2025-05-30T05:11:41,796 Created temporary directory: /tmp/pip-build-tracker-b6u9j2hy 2025-05-30T05:11:41,797 Initialized build tracking at /tmp/pip-build-tracker-b6u9j2hy 2025-05-30T05:11:41,797 Created build tracker: /tmp/pip-build-tracker-b6u9j2hy 2025-05-30T05:11:41,798 Entered build tracker: /tmp/pip-build-tracker-b6u9j2hy 2025-05-30T05:11:41,799 Created temporary directory: /tmp/pip-wheel-n2pymn4f 2025-05-30T05:11:41,803 Created temporary directory: /tmp/pip-ephem-wheel-cache-3rjvbsgq 2025-05-30T05:11:41,849 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-05-30T05:11:41,851 2 location(s) to search for versions of kssdtree: 2025-05-30T05:11:41,851 * https://pypi.org/simple/kssdtree/ 2025-05-30T05:11:41,851 * https://www.piwheels.org/simple/kssdtree/ 2025-05-30T05:11:41,852 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2025-05-30T05:11:41,853 Getting page https://pypi.org/simple/kssdtree/ 2025-05-30T05:11:41,854 Found index url https://pypi.org/simple/ 2025-05-30T05:11:42,072 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2025-05-30T05:11:42,075 Found link https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.1 2025-05-30T05:11:42,076 Found link https://files.pythonhosted.org/packages/9a/4c/6516f734f5860e4b30f9091aaac5811663bfae72c4de4ae6566c89192767/kssdtree-1.1.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.2 2025-05-30T05:11:42,077 Found link https://files.pythonhosted.org/packages/a4/cd/f2954686c636e853cc3fda197c459195377b78288874cf7d68218a8bdbf4/kssdtree-1.1.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.3 2025-05-30T05:11:42,077 Found link https://files.pythonhosted.org/packages/20/ea/b0301924e3f7d367cbb7b8da66837dba9af2a332bf56ed35e03a33faee76/kssdtree-1.1.4.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.4 2025-05-30T05:11:42,078 Found link https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.6 2025-05-30T05:11:42,079 Found link https://files.pythonhosted.org/packages/cd/4b/d886cbcc573ff0969da7d9c756049925b86141e60ee6708dfbbe0644d008/kssdtree-1.1.7.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.7 2025-05-30T05:11:42,079 Found link https://files.pythonhosted.org/packages/7e/8a/a62c8adc92df69ab8cb242827ee64a3e2b6d5c89b83425785dd00605af17/kssdtree-1.1.8.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.8 2025-05-30T05:11:42,080 Found link https://files.pythonhosted.org/packages/da/db/e458cca6427752c05428d2378ccdee631d32f760174fdaba65f73125e71b/kssdtree-1.1.9.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.9 2025-05-30T05:11:42,081 Found link https://files.pythonhosted.org/packages/9d/47/017180a30e73e421372377cbe6d01c5e51a5108ea2177f20ccd7d283f8d1/kssdtree-2.0.0.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.0 2025-05-30T05:11:42,082 Found link https://files.pythonhosted.org/packages/ba/39/d443cac955912a0371c93b797311cb9ec3a8d6ee0a5d7673376d826aa6b2/kssdtree-2.0.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.1 2025-05-30T05:11:42,082 Found link https://files.pythonhosted.org/packages/2e/32/e53c0e3735cbc913b2c96b4e0e1c1005fe816a4d71b38b80cdcfb5c67fa8/kssdtree-2.0.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.2 2025-05-30T05:11:42,083 Found link https://files.pythonhosted.org/packages/c0/0f/effc10c8e76dbe3b9a35a4b4d9e65a0a889ee805e10334541c3ca7ae3b94/kssdtree-2.0.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.3 2025-05-30T05:11:42,084 Found link https://files.pythonhosted.org/packages/fc/8d/d3790baa2f2f0a01c913005b94a82dc13ef601e7015e662ccff94bb1b458/kssdtree-2.0.4.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.4 2025-05-30T05:11:42,084 Found link https://files.pythonhosted.org/packages/b5/f8/19480a4c57704944f973ebf534f9582054949cca20170a33c6f874974440/kssdtree-2.0.5.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.5 2025-05-30T05:11:42,085 Found link https://files.pythonhosted.org/packages/46/ef/2d920d5d2fceded48c7add363e04f49ae85414bcd4360e1295d6fddc4a24/kssdtree-2.0.6.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.6 2025-05-30T05:11:42,086 Found link https://files.pythonhosted.org/packages/9c/1c/c6b3f05465d145856ac992328bd59e776286a59b120254620c1dbffcf67f/kssdtree-2.0.7.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.7 2025-05-30T05:11:42,086 Found link https://files.pythonhosted.org/packages/82/9b/dac2af6572f0c4421e5ba8341dcfddac466de30c62acfa019d9ef70b2670/kssdtree-2.0.8.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.8 2025-05-30T05:11:42,087 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2025-05-30T05:11:42,088 Getting page https://www.piwheels.org/simple/kssdtree/ 2025-05-30T05:11:42,089 Found index url https://www.piwheels.org/simple/ 2025-05-30T05:11:42,241 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kssdtree/ 2025-05-30T05:11:42,893 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kssdtree/ 2025-05-30T05:11:44,048 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kssdtree/ 2025-05-30T05:11:46,258 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kssdtree/ 2025-05-30T05:11:50,472 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kssdtree/ 2025-05-30T05:11:50,683 Could not fetch URL https://www.piwheels.org/simple/kssdtree/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/kssdtree/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-05-30T05:11:50,685 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2025-05-30T05:11:50,685 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2025-05-30T05:11:50,704 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2025-05-30T05:11:50,706 Collecting kssdtree==2.0.6 2025-05-30T05:11:50,708 Created temporary directory: /tmp/pip-unpack-uuk4lttt 2025-05-30T05:11:50,925 Downloading kssdtree-2.0.6.tar.gz (113 kB) 2025-05-30T05:11:51,148 Added kssdtree==2.0.6 from https://files.pythonhosted.org/packages/46/ef/2d920d5d2fceded48c7add363e04f49ae85414bcd4360e1295d6fddc4a24/kssdtree-2.0.6.tar.gz to build tracker '/tmp/pip-build-tracker-b6u9j2hy' 2025-05-30T05:11:51,150 Running setup.py (path:/tmp/pip-wheel-n2pymn4f/kssdtree_8f041400137f488e9b9988ebc230b542/setup.py) egg_info for package kssdtree 2025-05-30T05:11:51,151 Created temporary directory: /tmp/pip-pip-egg-info-g0ukqq4x 2025-05-30T05:11:51,151 Preparing metadata (setup.py): started 2025-05-30T05:11:51,152 Running command python setup.py egg_info 2025-05-30T05:11:52,005 running egg_info 2025-05-30T05:11:52,032 creating /tmp/pip-pip-egg-info-g0ukqq4x/kssdtree.egg-info 2025-05-30T05:11:52,033 writing /tmp/pip-pip-egg-info-g0ukqq4x/kssdtree.egg-info/PKG-INFO 2025-05-30T05:11:52,036 writing dependency_links to /tmp/pip-pip-egg-info-g0ukqq4x/kssdtree.egg-info/dependency_links.txt 2025-05-30T05:11:52,038 writing requirements to /tmp/pip-pip-egg-info-g0ukqq4x/kssdtree.egg-info/requires.txt 2025-05-30T05:11:52,039 writing top-level names to /tmp/pip-pip-egg-info-g0ukqq4x/kssdtree.egg-info/top_level.txt 2025-05-30T05:11:52,041 writing manifest file '/tmp/pip-pip-egg-info-g0ukqq4x/kssdtree.egg-info/SOURCES.txt' 2025-05-30T05:11:52,149 reading manifest file '/tmp/pip-pip-egg-info-g0ukqq4x/kssdtree.egg-info/SOURCES.txt' 2025-05-30T05:11:52,151 reading manifest template 'MANIFEST.in' 2025-05-30T05:11:52,169 writing manifest file '/tmp/pip-pip-egg-info-g0ukqq4x/kssdtree.egg-info/SOURCES.txt' 2025-05-30T05:11:52,276 Preparing metadata (setup.py): finished with status 'done' 2025-05-30T05:11:52,280 Source in /tmp/pip-wheel-n2pymn4f/kssdtree_8f041400137f488e9b9988ebc230b542 has version 2.0.6, which satisfies requirement kssdtree==2.0.6 from https://files.pythonhosted.org/packages/46/ef/2d920d5d2fceded48c7add363e04f49ae85414bcd4360e1295d6fddc4a24/kssdtree-2.0.6.tar.gz 2025-05-30T05:11:52,281 Removed kssdtree==2.0.6 from https://files.pythonhosted.org/packages/46/ef/2d920d5d2fceded48c7add363e04f49ae85414bcd4360e1295d6fddc4a24/kssdtree-2.0.6.tar.gz from build tracker '/tmp/pip-build-tracker-b6u9j2hy' 2025-05-30T05:11:52,285 Created temporary directory: /tmp/pip-unpack-p8uyct4q 2025-05-30T05:11:52,286 Created temporary directory: /tmp/pip-unpack-rbhngndc 2025-05-30T05:11:52,287 Building wheels for collected packages: kssdtree 2025-05-30T05:11:52,291 Created temporary directory: /tmp/pip-wheel-oiwrakqj 2025-05-30T05:11:52,292 DEPRECATION: Building 