2026-03-05T13:52:27,453 Created temporary directory: /tmp/pip-ephem-wheel-cache-moy_ph6w 2026-03-05T13:52:27,455 Created temporary directory: /tmp/pip-build-tracker-2a_sr__3 2026-03-05T13:52:27,456 Initialized build tracking at /tmp/pip-build-tracker-2a_sr__3 2026-03-05T13:52:27,456 Created build tracker: /tmp/pip-build-tracker-2a_sr__3 2026-03-05T13:52:27,457 Entered build tracker: /tmp/pip-build-tracker-2a_sr__3 2026-03-05T13:52:27,458 Created temporary directory: /tmp/pip-wheel-ge8oau1a 2026-03-05T13:52:27,460 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-03-05T13:52:27,463 Created temporary directory: /tmp/pip-ephem-wheel-cache-anzk74zv 2026-03-05T13:52:27,486 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-03-05T13:52:27,490 2 location(s) to search for versions of kssdutils: 2026-03-05T13:52:27,490 * https://pypi.org/simple/kssdutils/ 2026-03-05T13:52:27,490 * https://www.piwheels.org/simple/kssdutils/ 2026-03-05T13:52:27,490 Fetching project page and analyzing links: https://pypi.org/simple/kssdutils/ 2026-03-05T13:52:27,491 Getting page https://pypi.org/simple/kssdutils/ 2026-03-05T13:52:27,493 Found index url https://pypi.org/simple 2026-03-05T13:52:27,706 Fetched page https://pypi.org/simple/kssdutils/ as application/vnd.pypi.simple.v1+json 2026-03-05T13:52:27,710 Found link https://files.pythonhosted.org/packages/61/ef/1bdb91b53dbe31ea0be28ab2c2292994b6228b357a8d54b69ac642f81f01/kssdutils-1.0.0.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.0.0 2026-03-05T13:52:27,711 Found link https://files.pythonhosted.org/packages/6f/f6/cc67acf92ea770b5f6a8bd97d375432881861935beafe9ebd4031a73482c/kssdutils-1.0.1.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.0.1 2026-03-05T13:52:27,712 Found link https://files.pythonhosted.org/packages/57/17/dd41697db7220423d0ab77f9f035b9a347edc1edefc2c35d9890178cbe17/kssdutils-1.0.2.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.0.2 2026-03-05T13:52:27,712 Found link https://files.pythonhosted.org/packages/3e/92/7a94130bd54e0e3dd20c1a609aef2f24875b86e9d61752f63b500d3f86f5/kssdutils-1.0.3.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.0.3 2026-03-05T13:52:27,713 Found link https://files.pythonhosted.org/packages/42/01/15ec102f7ac6b4fc3158ba60de64598a005cefffc773fa69eecbd3c9b016/kssdutils-1.0.5.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.0.5 2026-03-05T13:52:27,714 Found link https://files.pythonhosted.org/packages/aa/08/08fa5f76478fd3dbe9534ad21332b5dc03826197935c2b696e189af49f0b/kssdutils-1.0.6.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.0.6 2026-03-05T13:52:27,715 Found link https://files.pythonhosted.org/packages/78/17/7776b7c3b149fedfb0fba98bce07fdf08cb53773dafa174f7fda9ce4df55/kssdutils-1.0.7.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.0.7 2026-03-05T13:52:27,715 Found link https://files.pythonhosted.org/packages/a7/50/138f2b5f98dcd2327609362e505af19857468da67dba88eaf6c8d8fdb83a/kssdutils-1.1.0.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.1.0 2026-03-05T13:52:27,716 Found link https://files.pythonhosted.org/packages/be/be/659d775f3dd37e727d782fa46b7b665e69a59c78312fa5fc1bad8640f980/kssdutils-1.1.2.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.1.2 2026-03-05T13:52:27,717 Found link https://files.pythonhosted.org/packages/d0/e9/badb25888a9e48aa82e2389e848aff81ae6affd17af96622974dc314ae52/kssdutils-1.1.3.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.1.3 2026-03-05T13:52:27,717 Found link https://files.pythonhosted.org/packages/b3/43/18e812a7529c356cfa20627f201f1956e4b8203e1db782861ad6e5900bf8/kssdutils-1.1.4.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.1.4 2026-03-05T13:52:27,718 Found link https://files.pythonhosted.org/packages/98/8c/0eb4850f10a9da51072d7be474ecffd0f808423f21838f543dc88db7ddd2/kssdutils-1.1.5.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.1.5 2026-03-05T13:52:27,719 Found link https://files.pythonhosted.org/packages/c3/44/c52bfc36ee73ebbc978099403a176e76446f23b1691c9df71bd38bbe6430/kssdutils-1.1.7.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.1.7 2026-03-05T13:52:27,720 Found link https://files.pythonhosted.org/packages/a8/d7/8426d81d46965dcb35320a45f5b457453be5160b18551902b31860952f69/kssdutils-1.1.8.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.1.8 2026-03-05T13:52:27,720 Found link https://files.pythonhosted.org/packages/4e/b4/5e5af5267d953d53d92b1f74c11fac8874cc94a7e1f5a0e699ba3ecc57f2/kssdutils-1.1.9.