-06-01T08:27:17,909 | ~~~~~~~ 2025-06-01T08:27:17,909 | | 2025-06-01T08:27:17,909 | size_t {aka unsigned int} 2025-06-01T08:27:17,910 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=] 2025-06-01T08:27:17,911 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-06-01T08:27:17,911 | ~~^ 2025-06-01T08:27:17,912 | | 2025-06-01T08:27:17,912 | long unsigned int 2025-06-01T08:27:17,913 | %u 2025-06-01T08:27:17,913 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-06-01T08:27:17,914 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2025-06-01T08:27:17,915 | ~~~~~~~~~ 2025-06-01T08:27:17,915 | | 2025-06-01T08:27:17,916 | size_t {aka unsigned int} 2025-06-01T08:27:17,917 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-06-01T08:27:17,918 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-06-01T08:27:17,918 | ~~^ 2025-06-01T08:27:17,919 | | 2025-06-01T08:27:17,920 | long unsigned int 2025-06-01T08:27:17,921 | %u 2025-06-01T08:27:17,921 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-06-01T08:27:17,922 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2025-06-01T08:27:17,923 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:17,923 | | 2025-06-01T08:27:17,924 | unsigned int 2025-06-01T08:27:17,925 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2025-06-01T08:27:17,926 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2025-06-01T08:27:17,927 | ^ 2025-06-01T08:27:17,928 command_dist.c: In function ‘mco_co_dist_core’: 2025-06-01T08:27:17,929 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-06-01T08:27:17,930 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2025-06-01T08:27:17,931 | ^ 2025-06-01T08:27:17,933 command_dist.c: In function ‘koc_dist_print_nobin’: 2025-06-01T08:27:17,934 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-06-01T08:27:17,934 1239 | for (int rid = 0; rid < ref_num; rid++) 2025-06-01T08:27:17,935 | ^ 2025-06-01T08:27:17,936 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-06-01T08:27:17,936 1245 | for (int rid = 0; rid < ref_num; rid++) { 2025-06-01T08:27:17,937 | ^ 2025-06-01T08:27:17,937 command_dist.c: In function ‘dist_print_nobin’: 2025-06-01T08:27:17,938 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-06-01T08:27:17,939 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2025-06-01T08:27:17,939 | ^ 2025-06-01T08:27:17,941 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-06-01T08:27:17,942 1356 | for (int rid = 0; rid < ref_num; rid++) { 2025-06-01T08:27:17,942 | ^ 2025-06-01T08:27:17,944 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-06-01T08:27:17,945 1382 | for (int rid = 0; rid < ref_num; rid++) 2025-06-01T08:27:17,945 | ^ 2025-06-01T08:27:18,308 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2025-06-01T08:27:18,308 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2025-06-01T08:27:18,309 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2025-06-01T08:27:18,310 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:18,311 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2025-06-01T08:27:18,311 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2025-06-01T08:27:18,312 | ^~~~~~~~~~~~ 2025-06-01T08:27:19,150 command_dist.c: In function ‘get_dim_shuffle’: 2025-06-01T08:27:19,150 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2025-06-01T08:27:19,151 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2025-06-01T08:27:19,151 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:19,152 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2025-06-01T08:27:19,153 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2025-06-01T08:27:19,153 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,058 command_dist.c: In function ‘mco_cbd_co_dist’: 2025-06-01T08:27:20,059 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:20,059 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-06-01T08:27:20,060 | ^~ ~~~~~~~~~ 2025-06-01T08:27:20,061 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-06-01T08:27:20,061 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-06-01T08:27:20,062 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,063 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-06-01T08:27:20,064 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-06-01T08:27:20,064 | ^~~~~~~~~~~~~~~ 2025-06-01T08:27:20,065 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-06-01T08:27:20,065 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-06-01T08:27:20,066 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,066 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-06-01T08:27:20,066 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-06-01T08:27:20,067 | ^~~~~~~~~~~ 2025-06-01T08:27:20,067 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:20,068 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-06-01T08:27:20,068 | ^~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,069 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2025-06-01T08:27:20,069 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-06-01T08:27:20,070 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,071 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-06-01T08:27:20,071 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-06-01T08:27:20,072 | ^~~~~ 2025-06-01T08:27:20,073 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:20,074 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-06-01T08:27:20,074 | ^~~~~~~~~~~ 2025-06-01T08:27:20,075 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-06-01T08:27:20,076 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-06-01T08:27:20,076 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,311 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2025-06-01T08:27:20,312 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:20,313 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-06-01T08:27:20,313 | ^~ ~~~~~~~~~ 