'kssdtree' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'kssdtree'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-05-30T05:11:52,293 Building wheel for kssdtree (setup.py): started 2025-05-30T05:11:52,294 Destination directory: /tmp/pip-wheel-oiwrakqj 2025-05-30T05:11:52,295 Running command python setup.py bdist_wheel 2025-05-30T05:11:53,098 running bdist_wheel 2025-05-30T05:11:53,225 running build 2025-05-30T05:11:53,226 running build_py 2025-05-30T05:11:53,254 creating build/lib.linux-armv7l-cpython-311 2025-05-30T05:11:53,256 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2025-05-30T05:11:53,259 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2025-05-30T05:11:53,261 running egg_info 2025-05-30T05:11:53,288 writing kssdtree.egg-info/PKG-INFO 2025-05-30T05:11:53,291 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2025-05-30T05:11:53,293 writing requirements to kssdtree.egg-info/requires.txt 2025-05-30T05:11:53,294 writing top-level names to kssdtree.egg-info/top_level.txt 2025-05-30T05:11:53,322 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2025-05-30T05:11:53,327 reading manifest template 'MANIFEST.in' 2025-05-30T05:11:53,344 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2025-05-30T05:11:53,346 running build_ext 2025-05-30T05:11:53,758 building 'kssd' extension 2025-05-30T05:11:53,759 creating build/temp.linux-armv7l-cpython-311 2025-05-30T05:11:53,761 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c co2mco.c -o build/temp.linux-armv7l-cpython-311/co2mco.o -fopenmp 2025-05-30T05:11:53,939 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2025-05-30T05:11:53,940 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T05:11:53,941 109 | for (unsigned int i = 0; i < comp_num; i++) { 2025-05-30T05:11:53,942 | ^ 2025-05-30T05:11:53,943 co2mco.c: In function ‘co2unitllmco’: 2025-05-30T05:11:53,944 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T05:11:53,945 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2025-05-30T05:11:53,945 | ^ 2025-05-30T05:11:54,679 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_composite.c -o build/temp.linux-armv7l-cpython-311/command_composite.o -fopenmp 2025-05-30T05:11:55,056 command_composite.c: In function ‘get_species_abundance’: 2025-05-30T05:11:55,057 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2025-05-30T05:11:55,057 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2025-05-30T05:11:55,058 | ^~ 2025-05-30T05:11:55,058 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2025-05-30T05:11:55,059 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2025-05-30T05:11:55,059 | ^~ 2025-05-30T05:11:55,060 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:55,061 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-05-30T05:11:55,061 | ^ 2025-05-30T05:11:55,062 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:55,063 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-05-30T05:11:55,063 | ^~~~~~~~~~ 2025-05-30T05:11:55,064 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-05-30T05:11:55,065 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-05-30T05:11:55,066 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:55,066 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:55,067 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-05-30T05:11:55,068 | ^ 2025-05-30T05:11:55,068 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:55,069 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-05-30T05:11:55,070 | ^~~~~~~~~~ 2025-05-30T05:11:55,070 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-05-30T05:11:55,071 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-05-30T05:11:55,072 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:55,072 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:55,073 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-05-30T05:11:55,074 | ^ 2025-05-30T05:11:55,075 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:55,076 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-05-30T05:11:55,077 | ^~~~~~~~~~ 2025-05-30T05:11:55,077 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-05-30T05:11:55,078 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-05-30T05:11:55,078 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:55,079 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:55,079 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-05-30T05:11:55,080 | ^ 2025-05-30T05:11:55,080 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:55,081 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-05-30T05:11:55,082 | ^~~~~~~~~~ 2025-05-30T05:11:55,082 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-05-30T05:11:55,083 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-05-30T05:11:55,083 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:55,084 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:55,084 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-05-30T05:11:55,085 | ^ 2025-05-30T05:11:55,086 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:55,086 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-05-30T05:11:55,087 | ^~~~~~~~~~~~ 2025-05-30T05:11:55,088 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2025-05-30T05:11:55,089 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-05-30T05:11:55,089 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:55,321 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist.c -o build/temp.linux-armv7l-cpython-311/command_dist.o -fopenmp 2025-05-30T05:11:55,557 command_dist.c: In function ‘mco_cbd_co_dist’: 2025-05-30T05:11:55,558 command_dist.c:677:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T05:11:55,559 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T05:11:55,559 | ~~^ 2025-05-30T05:11:55,560 | | 2025-05-30T05:11:55,561 | long unsigned int 2025-05-30T05:11:55,561 | %u 2025-05-30T05:11:55,562 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T05:11:55,562 | ~~~~~~~ 2025-05-30T05:11:55,563 | | 2025-05-30T05:11:55,564 | size_t {aka unsigned int} 2025-05-30T05:11:55,564 command_dist.c:677:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T05:11:55,565 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T05:11:55,566 | ~~^ 2025-05-30T05:11:55,566 | | 2025-05-30T05:11:55,567 | long unsigned int 2025-05-30T05:11:55,567 | %u 2025-05-30T05:11:55,568 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T05:11:55,568 679 | maplength, (size_t) b * unitsz_distf_mapped); 2025-05-30T05:11:55,569 | ~~~~~~~~~ 2025-05-30T05:11:55,570 | | 2025-05-30T05:11:55,570 | size_t {aka unsigned int} 2025-05-30T05:11:55,571 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-05-30T05:11:55,571 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T05:11:55,572 | ~~^ 2025-05-30T05:11:55,572 | | 2025-05-30T05:11:55,573 | long unsigned int 2025-05-30T05:11:55,573 | %u 2025-05-30T05:11:55,574 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T05:11:55,575 679 | maplength, (size_t) b * unitsz_distf_mapped); 2025-05-30T05:11:55,575 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:55,576 | | 2025-05-30T05:11:55,576 | unsigned int 2025-05-30T05:11:55,577 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-05-30T05:11:55,578 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2025-05-30T05:11:55,578 | ^ 2025-05-30T05:11:55,579 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2025-05-30T05:11:55,579 command_dist.c:863:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T05:11:55,580 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-05-30T05:11:55,580 | ~~^ ~~~~~~~ 2025-05-30T05:11:55,581 | | | 2025-05-30T05:11:55,582 | long unsigned int size_t {aka unsigned int} 2025-05-30T05:11:55,582 | %u 2025-05-30T05:11:55,583 command_dist.c:863:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T05:11:55,584 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-05-30T05:11:55,585 | ~~^ 2025-05-30T05:11:55,585 | | 2025-05-30T05:11:55,585 | long unsigned int 2025-05-30T05:11:55,586 | %u 2025-05-30T05:11:55,586 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2025-05-30T05:11:55,587 | ~~~~~~~~~ 2025-05-30T05:11:55,587 | | 2025-05-30T05:11:55,588 | size_t {aka unsigned int} 2025-05-30T05:11:55,588 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-05-30T05:11:55,589 