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.1.9 2026-03-05T13:52:27,721 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdutils/ 2026-03-05T13:52:27,721 Getting page https://www.piwheels.org/simple/kssdutils/ 2026-03-05T13:52:27,722 Found index url https://www.piwheels.org/simple 2026-03-05T13:52:27,882 Fetched page https://www.piwheels.org/simple/kssdutils/ as text/html 2026-03-05T13:52:27,896 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.1.8-cp311-cp311-linux_armv6l.whl#sha256=1ca8d1a14ea2253a85ab097f8a97a065c394460f12019e954e44a8de87f5392c (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,896 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.1.8-cp311-cp311-linux_armv7l.whl#sha256=1ca8d1a14ea2253a85ab097f8a97a065c394460f12019e954e44a8de87f5392c (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,897 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.7-cp311-cp311-linux_armv6l.whl#sha256=5beb32a7772765a880c50ab75f1b8a504d6c960523a444ea7829d7fef3671c4c (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,897 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.7-cp311-cp311-linux_armv7l.whl#sha256=5beb32a7772765a880c50ab75f1b8a504d6c960523a444ea7829d7fef3671c4c (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,898 Skipping link: No binaries permitted for kssdutils: 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https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.5-cp39-cp39-linux_armv7l.whl#sha256=fb21de5c7d85619ac9cc1fafe3280f0130178032b169f1cf7ceac0cb6326d42e (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,917 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp311-cp311-linux_armv6l.whl#sha256=85c10f6c3223fb99e39dfddbef722fd2913bd5c63f089283ce23dae20c6a4a4d (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,918 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp311-cp311-linux_armv7l.whl#sha256=85c10f6c3223fb99e39dfddbef722fd2913bd5c63f089283ce23dae20c6a4a4d (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,919 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp39-cp39-linux_armv6l.whl#sha256=809195defd92c452797e9a87d99cfa8217c9ca4800c4a57d3e669846368160b1 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,919 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp39-cp39-linux_armv7l.whl#sha256=809195defd92c452797e9a87d99cfa8217c9ca4800c4a57d3e669846368160b1 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,919 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp311-cp311-linux_armv6l.whl#sha256=88788d94e7e118cfdf4e2cb04c558d2032ffa4f9352b663efd1a76f098c9f31d (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,920 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp311-cp311-linux_armv7l.whl#sha256=88788d94e7e118cfdf4e2cb04c558d2032ffa4f9352b663efd1a76f098c9f31d (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,920 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp39-cp39-linux_armv6l.whl#sha256=29a695a62aae6fa18fcad3ae6bfc6bbe19f545f66740fde177ddbf23efa45d15 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,921 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp39-cp39-linux_armv7l.whl#sha256=29a695a62aae6fa18fcad3ae6bfc6bbe19f545f66740fde177ddbf23efa45d15 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,922 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp311-cp311-linux_armv6l.whl#sha256=e93f43f34a8ab412f6a0c97bc930a5c9c72997258d109e3f069a56b6270ff331 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,922 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp311-cp311-linux_armv7l.whl#sha256=e93f43f34a8ab412f6a0c97bc930a5c9c72997258d109e3f069a56b6270ff331 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,923 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp39-cp39-linux_armv6l.whl#sha256=0d9c0566cba326dbedbea1c1ea643cc81efe1b0b47b292f956e933d1a9fedb35 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,923 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp39-cp39-linux_armv7l.whl#sha256=0d9c0566cba326dbedbea1c1ea643cc81efe1b0b47b292f956e933d1a9fedb35 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T13:52:27,924 Skipping link: not a file: https://www.piwheels.org/simple/kssdutils/ 2026-03-05T13:52:27,924 Skipping link: not a file: https://pypi.org/simple/kssdutils/ 2026-03-05T13:52:27,945 Given no hashes to check 1 links for project 'kssdutils': discarding no