2025-06-01T08:27:20,314 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-06-01T08:27:20,314 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-06-01T08:27:20,315 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,316 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-06-01T08:27:20,316 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-06-01T08:27:20,317 | ^~~~~~~~~~~~~~~ 2025-06-01T08:27:20,317 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-06-01T08:27:20,318 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-06-01T08:27:20,319 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,319 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-06-01T08:27:20,320 823 | sprintf(distf, "%s/distance.out", distout_dir); 2025-06-01T08:27:20,321 | ^~~~~~~~~~~~~ 2025-06-01T08:27:20,321 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-06-01T08:27:20,321 823 | sprintf(distf, "%s/distance.out", distout_dir); 2025-06-01T08:27:20,322 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,322 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:20,323 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-06-01T08:27:20,323 | ^ 2025-06-01T08:27:20,324 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2025-06-01T08:27:20,324 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-06-01T08:27:20,325 | ^~~~~~~~~~ 2025-06-01T08:27:20,325 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2025-06-01T08:27:20,326 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-06-01T08:27:20,326 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,327 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:20,327 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-06-01T08:27:20,328 | ^ 2025-06-01T08:27:20,329 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2025-06-01T08:27:20,329 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-06-01T08:27:20,330 | ^~~~~~~~~~ 2025-06-01T08:27:20,331 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2025-06-01T08:27:20,331 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-06-01T08:27:20,332 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,592 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2025-06-01T08:27:20,594 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:20,594 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-06-01T08:27:20,595 | ^~ ~~~~~~~~~ 2025-06-01T08:27:20,595 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-06-01T08:27:20,596 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-06-01T08:27:20,596 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,597 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-06-01T08:27:20,597 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-06-01T08:27:20,598 | ^~~~~~~~~~~~~~~ 2025-06-01T08:27:20,599 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-06-01T08:27:20,599 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-06-01T08:27:20,600 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,601 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-06-01T08:27:20,601 990 | sprintf(distf, "%s/distance.out", distout_dir); 2025-06-01T08:27:20,602 | ^~~~~~~~~~~~~ 2025-06-01T08:27:20,603 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-06-01T08:27:20,603 990 | sprintf(distf, "%s/distance.out", distout_dir); 2025-06-01T08:27:20,603 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,604 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-06-01T08:27:20,604 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-06-01T08:27:20,605 | ^~~~~~~~~~~ 2025-06-01T08:27:20,605 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:20,605 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-06-01T08:27:20,606 | ^~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,606 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2025-06-01T08:27:20,607 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-06-01T08:27:20,607 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,607 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-06-01T08:27:20,608 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-06-01T08:27:20,608 | ^~~~~ 2025-06-01T08:27:20,609 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:20,610 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-06-01T08:27:20,611 | ^~~~~~~~~~~ 2025-06-01T08:27:20,612 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-06-01T08:27:20,612 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-06-01T08:27:20,613 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,893 command_dist.c: In function ‘combine_queries’: 2025-06-01T08:27:20,895 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-06-01T08:27:20,895 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2025-06-01T08:27:20,896 | ^ 2025-06-01T08:27:20,897 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-06-01T08:27:20,897 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2025-06-01T08:27:20,898 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,898 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-06-01T08:27:20,899 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2025-06-01T08:27:20,899 | ^ 2025-06-01T08:27:20,900 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-06-01T08:27:20,901 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2025-06-01T08:27:20,901 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:20,903 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:20,904 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2025-06-01T08:27:20,905 | ^~ ~~~~~~~~ 2025-06-01T08:27:20,905 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-06-01T08:27:20,906 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2025-06-01T08:27:20,906 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:21,392 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 2025-06-01T08:27:21,577 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 