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-05-30T05:11:55,589 | ~~^ 2025-05-30T05:11:55,590 | | 2025-05-30T05:11:55,590 | long unsigned int 2025-05-30T05:11:55,591 | %u 2025-05-30T05:11:55,592 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2025-05-30T05:11:55,592 865 | (size_t) b * unitsz_distf_mapped); 2025-05-30T05:11:55,593 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:55,594 | | 2025-05-30T05:11:55,595 | unsigned int 2025-05-30T05:11:55,596 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2025-05-30T05:11:55,596 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2025-05-30T05:11:55,597 | ^~~~~~~ 2025-05-30T05:11:55,597 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2025-05-30T05:11:55,598 809 | struct stat cbd_fcode_stat; 2025-05-30T05:11:55,598 | ^~~~~~~~~~~~~~ 2025-05-30T05:11:55,599 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2025-05-30T05:11:55,600 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2025-05-30T05:11:55,600 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:55,601 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2025-05-30T05:11:55,601 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2025-05-30T05:11:55,602 | ^~~~~~~~~~~~~~~~~ 2025-05-30T05:11:55,602 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2025-05-30T05:11:55,603 command_dist.c:1018:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T05:11:55,603 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T05:11:55,604 | ~~^ 2025-05-30T05:11:55,605 | | 2025-05-30T05:11:55,605 | long unsigned int 2025-05-30T05:11:55,606 | %u 2025-05-30T05:11:55,606 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T05:11:55,607 | ~~~~~~~ 2025-05-30T05:11:55,607 | | 2025-05-30T05:11:55,608 | size_t {aka unsigned int} 2025-05-30T05:11:55,608 command_dist.c:1018:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T05:11:55,609 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T05:11:55,609 | ~~^ 2025-05-30T05:11:55,610 | | 2025-05-30T05:11:55,610 | long unsigned int 2025-05-30T05:11:55,611 | %u 2025-05-30T05:11:55,611 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T05:11:55,612 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2025-05-30T05:11:55,612 | ~~~~~~~~~ 2025-05-30T05:11:55,613 | | 2025-05-30T05:11:55,614 | size_t {aka unsigned int} 2025-05-30T05:11:55,615 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-05-30T05:11:55,615 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-05-30T05:11:55,616 | ~~^ 2025-05-30T05:11:55,617 | | 2025-05-30T05:11:55,618 | long unsigned int 2025-05-30T05:11:55,618 | %u 2025-05-30T05:11:55,619 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-05-30T05:11:55,620 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2025-05-30T05:11:55,621 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:55,621 | | 2025-05-30T05:11:55,622 | unsigned int 2025-05-30T05:11:55,622 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2025-05-30T05:11:55,623 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2025-05-30T05:11:55,624 | ^ 2025-05-30T05:11:55,624 command_dist.c: In function ‘mco_co_dist_core’: 2025-05-30T05:11:55,625 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-05-30T05:11:55,626 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2025-05-30T05:11:55,626 | ^ 2025-05-30T05:11:55,627 command_dist.c: In function ‘koc_dist_print_nobin’: 2025-05-30T05:11:55,627 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T05:11:55,628 1239 | for (int rid = 0; rid < ref_num; rid++) 2025-05-30T05:11:55,628 | ^ 2025-05-30T05:11:55,630 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T05:11:55,630 1245 | for (int rid = 0; rid < ref_num; rid++) { 2025-05-30T05:11:55,631 | ^ 2025-05-30T05:11:55,637 command_dist.c: In function ‘dist_print_nobin’: 2025-05-30T05:11:55,638 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T05:11:55,639 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2025-05-30T05:11:55,639 | ^ 2025-05-30T05:11:55,641 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T05:11:55,642 1356 | for (int rid = 0; rid < ref_num; rid++) { 2025-05-30T05:11:55,643 | ^ 2025-05-30T05:11:55,645 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T05:11:55,645 1382 | for (int rid = 0; rid < ref_num; rid++) 2025-05-30T05:11:55,646 | ^ 2025-05-30T05:11:56,006 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2025-05-30T05:11:56,006 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2025-05-30T05:11:56,007 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2025-05-30T05:11:56,007 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:56,008 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2025-05-30T05:11:56,009 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2025-05-30T05:11:56,009 | ^~~~~~~~~~~~ 2025-05-30T05:11:56,851 command_dist.c: In function ‘get_dim_shuffle’: 2025-05-30T05:11:56,852 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2025-05-30T05:11:56,852 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2025-05-30T05:11:56,853 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:56,854 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2025-05-30T05:11:56,854 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2025-05-30T05:11:56,855 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:57,758 command_dist.c: In function ‘mco_cbd_co_dist’: 2025-05-30T05:11:57,759 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:57,760 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T05:11:57,760 | ^~ ~~~~~~~~~ 2025-05-30T05:11:57,761 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-05-30T05:11:57,762 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T05:11:57,762 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:57,763 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T05:11:57,764 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T05:11:57,764 | ^~~~~~~~~~~~~~~ 2025-05-30T05:11:57,765 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-05-30T05:11:57,765 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T05:11:57,766 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:57,766 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T05:11:57,767 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T05:11:57,767 | ^~~~~~~~~~~ 2025-05-30T05:11:57,767 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:57,768 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T05:11:57,768 | ^~~~~~~~~~~~~~~~~ 2025-05-30T05:11:57,769 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2025-05-30T05:11:57,769 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T05:11:57,770 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:57,770 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T05:11:57,771 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T05:11:57,771 | ^~~~~ 2025-05-30T05:11:57,772 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:57,773 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T05:11:57,773 | ^~~~~~~~~~~ 2025-05-30T05:11:57,774 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-05-30T05:11:57,775 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T05:11:57,775 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,013 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2025-05-30T05:11:58,014 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:58,014 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T05:11:58,015 | ^~ ~~~~~~~~~ 2025-05-30T05:11:58,016 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-05-30T05:11:58,016 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T05:11:58,017 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,018 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T05:11:58,018 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T05:11:58,019 | ^~~~~~~~~~~~~~~ 2025-05-30T05:11:58,019 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-05-30T05:11:58,020 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T05:11:58,021 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,021 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T05:11:58,022 823 | sprintf(distf, "%s/distance.out", distout_dir); 2025-05-30T05:11:58,022 | ^~~~~~~~~~~~~ 2025-05-30T05:11:58,023 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-05-30T05:11:58,023 823 | sprintf(distf, "%s/distance.out", distout_dir); 