candidates 2026-03-05T13:52:27,962 Collecting kssdutils==1.1.9 2026-03-05T13:52:27,965 Created temporary directory: /tmp/pip-unpack-sitehgcc 2026-03-05T13:52:28,189 Downloading kssdutils-1.1.9.tar.gz (44 kB) 2026-03-05T13:52:28,309 Added kssdutils==1.1.9 from https://files.pythonhosted.org/packages/4e/b4/5e5af5267d953d53d92b1f74c11fac8874cc94a7e1f5a0e699ba3ecc57f2/kssdutils-1.1.9.tar.gz to build tracker '/tmp/pip-build-tracker-2a_sr__3' 2026-03-05T13:52:28,311 Running setup.py (path:/tmp/pip-wheel-ge8oau1a/kssdutils_2fbae817142b402eb3496e5548b53829/setup.py) egg_info for package kssdutils 2026-03-05T13:52:28,312 Created temporary directory: /tmp/pip-pip-egg-info-qe1mq8tq 2026-03-05T13:52:28,313 Preparing metadata (setup.py): started 2026-03-05T13:52:28,314 Running command python setup.py egg_info 2026-03-05T13:52:29,239 running egg_info 2026-03-05T13:52:29,266 creating /tmp/pip-pip-egg-info-qe1mq8tq/kssdutils.egg-info 2026-03-05T13:52:29,267 writing /tmp/pip-pip-egg-info-qe1mq8tq/kssdutils.egg-info/PKG-INFO 2026-03-05T13:52:29,270 writing dependency_links to /tmp/pip-pip-egg-info-qe1mq8tq/kssdutils.egg-info/dependency_links.txt 2026-03-05T13:52:29,272 writing top-level names to /tmp/pip-pip-egg-info-qe1mq8tq/kssdutils.egg-info/top_level.txt 2026-03-05T13:52:29,274 writing manifest file '/tmp/pip-pip-egg-info-qe1mq8tq/kssdutils.egg-info/SOURCES.txt' 2026-03-05T13:52:29,361 reading manifest file '/tmp/pip-pip-egg-info-qe1mq8tq/kssdutils.egg-info/SOURCES.txt' 2026-03-05T13:52:29,363 reading manifest template 'MANIFEST.in' 2026-03-05T13:52:29,371 writing manifest file '/tmp/pip-pip-egg-info-qe1mq8tq/kssdutils.egg-info/SOURCES.txt' 2026-03-05T13:52:29,479 Preparing metadata (setup.py): finished with status 'done' 2026-03-05T13:52:29,482 Source in /tmp/pip-wheel-ge8oau1a/kssdutils_2fbae817142b402eb3496e5548b53829 has version 1.1.9, which satisfies requirement kssdutils==1.1.9 from https://files.pythonhosted.org/packages/4e/b4/5e5af5267d953d53d92b1f74c11fac8874cc94a7e1f5a0e699ba3ecc57f2/kssdutils-1.1.9.tar.gz 2026-03-05T13:52:29,483 Removed kssdutils==1.1.9 from https://files.pythonhosted.org/packages/4e/b4/5e5af5267d953d53d92b1f74c11fac8874cc94a7e1f5a0e699ba3ecc57f2/kssdutils-1.1.9.tar.gz from build tracker '/tmp/pip-build-tracker-2a_sr__3' 2026-03-05T13:52:29,487 Created temporary directory: /tmp/pip-unpack-12nwwshl 2026-03-05T13:52:29,488 Building wheels for collected packages: kssdutils 2026-03-05T13:52:29,493 Created temporary directory: /tmp/pip-wheel-z4w0apcq 2026-03-05T13:52:29,493 Building wheel for kssdutils (setup.py): started 2026-03-05T13:52:29,495 Destination directory: /tmp/pip-wheel-z4w0apcq 2026-03-05T13:52:29,495 Running command python setup.py bdist_wheel 2026-03-05T13:52:30,323 running bdist_wheel 2026-03-05T13:52:30,431 running build 2026-03-05T13:52:30,432 running build_py 2026-03-05T13:52:30,463 creating build/lib.linux-armv7l-cpython-311 2026-03-05T13:52:30,465 copying kssdutils.py -> build/lib.linux-armv7l-cpython-311 2026-03-05T13:52:30,467 running egg_info 2026-03-05T13:52:30,494 writing kssdutils.egg-info/PKG-INFO 2026-03-05T13:52:30,497 writing dependency_links to kssdutils.egg-info/dependency_links.txt 2026-03-05T13:52:30,499 writing top-level names to kssdutils.egg-info/top_level.txt 2026-03-05T13:52:30,528 reading manifest file 'kssdutils.egg-info/SOURCES.txt' 2026-03-05T13:52:30,531 reading manifest template 'MANIFEST.in' 2026-03-05T13:52:30,539 writing manifest file 'kssdutils.egg-info/SOURCES.txt' 2026-03-05T13:52:30,540 running build_ext 2026-03-05T13:52:31,077 building 'kssdtool' extension 2026-03-05T13:52:31,079 creating build/temp.linux-armv7l-cpython-311 2026-03-05T13:52:31,080 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 2026-03-05T13:52:31,256 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2026-03-05T13:52:31,257 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-03-05T13:52:31,257 109 | for (unsigned int i = 0; i < comp_num; i++) { 2026-03-05T13:52:31,258 | ^ 2026-03-05T13:52:31,261 co2mco.c: In function ‘co2unitllmco’: 2026-03-05T13:52:31,262 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-03-05T13:52:31,263 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2026-03-05T13:52:31,263 | ^ 2026-03-05T13:52:31,966 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 2026-03-05T13:52:32,341 command_composite.c: In function ‘get_species_abundance’: 2026-03-05T13:52:32,341 