2025-06-01T08:27:21,762 command_set.c: In function ‘sketch_operate’: 2025-06-01T08:27:21,762 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-06-01T08:27:21,763 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2025-06-01T08:27:21,764 | ^ 2025-06-01T08:27:21,775 command_set.c: In function ‘combin_subset_pans’: 2025-06-01T08:27:21,776 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2025-06-01T08:27:21,777 457 | free(co_dstat_fpath); 2025-06-01T08:27:21,777 | ^~~~~~~~~~~~~~ 2025-06-01T08:27:21,778 In file included from kssdheaders/global_basic.h:159, 2025-06-01T08:27:21,778 from command_set.c:15: 2025-06-01T08:27:21,779 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2025-06-01T08:27:21,780 568 | extern void free (void *__ptr) __THROW; 2025-06-01T08:27:21,781 | ~~~~~~^~~~~ 2025-06-01T08:27:21,783 command_set.c: In function ‘grouping_genomes’: 2025-06-01T08:27:21,784 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2025-06-01T08:27:21,785 562 | free(co_dstat_fpath); 2025-06-01T08:27:21,786 | ^~~~~~~~~~~~~~ 2025-06-01T08:27:21,787 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2025-06-01T08:27:21,787 568 | extern void free (void *__ptr) __THROW; 2025-06-01T08:27:21,788 | ~~~~~~^~~~~ 2025-06-01T08:27:21,958 command_set.c: In function ‘sketch_union’: 2025-06-01T08:27:21,958 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-06-01T08:27:21,959 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:21,960 | ^ 2025-06-01T08:27:21,961 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-06-01T08:27:21,962 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:21,962 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:21,963 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:21,964 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-06-01T08:27:21,964 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:21,965 command_set.c:82:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:21,966 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-06-01T08:27:21,966 | ^~~~~~~~~~ 2025-06-01T08:27:21,967 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-06-01T08:27:21,968 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-06-01T08:27:21,968 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:21,969 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:21,970 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-06-01T08:27:21,970 | ^~ ~~~~~~~~~~ 2025-06-01T08:27:21,971 command_set.c:92:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:21,971 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-06-01T08:27:21,972 | ^~~~~~~~~~ 2025-06-01T08:27:21,972 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-06-01T08:27:21,973 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-06-01T08:27:21,973 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,094 command_set.c: In function ‘sketch_operate’: 2025-06-01T08:27:22,095 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,095 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-06-01T08:27:22,096 | ^~ ~~~~~~~~~~ 2025-06-01T08:27:22,096 command_set.c:153:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,097 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-06-01T08:27:22,098 | ^~~~~~~~~~ 2025-06-01T08:27:22,099 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-06-01T08:27:22,099 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-06-01T08:27:22,100 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,101 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,102 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-06-01T08:27:22,103 | ^~ ~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,103 command_set.c:155:29: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,104 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-06-01T08:27:22,104 | ^~~~~~~~~~ 2025-06-01T08:27:22,105 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2025-06-01T08:27:22,106 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-06-01T08:27:22,106 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,107 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,108 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-06-01T08:27:22,108 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:22,109 command_set.c:165:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,110 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-06-01T08:27:22,111 | ^~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,112 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-06-01T08:27:22,112 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-06-01T08:27:22,113 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,113 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,114 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-06-01T08:27:22,114 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:22,115 command_set.c:169:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,115 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-06-01T08:27:22,116 | ^~~~~~~~~~ 2025-06-01T08:27:22,116 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-06-01T08:27:22,117 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-06-01T08:27:22,117 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,118 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,118 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-06-01T08:27:22,119 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:22,120 command_set.c:174:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,120 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-06-01T08:27:22,121 | ^~~~~~~~~~ 2025-06-01T08:27:22,122 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-06-01T08:27:22,123 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-06-01T08:27:22,123 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,124 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,125 