2025-05-30T05:11:58,024 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,024 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:58,025 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-05-30T05:11:58,025 | ^ 2025-05-30T05:11:58,025 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2025-05-30T05:11:58,026 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-05-30T05:11:58,026 | ^~~~~~~~~~ 2025-05-30T05:11:58,027 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2025-05-30T05:11:58,027 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-05-30T05:11:58,028 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,028 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:58,029 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-05-30T05:11:58,029 | ^ 2025-05-30T05:11:58,030 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2025-05-30T05:11:58,030 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-05-30T05:11:58,031 | ^~~~~~~~~~ 2025-05-30T05:11:58,032 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2025-05-30T05:11:58,033 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-05-30T05:11:58,033 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,296 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2025-05-30T05:11:58,298 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:58,299 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T05:11:58,299 | ^~ ~~~~~~~~~ 2025-05-30T05:11:58,300 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-05-30T05:11:58,301 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-05-30T05:11:58,301 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,302 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T05:11:58,302 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T05:11:58,303 | ^~~~~~~~~~~~~~~ 2025-05-30T05:11:58,303 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-05-30T05:11:58,304 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-05-30T05:11:58,305 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,305 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T05:11:58,306 990 | sprintf(distf, "%s/distance.out", distout_dir); 2025-05-30T05:11:58,306 | ^~~~~~~~~~~~~ 2025-05-30T05:11:58,307 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-05-30T05:11:58,307 990 | sprintf(distf, "%s/distance.out", distout_dir); 2025-05-30T05:11:58,308 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,309 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T05:11:58,310 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T05:11:58,310 | ^~~~~~~~~~~ 2025-05-30T05:11:58,311 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:58,311 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T05:11:58,312 | ^~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,312 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2025-05-30T05:11:58,313 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-05-30T05:11:58,313 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,314 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-05-30T05:11:58,314 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T05:11:58,315 | ^~~~~ 2025-05-30T05:11:58,316 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:58,316 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T05:11:58,317 | ^~~~~~~~~~~ 2025-05-30T05:11:58,317 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-05-30T05:11:58,318 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-05-30T05:11:58,319 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,591 command_dist.c: In function ‘combine_queries’: 2025-05-30T05:11:58,593 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T05:11:58,594 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2025-05-30T05:11:58,594 | ^ 2025-05-30T05:11:58,595 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T05:11:58,596 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2025-05-30T05:11:58,596 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,597 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T05:11:58,598 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2025-05-30T05:11:58,599 | ^ 2025-05-30T05:11:58,600 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T05:11:58,600 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2025-05-30T05:11:58,601 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:58,603 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:58,604 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2025-05-30T05:11:58,604 | ^~ ~~~~~~~~ 2025-05-30T05:11:58,606 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-05-30T05:11:58,606 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2025-05-30T05:11:58,607 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,100 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o -fopenmp 2025-05-30T05:11:59,275 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_set.c -o build/temp.linux-armv7l-cpython-311/command_set.o -fopenmp 2025-05-30T05:11:59,444 command_set.c: In function ‘sketch_operate’: 2025-05-30T05:11:59,444 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-05-30T05:11:59,445 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2025-05-30T05:11:59,446 | ^ 2025-05-30T05:11:59,457 command_set.c: In function ‘combin_subset_pans’: 2025-05-30T05:11:59,458 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2025-05-30T05:11:59,459 457 | free(co_dstat_fpath); 2025-05-30T05:11:59,459 | ^~~~~~~~~~~~~~ 2025-05-30T05:11:59,460 In file included from kssdheaders/global_basic.h:159, 2025-05-30T05:11:59,460 from command_set.c:15: 2025-05-30T05:11:59,461 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2025-05-30T05:11:59,462 568 | extern void free (void *__ptr) __THROW; 2025-05-30T05:11:59,462 | ~~~~~~^~~~~ 2025-05-30T05:11:59,465 command_set.c: In function ‘grouping_genomes’: 2025-05-30T05:11:59,466 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2025-05-30T05:11:59,466 562 | free(co_dstat_fpath); 2025-05-30T05:11:59,467 | ^~~~~~~~~~~~~~ 2025-05-30T05:11:59,467 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2025-05-30T05:11:59,468 568 | extern void free (void *__ptr) __THROW; 2025-05-30T05:11:59,469 | ~~~~~~^~~~~ 2025-05-30T05:11:59,634 command_set.c: In function ‘sketch_union’: 2025-05-30T05:11:59,634 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T05:11:59,635 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:11:59,636 | ^ 2025-05-30T05:11:59,636 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T05:11:59,637 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:11:59,638 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,638 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:59,639 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T05:11:59,639 | ^~ ~~~~~~~~~~~ 2025-05-30T05:11:59,640 command_set.c:82:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:59,641 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T05:11:59,642 | ^~~~~~~~~~ 2025-05-30T05:11:59,642 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T05:11:59,643 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T05:11:59,644 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,644 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:59,645 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-05-30T05:11:59,645 | ^~ ~~~~~~~~~~ 2025-05-30T05:11:59,646 command_set.c:92:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:59,646 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-05-30T05:11:59,647 | ^~~~~~~~~~ 2025-05-30T05:11:59,647 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-05-30T05:11:59,648 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-05-30T05:11:59,648 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,767 command_set.c: In function ‘sketch_operate’: 2025-05-30T05:11:59,768 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:59,768 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-05-30T05:11:59,769 | ^~ ~~~~~~~~~~ 2025-05-30T05:11:59,769 command_set.c:153:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:59,770 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-05-30T05:11:59,770 | ^~~~~~~~~~ 2025-05-30T05:11:59,771 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-05-30T05:11:59,771 