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2026-03-05T13:52:32,342 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2026-03-05T13:52:32,342 | ^~ 2026-03-05T13:52:32,343 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2026-03-05T13:52:32,344 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2026-03-05T13:52:32,344 | ^~ 2026-03-05T13:52:32,344 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:32,345 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-03-05T13:52:32,346 | ^ 2026-03-05T13:52:32,346 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:32,347 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-03-05T13:52:32,347 | ^~~~~~~~~~ 2026-03-05T13:52:32,348 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-05T13:52:32,349 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-03-05T13:52:32,349 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:32,350 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:32,351 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-03-05T13:52:32,351 | ^ 2026-03-05T13:52:32,352 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:32,352 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-03-05T13:52:32,353 | ^~~~~~~~~~ 2026-03-05T13:52:32,354 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-05T13:52:32,354 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-03-05T13:52:32,355 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:32,355 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:32,356 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-03-05T13:52:32,357 | ^ 2026-03-05T13:52:32,357 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:32,358 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-03-05T13:52:32,359 | ^~~~~~~~~~ 2026-03-05T13:52:32,359 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-05T13:52:32,360 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-03-05T13:52:32,360 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:32,361 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:32,361 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-03-05T13:52:32,362 | ^ 2026-03-05T13:52:32,362 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:32,363 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-03-05T13:52:32,363 | ^~~~~~~~~~ 2026-03-05T13:52:32,364 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-05T13:52:32,364 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-03-05T13:52:32,365 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:32,365 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:32,366 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-03-05T13:52:32,366 | ^ 2026-03-05T13:52:32,367 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:32,367 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-03-05T13:52:32,368 | ^~~~~~~~~~~~ 2026-03-05T13:52:32,368 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2026-03-05T13:52:32,369 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-03-05T13:52:32,370 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:32,616 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 2026-03-05T13:52:32,850 command_dist.c: In function ‘mco_cbd_co_dist’: 2026-03-05T13:52:32,852 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=] 2026-03-05T13:52:32,852 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T13:52:32,853 | ~~^ 2026-03-05T13:52:32,853 | | 2026-03-05T13:52:32,854 | long unsigned int 2026-03-05T13:52:32,854 | %u 2026-03-05T13:52:32,855 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T13:52:32,855 | ~~~~~~~ 2026-03-05T13:52:32,856 | | 2026-03-05T13:52:32,857 | size_t {aka unsigned int} 2026-03-05T13:52:32,857 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=] 2026-03-05T13:52:32,858 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T13:52:32,859 | ~~^ 2026-03-05T13:52:32,859 | | 2026-03-05T13:52:32,859 | long unsigned int 2026-03-05T13:52:32,860 | %u 2026-03-05T13:52:32,860 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T13:52:32,861 679 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-05T13:52:32,861 | ~~~~~~~~~ 2026-03-05T13:52:32,861 | | 2026-03-05T13:52:32,862 | size_t {aka unsigned int} 2026-03-05T13:52:32,862 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-03-05T13:52:32,863 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T13:52:32,863 | ~~^ 2026-03-05T13:52:32,864 | | 2026-03-05T13:52:32,864 | long unsigned int 2026-03-05T13:52:32,865 | %u 