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-06-01T08:27:22,126 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:22,126 command_set.c:187:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,127 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-06-01T08:27:22,128 | ^~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,128 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-06-01T08:27:22,129 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-06-01T08:27:22,130 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,131 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-06-01T08:27:22,131 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:22,132 | ^ 2025-06-01T08:27:22,133 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-06-01T08:27:22,133 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:22,134 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,273 command_set.c: In function ‘uniq_sketch_union’: 2025-06-01T08:27:22,274 command_set.c:219:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-06-01T08:27:22,275 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2025-06-01T08:27:22,275 | ^ 2025-06-01T08:27:22,276 command_set.c:219:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2025-06-01T08:27:22,276 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2025-06-01T08:27:22,277 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,277 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-06-01T08:27:22,278 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:22,278 | ^ 2025-06-01T08:27:22,279 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-06-01T08:27:22,280 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:22,280 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,281 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,281 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-06-01T08:27:22,282 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:22,282 command_set.c:247:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,283 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-06-01T08:27:22,284 | ^~~~~~~~~~ 2025-06-01T08:27:22,284 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-06-01T08:27:22,285 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-06-01T08:27:22,286 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,286 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,287 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-06-01T08:27:22,288 | ^~ ~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,289 command_set.c:259:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,289 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-06-01T08:27:22,290 | ^~~~~~~~~~ 2025-06-01T08:27:22,291 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2025-06-01T08:27:22,291 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-06-01T08:27:22,292 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,421 command_set.c: In function ‘combin_pans’: 2025-06-01T08:27:22,421 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,422 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-06-01T08:27:22,423 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:22,423 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2025-06-01T08:27:22,424 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-06-01T08:27:22,425 | ^~~~~~~~~~ 2025-06-01T08:27:22,425 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2025-06-01T08:27:22,426 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-06-01T08:27:22,427 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,427 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,428 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-06-01T08:27:22,429 | ^~ ~~~~~~~~~~ 2025-06-01T08:27:22,429 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2025-06-01T08:27:22,430 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-06-01T08:27:22,430 | ^~~~~~~~~~ 2025-06-01T08:27:22,431 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2025-06-01T08:27:22,431 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-06-01T08:27:22,432 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,433 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-06-01T08:27:22,434 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:22,434 | ^ 2025-06-01T08:27:22,435 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-06-01T08:27:22,435 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:22,436 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,639 command_set.c: In function ‘combin_subset_pans’: 2025-06-01T08:27:22,640 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,640 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-06-01T08:27:22,641 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:22,642 command_set.c:469:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,642 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-06-01T08:27:22,643 | ^~~~~~~~~~ 2025-06-01T08:27:22,644 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-06-01T08:27:22,644 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-06-01T08:27:22,645 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,646 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,646 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-06-01T08:27:22,647 | ^~ ~~~~~~~~~~ 2025-06-01T08:27:22,648 command_set.c:475:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,648 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-06-01T08:27:22,649 | ^~~~~~~~~~ 2025-06-01T08:27:22,649 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-06-01T08:27:22,650 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-06-01T08:27:22,651 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,651 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,652 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-06-01T08:27:22,653 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:22,654 