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-05-30T05:11:59,772 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,773 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:59,773 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-05-30T05:11:59,774 | ^~ ~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,775 command_set.c:155:29: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:59,776 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-05-30T05:11:59,776 | ^~~~~~~~~~ 2025-05-30T05:11:59,777 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2025-05-30T05:11:59,777 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-05-30T05:11:59,778 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,779 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:59,779 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T05:11:59,780 | ^~ ~~~~~~~~~~~ 2025-05-30T05:11:59,780 command_set.c:165:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:59,781 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T05:11:59,782 | ^~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,783 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T05:11:59,783 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T05:11:59,784 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,784 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:59,785 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T05:11:59,785 | ^~ ~~~~~~~~~~~ 2025-05-30T05:11:59,785 command_set.c:169:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:59,786 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T05:11:59,786 | ^~~~~~~~~~ 2025-05-30T05:11:59,787 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T05:11:59,787 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-05-30T05:11:59,788 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,788 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:59,789 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T05:11:59,789 | ^~ ~~~~~~~~~~~ 2025-05-30T05:11:59,790 command_set.c:174:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:59,790 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T05:11:59,791 | ^~~~~~~~~~ 2025-05-30T05:11:59,792 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T05:11:59,792 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T05:11:59,793 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,793 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:59,794 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T05:11:59,795 | ^~ ~~~~~~~~~~~ 2025-05-30T05:11:59,795 command_set.c:187:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:59,796 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T05:11:59,797 | ^~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,797 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T05:11:59,798 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-05-30T05:11:59,798 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,799 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T05:11:59,800 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:11:59,801 | ^ 2025-05-30T05:11:59,801 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T05:11:59,802 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:11:59,803 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,944 command_set.c: In function ‘uniq_sketch_union’: 2025-05-30T05:11:59,945 command_set.c:219:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T05:11:59,946 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2025-05-30T05:11:59,946 | ^ 2025-05-30T05:11:59,947 command_set.c:219:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2025-05-30T05:11:59,947 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2025-05-30T05:11:59,947 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,948 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T05:11:59,948 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:11:59,949 | ^ 2025-05-30T05:11:59,950 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T05:11:59,950 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:11:59,951 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,951 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:59,952 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T05:11:59,952 | ^~ ~~~~~~~~~~~ 2025-05-30T05:11:59,953 command_set.c:247:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:59,953 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T05:11:59,954 | ^~~~~~~~~~ 2025-05-30T05:11:59,955 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T05:11:59,955 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-05-30T05:11:59,956 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,957 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:11:59,958 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-05-30T05:11:59,958 | ^~ ~~~~~~~~~~~~~~~ 2025-05-30T05:11:59,959 command_set.c:259:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:11:59,960 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-05-30T05:11:59,961 | ^~~~~~~~~~ 2025-05-30T05:11:59,961 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2025-05-30T05:11:59,962 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-05-30T05:11:59,962 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,091 command_set.c: In function ‘combin_pans’: 2025-05-30T05:12:00,092 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:12:00,092 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T05:12:00,093 | ^~ ~~~~~~~~~~~ 2025-05-30T05:12:00,094 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2025-05-30T05:12:00,094 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T05:12:00,095 | ^~~~~~~~~~ 2025-05-30T05:12:00,096 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2025-05-30T05:12:00,096 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T05:12:00,097 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,098 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:12:00,098 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T05:12:00,099 | ^~ ~~~~~~~~~~ 2025-05-30T05:12:00,099 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2025-05-30T05:12:00,100 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T05:12:00,100 | ^~~~~~~~~~ 2025-05-30T05:12:00,101 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2025-05-30T05:12:00,101 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T05:12:00,102 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,103 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T05:12:00,103 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:12:00,104 | ^ 2025-05-30T05:12:00,104 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T05:12:00,105 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:12:00,105 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,310 command_set.c: In function ‘combin_subset_pans’: 2025-05-30T05:12:00,311 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:12:00,311 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T05:12:00,312 | ^~ ~~~~~~~~~~~ 2025-05-30T05:12:00,313 command_set.c:469:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:12:00,313 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T05:12:00,314 | ^~~~~~~~~~ 2025-05-30T05:12:00,314 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T05:12:00,315 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T05:12:00,316 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,316 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:12:00,317 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T05:12:00,317 | ^~ ~~~~~~~~~~ 2025-05-30T05:12:00,318 command_set.c:475:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:12:00,319 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T05:12:00,319 | ^~~~~~~~~~ 2025-05-30T05:12:00,320 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T05:12:00,320 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T05:12:00,321 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,322 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:12:00,322 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T05:12:00,323 | ^~ ~~~~~~~~~~~ 2025-05-30T05:12:00,324 command_set.c:481:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:12:00,325 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T05:12:00,325 | ^~~~~~~~~~ 2025-05-30T05:12:00,326 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T05:12:00,326 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T05:12:00,327 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,327 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:12:00,328 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T05:12:00,328 | ^~ ~~~~~~~~~~ 2025-05-30T05:12:00,329 command_set.c:512:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:12:00,329 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T05:12:00,330 | ^~~~~~~~~~ 2025-05-30T05:12:00,330 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T05:12:00,330 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T05:12:00,331 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,331 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T05:12:00,332 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:12:00,333 | ^ 2025-05-30T05:12:00,333 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T05:12:00,334 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:12:00,335 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,560 command_set.c: In function ‘grouping_genomes’: 2025-05-30T05:12:00,561 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:12:00,561 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T05:12:00,562 | ^~ ~~~~~~~~~~~ 2025-05-30T05:12:00,562 command_set.c:574:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:12:00,563 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T05:12:00,564 | ^~~~~~~~~~ 2025-05-30T05:12:00,564 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T05:12:00,565 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-05-30T05:12:00,565 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,566 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:12:00,567 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T05:12:00,567 | ^~ ~~~~~~~~~~ 2025-05-30T05:12:00,568 command_set.c:580:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:12:00,568 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T05:12:00,569 | ^~~~~~~~~~ 2025-05-30T05:12:00,570 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T05:12:00,570 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-05-30T05:12:00,571 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,572 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:12:00,572 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T05:12:00,572 | ^~ ~~~~~~~~~~~ 2025-05-30T05:12:00,573 command_set.c:612:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:12:00,573 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T05:12:00,574 | ^~~~~~~~~~ 2025-05-30T05:12:00,574 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-05-30T05:12:00,575 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-05-30T05:12:00,575 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,576 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-05-30T05:12:00,576 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T05:12:00,577 | ^~ ~~~~~~~~~~ 2025-05-30T05:12:00,577 command_set.c:634:25: note: directive argument in the range [-2147483644, 2147483646] 2025-05-30T05:12:00,578 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T05:12:00,579 | ^~~~~~~~~~ 2025-05-30T05:12:00,579 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-05-30T05:12:00,580 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-05-30T05:12:00,580 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,581 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-05-30T05:12:00,582 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:12:00,583 | ^ 2025-05-30T05:12:00,583 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-05-30T05:12:00,584 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-05-30T05:12:00,584 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:00,858 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-311/command_shuffle.o -fopenmp 2025-05-30T05:12:01,171 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c global_basic.c -o build/temp.linux-armv7l-cpython-311/global_basic.o -fopenmp 2025-05-30T05:12:01,359 global_basic.c: In function ‘organize_infile_list’: 2025-05-30T05:12:01,360 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2025-05-30T05:12:01,361 195 | while (isspace(*buf)) buf++; 2025-05-30T05:12:01,362 | ^~~~~~~ 2025-05-30T05:12:01,363 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2025-05-30T05:12:01,364 34 | #include 2025-05-30T05:12:01,364 +++ |+#include 2025-05-30T05:12:01,365 35 | 2025-05-30T05:12:01,366 global_basic.c:201:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T05:12:01,367 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2025-05-30T05:12:01,368 | ~~^ 2025-05-30T05:12:01,369 | | 2025-05-30T05:12:01,370 | long unsigned int 2025-05-30T05:12:01,370 | %u 2025-05-30T05:12:01,371 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2025-05-30T05:12:01,372 | ~~~~~~~~~~~ 2025-05-30T05:12:01,372 | | 2025-05-30T05:12:01,373 | size_t {aka unsigned int} 2025-05-30T05:12:01,374 global_basic.c:233:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-05-30T05:12:01,374 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2025-05-30T05:12:01,375 | ~~^ 2025-05-30T05:12:01,376 | | 2025-05-30T05:12:01,377 | long unsigned int 2025-05-30T05:12:01,378 | %u 2025-05-30T05:12:01,379 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2025-05-30T05:12:01,380 | ~~~~~~~~~~~ 2025-05-30T05:12:01,380 | | 2025-05-30T05:12:01,381 | size_t {aka unsigned int} 2025-05-30T05:12:02,131 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-311/iseq2comem.o -fopenmp 2025-05-30T05:12:02,320 iseq2comem.c: In function ‘reads2mco’: 2025-05-30T05:12:02,321 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,322 156 | if (base > TL) { 2025-05-30T05:12:02,322 | ^ 2025-05-30T05:12:02,323 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,324 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T05:12:02,324 | ^~ 2025-05-30T05:12:02,325 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,326 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T05:12:02,326 | ^ 2025-05-30T05:12:02,328 iseq2comem.c: In function ‘fasta2co’: 2025-05-30T05:12:02,328 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,329 239 | if (base > TL) { 2025-05-30T05:12:02,330 | ^ 2025-05-30T05:12:02,331 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,331 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T05:12:02,332 | ^~ 2025-05-30T05:12:02,333 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,333 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T05:12:02,334 | ^ 2025-05-30T05:12:02,334 iseq2comem.c: In function ‘fastq2co’: 2025-05-30T05:12:02,335 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2025-05-30T05:12:02,335 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2025-05-30T05:12:02,336 | ^~ 2025-05-30T05:12:02,337 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,337 318 | if (base > TL) { 2025-05-30T05:12:02,338 | ^ 2025-05-30T05:12:02,338 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,339 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T05:12:02,339 | ^~ 2025-05-30T05:12:02,340 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,341 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T05:12:02,341 | ^ 2025-05-30T05:12:02,343 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,344 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2025-05-30T05:12:02,345 | ^ 2025-05-30T05:12:02,346 iseq2comem.c: In function ‘fastq2koc’: 2025-05-30T05:12:02,347 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,348 402 | if (base > TL) { 2025-05-30T05:12:02,349 | ^ 2025-05-30T05:12:02,349 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,350 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T05:12:02,351 | ^~ 2025-05-30T05:12:02,351 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,352 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T05:12:02,352 | ^ 2025-05-30T05:12:02,359 iseq2comem.c: In function ‘mt_shortreads2koc’: 2025-05-30T05:12:02,360 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,360 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T05:12:02,361 | ^~ 2025-05-30T05:12:02,362 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:02,363 