command_set.c:481:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,655 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-06-01T08:27:22,655 | ^~~~~~~~~~ 2025-06-01T08:27:22,656 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-06-01T08:27:22,656 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-06-01T08:27:22,657 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,657 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,658 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-06-01T08:27:22,658 | ^~ ~~~~~~~~~~ 2025-06-01T08:27:22,659 command_set.c:512:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,659 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-06-01T08:27:22,660 | ^~~~~~~~~~ 2025-06-01T08:27:22,660 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-06-01T08:27:22,661 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-06-01T08:27:22,661 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,662 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-06-01T08:27:22,662 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:22,663 | ^ 2025-06-01T08:27:22,664 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-06-01T08:27:22,664 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:22,665 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,887 command_set.c: In function ‘grouping_genomes’: 2025-06-01T08:27:22,888 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,889 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-06-01T08:27:22,889 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:22,890 command_set.c:574:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,891 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-06-01T08:27:22,891 | ^~~~~~~~~~ 2025-06-01T08:27:22,892 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-06-01T08:27:22,893 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-06-01T08:27:22,893 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,894 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,895 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-06-01T08:27:22,895 | ^~ ~~~~~~~~~~ 2025-06-01T08:27:22,896 command_set.c:580:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,896 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-06-01T08:27:22,897 | ^~~~~~~~~~ 2025-06-01T08:27:22,898 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-06-01T08:27:22,899 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-06-01T08:27:22,899 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,900 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,901 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-06-01T08:27:22,901 | ^~ ~~~~~~~~~~~ 2025-06-01T08:27:22,902 command_set.c:612:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,903 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-06-01T08:27:22,903 | ^~~~~~~~~~ 2025-06-01T08:27:22,904 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-06-01T08:27:22,904 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-06-01T08:27:22,905 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,906 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-06-01T08:27:22,906 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-06-01T08:27:22,907 | ^~ ~~~~~~~~~~ 2025-06-01T08:27:22,907 command_set.c:634:25: note: directive argument in the range [-2147483644, 2147483646] 2025-06-01T08:27:22,908 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-06-01T08:27:22,908 | ^~~~~~~~~~ 2025-06-01T08:27:22,909 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-06-01T08:27:22,910 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-06-01T08:27:22,910 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:22,911 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-06-01T08:27:22,912 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:22,912 | ^ 2025-06-01T08:27:22,913 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-06-01T08:27:22,914 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-06-01T08:27:22,914 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:23,199 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 2025-06-01T08:27:23,528 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 2025-06-01T08:27:23,715 global_basic.c: In function ‘organize_infile_list’: 2025-06-01T08:27:23,716 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2025-06-01T08:27:23,716 195 | while (isspace(*buf)) buf++; 2025-06-01T08:27:23,717 | ^~~~~~~ 2025-06-01T08:27:23,718 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2025-06-01T08:27:23,718 34 | #include 2025-06-01T08:27:23,719 +++ |+#include 2025-06-01T08:27:23,720 35 | 2025-06-01T08:27:23,721 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=] 2025-06-01T08:27:23,722 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2025-06-01T08:27:23,722 | ~~^ 2025-06-01T08:27:23,723 | | 2025-06-01T08:27:23,723 | long unsigned int 2025-06-01T08:27:23,724 | %u 2025-06-01T08:27:23,724 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2025-06-01T08:27:23,725 | ~~~~~~~~~~~ 2025-06-01T08:27:23,725 | | 2025-06-01T08:27:23,726 | size_t {aka unsigned int} 2025-06-01T08:27:23,726 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=] 2025-06-01T08:27:23,727 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2025-06-01T08:27:23,727 | ~~^ 2025-06-01T08:27:23,728 | | 2025-06-01T08:27:23,728 | long unsigned int 2025-06-01T08:27:23,729 | %u 2025-06-01T08:27:23,729 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2025-06-01T08:27:23,730 | ~~~~~~~~~~~ 2025-06-01T08:27:23,731 | | 2025-06-01T08:27:23,731 | size_t {aka unsigned int} 2025-06-01T08:27:24,490 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 2025-06-01T08:27:24,687 iseq2comem.c: In function ‘reads2mco’: 2025-06-01T08:27:24,688 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,689 156 | if (base > TL) { 2025-06-01T08:27:24,689 | ^ 2025-06-01T08:27:24,690 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,691 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-06-01T08:27:24,691 | ^~ 2025-06-01T08:27:24,692 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,693 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-06-01T08:27:24,693 | ^ 2025-06-01T08:27:24,695 iseq2comem.c: In function ‘fasta2co’: 2025-06-01T08:27:24,696 iseq2comem.c:213:69: warning: too many arguments for format [-Wformat-extra-args] 2025-06-01T08:27:24,696 213 | if ((infp = popen(fas_fname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2025-06-01T08:27:24,697 | ^~~~~~~~~~~~~~~ 2025-06-01T08:27:24,697 iseq2comem.c:219:69: warning: too many arguments for format [-Wformat-extra-args] 2025-06-01T08:27:24,698 219 | if ((infp = popen(fas_fname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2025-06-01T08:27:24,699 | ^~~~~~~~~~~~~~~ 2025-06-01T08:27:24,700 iseq2comem.c:261:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,701 261 | if (base > TL) { 2025-06-01T08:27:24,701 | ^ 2025-06-01T08:27:24,702 iseq2comem.c:265:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,702 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-06-01T08:27:24,703 | ^~ 2025-06-01T08:27:24,703 iseq2comem.c:265:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,704 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-06-01T08:27:24,705 | ^ 2025-06-01T08:27:24,705 iseq2comem.c: In function ‘fastq2co’: 2025-06-01T08:27:24,706 iseq2comem.c:295:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2025-06-01T08:27:24,707 295 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2025-06-01T08:27:24,707 | ^~ 2025-06-01T08:27:24,708 iseq2comem.c:307:68: warning: too many arguments for format [-Wformat-extra-args] 2025-06-01T08:27:24,709 307 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2025-06-01T08:27:24,710 | ^~~~~~~~~~~~~~~ 2025-06-01T08:27:24,710 iseq2comem.c:313:68: warning: too many arguments for format [-Wformat-extra-args] 2025-06-01T08:27:24,711 313 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2025-06-01T08:27:24,711 | ^~~~~~~~~~~~~~~ 2025-06-01T08:27:24,714 iseq2comem.c:352:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,715 352 | if (base > TL) { 2025-06-01T08:27:24,715 | ^ 2025-06-01T08:27:24,716 iseq2comem.c:356:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,717 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-06-01T08:27:24,717 | ^~ 2025-06-01T08:27:24,718 iseq2comem.c:356:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,718 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-06-01T08:27:24,719 | ^ 2025-06-01T08:27:24,721 iseq2comem.c:375:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,721 375 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2025-06-01T08:27:24,722 | ^ 2025-06-01T08:27:24,723 iseq2comem.c: In function ‘fastq2koc’: 2025-06-01T08:27:24,724 iseq2comem.c:403:68: warning: too many arguments for format [-Wformat-extra-args] 2025-06-01T08:27:24,725 403 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2025-06-01T08:27:24,725 | ^~~~~~~~~~~~~~~~ 2025-06-01T08:27:24,726 iseq2comem.c:409:68: warning: too many arguments for format [-Wformat-extra-args] 2025-06-01T08:27:24,727 409 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2025-06-01T08:27:24,727 | ^~~~~~~~~~~~~~~~ 2025-06-01T08:27:24,729 iseq2comem.c:448:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,729 448 | if (base > TL) { 2025-06-01T08:27:24,730 | ^ 2025-06-01T08:27:24,730 iseq2comem.c:452:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,731 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-06-01T08:27:24,731 | ^~ 2025-06-01T08:27:24,732 iseq2comem.c:452:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,732 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-06-01T08:27:24,733 | ^ 2025-06-01T08:27:24,740 iseq2comem.c: In function ‘mt_shortreads2koc’: 2025-06-01T08:27:24,741 iseq2comem.c:628:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,741 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-06-01T08:27:24,742 | ^~ 2025-06-01T08:27:24,742 iseq2comem.c:628:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:24,743 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-06-01T08:27:24,744 | ^ 2025-06-01T08:27:26,140 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 2025-06-01T08:27:26,201 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 2025-06-01T08:27:26,334 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 2025-06-01T08:27:26,750 pykssd.c: In function ‘py_dist_dispatch’: 2025-06-01T08:27:26,751 pykssd.c:334:13: warning: unused variable ‘state1’ [-Wunused-variable] 2025-06-01T08:27:26,751 334 | int state1 = dist_dispatch(&dist_opt_val1); 2025-06-01T08:27:26,752 | ^~~~~~ 2025-06-01T08:27:26,753 pykssd.c:396:13: warning: unused variable ‘state2’ [-Wunused-variable] 2025-06-01T08:27:26,754 396 | int state2 = dist_dispatch(&dist_opt_val2); 2025-06-01T08:27:26,754 | ^~~~~~ 2025-06-01T08:27:26,755 pykssd.c:530:13: warning: unused variable ‘state4’ [-Wunused-variable] 2025-06-01T08:27:26,756 530 | int state4 = dist_dispatch(&dist_opt_val4); 2025-06-01T08:27:26,757 | ^~~~~~ 2025-06-01T08:27:27,417 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 2025-06-01T08:27:27,583 building 'nj' extension 2025-06-01T08:27:27,586 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 2025-06-01T08:27:28,063 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 2025-06-01T08:27:28,228 buildtree.c: In function ‘UPGMA_buildtree’: 2025-06-01T08:27:28,228 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-06-01T08:27:28,229 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2025-06-01T08:27:28,229 | ^~ 2025-06-01T08:27:28,230 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-06-01T08:27:28,231 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2025-06-01T08:27:28,232 | ^~ 2025-06-01T08:27:28,892 