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-05-30T05:12:02,363 | ^ 2025-05-30T05:12:03,712 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2025-05-30T05:12:03,764 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mytime.c -o build/temp.linux-armv7l-cpython-311/mytime.o -fopenmp 2025-05-30T05:12:03,884 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c pykssd.c -o build/temp.linux-armv7l-cpython-311/pykssd.o -fopenmp 2025-05-30T05:12:04,265 pykssd.c: In function ‘py_dist_dispatch’: 2025-05-30T05:12:04,265 pykssd.c:334:13: warning: unused variable ‘state1’ [-Wunused-variable] 2025-05-30T05:12:04,266 334 | int state1 = dist_dispatch(&dist_opt_val1); 2025-05-30T05:12:04,266 | ^~~~~~ 2025-05-30T05:12:04,267 pykssd.c:396:13: warning: unused variable ‘state2’ [-Wunused-variable] 2025-05-30T05:12:04,268 396 | int state2 = dist_dispatch(&dist_opt_val2); 2025-05-30T05:12:04,268 | ^~~~~~ 2025-05-30T05:12:04,269 pykssd.c:530:13: warning: unused variable ‘state4’ [-Wunused-variable] 2025-05-30T05:12:04,270 530 | int state4 = dist_dispatch(&dist_opt_val4); 2025-05-30T05:12:04,270 | ^~~~~~ 2025-05-30T05:12:04,920 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/co2mco.o build/temp.linux-armv7l-cpython-311/command_composite.o build/temp.linux-armv7l-cpython-311/command_dist.o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o build/temp.linux-armv7l-cpython-311/command_set.o build/temp.linux-armv7l-cpython-311/command_shuffle.o build/temp.linux-armv7l-cpython-311/global_basic.o build/temp.linux-armv7l-cpython-311/iseq2comem.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/mytime.o build/temp.linux-armv7l-cpython-311/pykssd.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -fopenmp 2025-05-30T05:12:05,073 building 'nj' extension 2025-05-30T05:12:05,074 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c align.c -o build/temp.linux-armv7l-cpython-311/align.o 2025-05-30T05:12:05,528 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c buildtree.c -o build/temp.linux-armv7l-cpython-311/buildtree.o 2025-05-30T05:12:05,675 buildtree.c: In function ‘UPGMA_buildtree’: 2025-05-30T05:12:05,676 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T05:12:05,677 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2025-05-30T05:12:05,677 | ^~ 2025-05-30T05:12:05,679 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T05:12:05,680 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2025-05-30T05:12:05,680 | ^~ 2025-05-30T05:12:06,335 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c cluster.c -o build/temp.linux-armv7l-cpython-311/cluster.o 2025-05-30T05:12:06,702 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c distancemat.c -o build/temp.linux-armv7l-cpython-311/distancemat.o 2025-05-30T05:12:06,836 distancemat.c: In function ‘clone_DistanceMatrix’: 2025-05-30T05:12:06,837 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T05:12:06,837 226 | for( i=0; i < dest->size; i++) { 2025-05-30T05:12:06,838 | ^ 2025-05-30T05:12:06,838 distancemat.c: In function ‘empty_DistanceMatrix’: 2025-05-30T05:12:06,839 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T05:12:06,840 260 | for( i=0; i < mat->size; i++) { 2025-05-30T05:12:06,840 | ^ 2025-05-30T05:12:06,841 distancemat.c: In function ‘print_DistanceMatrix’: 2025-05-30T05:12:06,841 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T05:12:06,842 349 | for(row=0; row < mat->size; row++) { 2025-05-30T05:12:06,843 | ^ 2025-05-30T05:12:06,844 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2025-05-30T05:12:06,844 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2025-05-30T05:12:06,845 410 | while(c = fgetc(handle)) { 2025-05-30T05:12:06,846 | ^ 2025-05-30T05:12:07,227 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c pynj.c -o build/temp.linux-armv7l-cpython-311/pynj.o 2025-05-30T05:12:07,664 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c sequence.c -o build/temp.linux-armv7l-cpython-311/sequence.o 2025-05-30T05:12:07,877 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c tree.c -o build/temp.linux-armv7l-cpython-311/tree.o 2025-05-30T05:12:08,695 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c util.c -o build/temp.linux-armv7l-cpython-311/util.o 2025-05-30T05:12:08,868 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/align.o build/temp.linux-armv7l-cpython-311/buildtree.o build/temp.linux-armv7l-cpython-311/cluster.o build/temp.linux-armv7l-cpython-311/distancemat.o build/temp.linux-armv7l-cpython-311/pynj.o build/temp.linux-armv7l-cpython-311/sequence.o build/temp.linux-armv7l-cpython-311/tree.o build/temp.linux-armv7l-cpython-311/util.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so 2025-05-30T05:12:08,982 building 'dnj' extension 2025-05-30T05:12:08,983 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c bytescale.c -o build/temp.linux-armv7l-cpython-311/bytescale.o -fopenmp 2025-05-30T05:12:09,037 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c dnj.c -o build/temp.linux-armv7l-cpython-311/dnj.o -fopenmp 2025-05-30T05:12:09,171 dnj.c: In function ‘minQpair’: 2025-05-30T05:12:09,172 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,173 70 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,173 | ^~~ 2025-05-30T05:12:09,174 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,174 126 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,175 | ^~~ 2025-05-30T05:12:09,175 dnj.c: In function ‘maxQpair’: 2025-05-30T05:12:09,176 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,176 157 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,177 | ^~~ 2025-05-30T05:12:09,177 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,178 213 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,179 | ^~~ 2025-05-30T05:12:09,179 dnj.c: In function ‘UPGMApair’: 2025-05-30T05:12:09,180 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,180 237 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,180 | ^~~ 2025-05-30T05:12:09,181 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,182 284 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,182 | ^~~ 2025-05-30T05:12:09,183 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,184 291 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,184 | ^~~ 2025-05-30T05:12:09,185 dnj.c: In function ‘minQrow’: 2025-05-30T05:12:09,185 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,186 374 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,186 | ^~~ 2025-05-30T05:12:09,187 dnj.c: In function ‘maxQrow’: 2025-05-30T05:12:09,188 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,188 435 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,189 | ^~~ 2025-05-30T05:12:09,189 dnj.c: In function ‘UPGMArow’: 2025-05-30T05:12:09,190 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,191 488 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,191 | ^~~ 2025-05-30T05:12:09,192 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,192 494 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,193 | ^~~ 2025-05-30T05:12:09,194 dnj.c: In function ‘minQ_thread’: 2025-05-30T05:12:09,194 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:09,195 553 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:09,195 | ^~~ 2025-05-30T05:12:10,585 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c filebuff.c -o build/temp.linux-armv7l-cpython-311/filebuff.o -fopenmp 2025-05-30T05:12:10,702 filebuff.c: In function ‘BuffgzFileBuff’: 2025-05-30T05:12:10,703 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:10,704 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2025-05-30T05:12:10,704 | ^~ 2025-05-30T05:12:11,028 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c hclust.c -o build/temp.linux-armv7l-cpython-311/hclust.o -fopenmp 2025-05-30T05:12:11,163 hclust.c: In function ‘minQ’: 2025-05-30T05:12:11,164 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T05:12:11,164 364 | while(++i < Q->n) { 2025-05-30T05:12:11,165 | ^ 2025-05-30T05:12:11,165 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:11,166 377 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:11,166 | ^~~ 2025-05-30T05:12:11,167 hclust.c: In function ‘maxQ’: 2025-05-30T05:12:11,167 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-05-30T05:12:11,168 394 | while(++i < Q->n) { 2025-05-30T05:12:11,168 | ^ 2025-05-30T05:12:11,169 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:11,169 407 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:11,170 | ^~~ 2025-05-30T05:12:13,546 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c matrix.c -o build/temp.linux-armv7l-cpython-311/matrix.o -fopenmp 2025-05-30T05:12:13,677 matrix.c: In function ‘ltdMatrix_popArrange’: 2025-05-30T05:12:13,678 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-05-30T05:12:13,679 538 | if(pos != n) { 2025-05-30T05:12:13,679 | ^~ 2025-05-30T05:12:14,561 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2025-05-30T05:12:14,614 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nj.c -o build/temp.linux-armv7l-cpython-311/nj.o -fopenmp 2025-05-30T05:12:14,742 nj.c: In function ‘initQ’: 2025-05-30T05:12:14,743 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:14,743 243 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:14,744 | ^~~ 2025-05-30T05:12:14,745 nj.c: In function ‘initQ_MN’: 2025-05-30T05:12:14,745 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:14,746 358 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:14,747 | ^~~ 2025-05-30T05:12:14,750 nj.c: In function ‘minD’: 2025-05-30T05:12:14,751 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:14,751 559 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:14,752 | ^~~ 2025-05-30T05:12:14,752 nj.c: In function ‘maxD’: 2025-05-30T05:12:14,753 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:14,754 642 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:14,755 | ^~~ 2025-05-30T05:12:14,757 nj.c: In function ‘minPair’: 2025-05-30T05:12:14,758 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-05-30T05:12:14,759 826 | pos <<= sizeof(unsigned) * 8; 2025-05-30T05:12:14,760 | ^~~ 2025-05-30T05:12:17,150 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nwck.c -o build/temp.linux-armv7l-cpython-311/nwck.o -fopenmp 2025-05-30T05:12:17,687 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pherror.c -o build/temp.linux-armv7l-cpython-311/pherror.o -fopenmp 2025-05-30T05:12:17,783 pherror.c: In function ‘cfread’: 2025-05-30T05:12:17,784 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-05-30T05:12:17,784 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2025-05-30T05:12:17,785 | ^~ 2025-05-30T05:12:17,877 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c phy.c -o build/temp.linux-armv7l-cpython-311/phy.o -fopenmp 2025-05-30T05:12:18,938 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pydnj.c -o build/temp.linux-armv7l-cpython-311/pydnj.o -fopenmp 2025-05-30T05:12:19,305 In file included from pydnj.c:11: 2025-05-30T05:12:19,306 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2025-05-30T05:12:19,306 20 | #define _XOPEN_SOURCE 600 2025-05-30T05:12:19,307 | 2025-05-30T05:12:19,307 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2025-05-30T05:12:19,308 from /usr/include/stdlib.h:26, 2025-05-30T05:12:19,309 from /usr/include/python3.11/Python.h:23, 2025-05-30T05:12:19,309 from pydnj.c:1: 2025-05-30T05:12:19,310 /usr/include/features.h:214: note: this is the location of the previous definition 2025-05-30T05:12:19,310 214 | # define _XOPEN_SOURCE 700 2025-05-30T05:12:19,311 | 2025-05-30T05:12:19,329 pydnj.c: In function ‘py_build’: 2025-05-30T05:12:19,330 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2025-05-30T05:12:19,331 165 | p = omp_get_num_procs(); 2025-05-30T05:12:19,333 | ^~~~~~~~~~~~~~~~~ 2025-05-30T05:12:19,450 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2025-05-30T05:12:19,451 169 | free(file); 2025-05-30T05:12:19,451 | ^~~~~~~~~~ 2025-05-30T05:12:19,452 pydnj.c:125:12: note: returned from ‘fopen’ 2025-05-30T05:12:19,452 125 | file = fopen(inputfilename, "r"); 2025-05-30T05:12:19,453 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-05-30T05:12:19,524 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c qseqs.c -o build/temp.linux-armv7l-cpython-311/qseqs.o -fopenmp 2025-05-30T05:12:19,729 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c str.c -o build/temp.linux-armv7l-cpython-311/str.o -fopenmp 2025-05-30T05:12:19,839 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c tmp.c -o build/temp.linux-armv7l-cpython-311/tmp.o -fopenmp 2025-05-30T05:12:20,036 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c vector.c -o build/temp.linux-armv7l-cpython-311/vector.o -fopenmp 2025-05-30T05:12:20,239 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/bytescale.o build/temp.linux-armv7l-cpython-311/dnj.o build/temp.linux-armv7l-cpython-311/filebuff.o build/temp.linux-armv7l-cpython-311/hclust.o build/temp.linux-armv7l-cpython-311/matrix.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/nj.o build/temp.linux-armv7l-cpython-311/nwck.o build/temp.linux-armv7l-cpython-311/pherror.o build/temp.linux-armv7l-cpython-311/phy.o build/temp.linux-armv7l-cpython-311/pydnj.o build/temp.linux-armv7l-cpython-311/qseqs.o build/temp.linux-armv7l-cpython-311/str.o build/temp.linux-armv7l-cpython-311/tmp.o build/temp.linux-armv7l-cpython-311/vector.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -fopenmp 2025-05-30T05:12:20,428 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-05-30T05:12:20,429 !! 2025-05-30T05:12:20,430 ******************************************************************************** 2025-05-30T05:12:20,430 Please avoid running ``setup.py`` directly. 2025-05-30T05:12:20,431 Instead, use pypa/build, pypa/installer or other 2025-05-30T05:12:20,431 standards-based tools. 2025-05-30T05:12:20,433 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-05-30T05:12:20,433 or your builds will no longer be supported. 2025-05-30T05:12:20,434 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-05-30T05:12:20,435 ******************************************************************************** 2025-05-30T05:12:20,436 !! 2025-05-30T05:12:20,437 self.initialize_options() 2025-05-30T05:12:20,460 installing to build/bdist.linux-armv7l/wheel 2025-05-30T05:12:20,461 running install 2025-05-30T05:12:20,486 running install_lib 2025-05-30T05:12:20,513 creating build/bdist.linux-armv7l/wheel 2025-05-30T05:12:20,515 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-05-30T05:12:20,522 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel/. 2025-05-30T05:12:20,525 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-05-30T05:12:20,529 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-05-30T05:12:20,537 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel/. 2025-05-30T05:12:20,540 running install_egg_info 2025-05-30T05:12:20,572 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/./kssdtree-2.0.6-py3.11.egg-info 2025-05-30T05:12:20,584 running install_scripts 2025-05-30T05:12:20,632 creating build/bdist.linux-armv7l/wheel/kssdtree-2.0.6.dist-info/WHEEL 2025-05-30T05:12:20,635 creating '/tmp/pip-wheel-oiwrakqj/kssdtree-2.0.6-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-05-30T05:12:20,700 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2025-05-30T05:12:20,783 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2025-05-30T05:12:20,788 adding 'kssdtree.py' 2025-05-30T05:12:20,808 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2025-05-30T05:12:20,811 adding 'toolutils.py' 2025-05-30T05:12:20,813 adding 'kssdtree-2.0.6.dist-info/METADATA' 2025-05-30T05:12:20,814 adding 'kssdtree-2.0.6.dist-info/WHEEL' 2025-05-30T05:12:20,815 adding 'kssdtree-2.0.6.dist-info/dependency_links.txt' 2025-05-30T05:12:20,816 adding 'kssdtree-2.0.6.dist-info/top_level.txt' 2025-05-30T05:12:20,817 adding 'kssdtree-2.0.6.dist-info/RECORD' 2025-05-30T05:12:20,822 removing build/bdist.linux-armv7l/wheel 2025-05-30T05:12:20,962 Building wheel for kssdtree (setup.py): finished with status 'done' 2025-05-30T05:12:20,968 Created wheel for kssdtree: filename=kssdtree-2.0.6-cp311-cp311-linux_armv7l.whl size=381936 sha256=e1e02281e0fc8ed3b80b596a811ca2a9b50cb7affb3649479228d59c074c1f94 2025-05-30T05:12:20,969 Stored in directory: /tmp/pip-ephem-wheel-cache-3rjvbsgq/wheels/e4/e2/d1/ce47e4b0364eb50a3f500b52a8f4d85481e4672fe35242c9fe 2025-05-30T05:12:20,984 Successfully built kssdtree 2025-05-30T05:12:21,012 Removed build tracker: '/tmp/pip-build-tracker-b6u9j2hy'