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 2025-06-01T08:27:29,278 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 2025-06-01T08:27:29,432 distancemat.c: In function ‘clone_DistanceMatrix’: 2025-06-01T08:27:29,433 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-06-01T08:27:29,434 226 | for( i=0; i < dest->size; i++) { 2025-06-01T08:27:29,435 | ^ 2025-06-01T08:27:29,435 distancemat.c: In function ‘empty_DistanceMatrix’: 2025-06-01T08:27:29,436 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-06-01T08:27:29,437 260 | for( i=0; i < mat->size; i++) { 2025-06-01T08:27:29,438 | ^ 2025-06-01T08:27:29,438 distancemat.c: In function ‘print_DistanceMatrix’: 2025-06-01T08:27:29,439 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-06-01T08:27:29,441 349 | for(row=0; row < mat->size; row++) { 2025-06-01T08:27:29,441 | ^ 2025-06-01T08:27:29,442 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2025-06-01T08:27:29,443 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2025-06-01T08:27:29,444 410 | while(c = fgetc(handle)) { 2025-06-01T08:27:29,444 | ^ 2025-06-01T08:27:29,826 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 2025-06-01T08:27:30,293 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 2025-06-01T08:27:30,524 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 2025-06-01T08:27:31,410 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 2025-06-01T08:27:31,600 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 2025-06-01T08:27:31,720 building 'dnj' extension 2025-06-01T08:27:31,723 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 2025-06-01T08:27:31,791 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 2025-06-01T08:27:31,938 dnj.c: In function ‘minQpair’: 2025-06-01T08:27:31,939 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,940 70 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,940 | ^~~ 2025-06-01T08:27:31,941 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,942 126 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,943 | ^~~ 2025-06-01T08:27:31,943 dnj.c: In function ‘maxQpair’: 2025-06-01T08:27:31,944 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,945 157 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,945 | ^~~ 2025-06-01T08:27:31,946 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,947 213 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,947 | ^~~ 2025-06-01T08:27:31,948 dnj.c: In function ‘UPGMApair’: 2025-06-01T08:27:31,949 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,949 237 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,950 | ^~~ 2025-06-01T08:27:31,951 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,951 284 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,952 | ^~~ 2025-06-01T08:27:31,953 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,953 291 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,954 | ^~~ 2025-06-01T08:27:31,955 dnj.c: In function ‘minQrow’: 2025-06-01T08:27:31,955 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,956 374 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,956 | ^~~ 2025-06-01T08:27:31,957 dnj.c: In function ‘maxQrow’: 2025-06-01T08:27:31,957 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,958 435 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,959 | ^~~ 2025-06-01T08:27:31,959 dnj.c: In function ‘UPGMArow’: 2025-06-01T08:27:31,960 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,960 488 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,961 | ^~~ 2025-06-01T08:27:31,961 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,962 494 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,963 | ^~~ 2025-06-01T08:27:31,963 dnj.c: In function ‘minQ_thread’: 2025-06-01T08:27:31,964 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:31,964 553 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:31,965 | ^~~ 2025-06-01T08:27:33,325 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 2025-06-01T08:27:33,454 filebuff.c: In function ‘BuffgzFileBuff’: 2025-06-01T08:27:33,455 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:33,456 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2025-06-01T08:27:33,457 | ^~ 2025-06-01T08:27:33,783 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 2025-06-01T08:27:33,929 hclust.c: In function ‘minQ’: 2025-06-01T08:27:33,930 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-06-01T08:27:33,931 364 | while(++i < Q->n) { 2025-06-01T08:27:33,932 | ^ 2025-06-01T08:27:33,932 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:33,933 377 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:33,934 | ^~~ 2025-06-01T08:27:33,934 hclust.c: In function ‘maxQ’: 2025-06-01T08:27:33,935 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-06-01T08:27:33,936 394 | while(++i < Q->n) { 2025-06-01T08:27:33,936 | ^ 2025-06-01T08:27:33,937 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:33,938 407 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:33,939 | ^~~ 2025-06-01T08:27:36,325 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 2025-06-01T08:27:36,478 matrix.c: In function ‘ltdMatrix_popArrange’: 2025-06-01T08:27:36,479 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-06-01T08:27:36,480 538 | if(pos != n) { 2025-06-01T08:27:36,480 | ^~ 2025-06-01T08:27:37,361 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 2025-06-01T08:27:37,419 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 2025-06-01T08:27:37,566 nj.c: In function ‘initQ’: 2025-06-01T08:27:37,566 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:37,567 243 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:37,568 | ^~~ 2025-06-01T08:27:37,569 nj.c: In function ‘initQ_MN’: 2025-06-01T08:27:37,569 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:37,570 358 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:37,570 | ^~~ 2025-06-01T08:27:37,574 nj.c: In function ‘minD’: 2025-06-01T08:27:37,575 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:37,575 559 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:37,576 | ^~~ 2025-06-01T08:27:37,577 nj.c: In function ‘maxD’: 2025-06-01T08:27:37,577 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:37,578 642 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:37,579 | ^~~ 2025-06-01T08:27:37,582 nj.c: In function ‘minPair’: 2025-06-01T08:27:37,583 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-06-01T08:27:37,584 826 | pos <<= sizeof(unsigned) * 8; 2025-06-01T08:27:37,584 | ^~~ 2025-06-01T08:27:39,951 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 2025-06-01T08:27:40,506 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 2025-06-01T08:27:40,610 pherror.c: In function ‘cfread’: 2025-06-01T08:27:40,611 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-06-01T08:27:40,611 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2025-06-01T08:27:40,612 | ^~ 2025-06-01T08:27:40,706 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 2025-06-01T08:27:41,804 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 2025-06-01T08:27:42,202 In file included from pydnj.c:11: 2025-06-01T08:27:42,203 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2025-06-01T08:27:42,203 20 | #define _XOPEN_SOURCE 600 2025-06-01T08:27:42,204 | 2025-06-01T08:27:42,205 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2025-06-01T08:27:42,206 from /usr/include/stdlib.h:26, 2025-06-01T08:27:42,206 from /usr/include/python3.11/Python.h:23, 2025-06-01T08:27:42,207 from pydnj.c:1: 2025-06-01T08:27:42,208 /usr/include/features.h:214: note: this is the location of the previous definition 2025-06-01T08:27:42,208 214 | # define _XOPEN_SOURCE 700 2025-06-01T08:27:42,209 | 2025-06-01T08:27:42,230 pydnj.c: In function ‘py_build’: 2025-06-01T08:27:42,231 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2025-06-01T08:27:42,232 165 | p = omp_get_num_procs(); 2025-06-01T08:27:42,233 | ^~~~~~~~~~~~~~~~~ 2025-06-01T08:27:42,352 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2025-06-01T08:27:42,353 169 | free(file); 2025-06-01T08:27:42,354 | ^~~~~~~~~~ 2025-06-01T08:27:42,354 pydnj.c:125:12: note: returned from ‘fopen’ 2025-06-01T08:27:42,355 125 | file = fopen(inputfilename, "r"); 2025-06-01T08:27:42,355 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-06-01T08:27:42,428 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 2025-06-01T08:27:42,656 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 2025-06-01T08:27:42,773 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 2025-06-01T08:27:42,982 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 2025-06-01T08:27:43,157 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 2025-06-01T08:27:43,348 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-06-01T08:27:43,348 !! 2025-06-01T08:27:43,350 ******************************************************************************** 2025-06-01T08:27:43,351 Please avoid running ``setup.py`` directly. 2025-06-01T08:27:43,351 Instead, use pypa/build, pypa/installer or other 2025-06-01T08:27:43,352 standards-based tools. 2025-06-01T08:27:43,353 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-06-01T08:27:43,354 or your builds will no longer be supported. 2025-06-01T08:27:43,355 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-06-01T08:27:43,356 ******************************************************************************** 2025-06-01T08:27:43,357 !! 2025-06-01T08:27:43,358 self.initialize_options() 2025-06-01T08:27:43,381 installing to build/bdist.linux-armv7l/wheel 2025-06-01T08:27:43,382 running install 2025-06-01T08:27:43,407 running install_lib 2025-06-01T08:27:43,435 creating build/bdist.linux-armv7l/wheel 2025-06-01T08:27:43,437 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-06-01T08:27:43,445 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel/. 2025-06-01T08:27:43,448 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-06-01T08:27:43,453 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-06-01T08:27:43,464 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel/. 2025-06-01T08:27:43,466 running install_egg_info 2025-06-01T08:27:43,504 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/./kssdtree-2.0.8-py3.11.egg-info 2025-06-01T08:27:43,517 running install_scripts 2025-06-01T08:27:43,572 creating build/bdist.linux-armv7l/wheel/kssdtree-2.0.8.dist-info/WHEEL 2025-06-01T08:27:43,574 creating '/tmp/pip-wheel-24zd_2i2/kssdtree-2.0.8-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-06-01T08:27:43,642 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2025-06-01T08:27:43,725 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2025-06-01T08:27:43,730 adding 'kssdtree.py' 2025-06-01T08:27:43,750 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2025-06-01T08:27:43,753 adding 'toolutils.py' 2025-06-01T08:27:43,755 adding 'kssdtree-2.0.8.dist-info/METADATA' 2025-06-01T08:27:43,756 adding 'kssdtree-2.0.8.dist-info/WHEEL' 2025-06-01T08:27:43,757 adding 'kssdtree-2.0.8.dist-info/dependency_links.txt' 2025-06-01T08:27:43,758 adding 'kssdtree-2.0.8.dist-info/top_level.txt' 2025-06-01T08:27:43,759 adding 'kssdtree-2.0.8.dist-info/RECORD' 2025-06-01T08:27:43,764 removing build/bdist.linux-armv7l/wheel 2025-06-01T08:27:43,904 Building wheel for kssdtree (setup.py): finished with status 'done' 2025-06-01T08:27:43,910 Created wheel for kssdtree: filename=kssdtree-2.0.8-cp311-cp311-linux_armv7l.whl size=382407 sha256=af8a0b06198bfd1ce24b078cdad070d5c587b126973ade98efa6ab13b9c2fc32 2025-06-01T08:27:43,911 Stored in directory: /tmp/pip-ephem-wheel-cache-4jpnzwue/wheels/4a/4e/04/af31ed876e97c1adaa514a95a22c29f33f4906451bf35eb766 2025-06-01T08:27:43,922 Successfully built kssdtree 2025-06-01T08:27:43,936 Removed build tracker: '/tmp/pip-build-tracker-oxgxdj2h'