2026-03-05T13:52:32,866 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T13:52:32,866 679 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-05T13:52:32,867 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:32,868 | | 2026-03-05T13:52:32,869 | unsigned int 2026-03-05T13:52:32,870 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-03-05T13:52:32,871 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2026-03-05T13:52:32,872 | ^ 2026-03-05T13:52:32,879 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2026-03-05T13:52:32,882 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=] 2026-03-05T13:52:32,882 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-03-05T13:52:32,883 | ~~^ ~~~~~~~ 2026-03-05T13:52:32,883 | | | 2026-03-05T13:52:32,884 | long unsigned int size_t {aka unsigned int} 2026-03-05T13:52:32,884 | %u 2026-03-05T13:52:32,886 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=] 2026-03-05T13:52:32,886 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-03-05T13:52:32,887 | ~~^ 2026-03-05T13:52:32,888 | | 2026-03-05T13:52:32,888 | long unsigned int 2026-03-05T13:52:32,888 | %u 2026-03-05T13:52:32,889 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2026-03-05T13:52:32,889 | ~~~~~~~~~ 2026-03-05T13:52:32,890 | | 2026-03-05T13:52:32,890 | size_t {aka unsigned int} 2026-03-05T13:52:32,891 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-03-05T13:52:32,891 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-03-05T13:52:32,892 | ~~^ 2026-03-05T13:52:32,892 | | 2026-03-05T13:52:32,893 | long unsigned int 2026-03-05T13:52:32,893 | %u 2026-03-05T13:52:32,894 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2026-03-05T13:52:32,894 865 | (size_t) b * unitsz_distf_mapped); 2026-03-05T13:52:32,895 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:32,895 | | 2026-03-05T13:52:32,896 | unsigned int 2026-03-05T13:52:32,897 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2026-03-05T13:52:32,897 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2026-03-05T13:52:32,898 | ^~~~~~~ 2026-03-05T13:52:32,898 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2026-03-05T13:52:32,899 809 | struct stat cbd_fcode_stat; 2026-03-05T13:52:32,900 | ^~~~~~~~~~~~~~ 2026-03-05T13:52:32,901 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2026-03-05T13:52:32,901 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2026-03-05T13:52:32,902 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:32,902 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2026-03-05T13:52:32,903 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2026-03-05T13:52:32,903 | ^~~~~~~~~~~~~~~~~ 2026-03-05T13:52:32,904 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2026-03-05T13:52:32,904 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=] 2026-03-05T13:52:32,905 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T13:52:32,905 | ~~^ 2026-03-05T13:52:32,906 | | 2026-03-05T13:52:32,906 | long unsigned int 2026-03-05T13:52:32,907 | %u 2026-03-05T13:52:32,908 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T13:52:32,908 | ~~~~~~~ 2026-03-05T13:52:32,908 | | 2026-03-05T13:52:32,909 | size_t {aka unsigned int} 2026-03-05T13:52:32,909 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=] 2026-03-05T13:52:32,910 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T13:52:32,910 | ~~^ 2026-03-05T13:52:32,911 | | 2026-03-05T13:52:32,911 | long unsigned int 2026-03-05T13:52:32,912 | %u 2026-03-05T13:52:32,912 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T13:52:32,913 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-05T13:52:32,913 | ~~~~~~~~~ 2026-03-05T13:52:32,914 | | 2026-03-05T13:52:32,915 | size_t {aka unsigned int} 2026-03-05T13:52:32,915 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-03-05T13:52:32,916 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T13:52:32,916 | ~~^ 2026-03-05T13:52:32,917 | | 2026-03-05T13:52:32,918 | long unsigned int 2026-03-05T13:52:32,918 | %u 2026-03-05T13:52:32,919 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T13:52:32,919 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-05T13:52:32,920 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:32,921 | | 2026-03-05T13:52:32,921 | unsigned int 2026-03-05T13:52:32,922 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2026-03-05T13:52:32,923 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2026-03-05T13:52:32,923 | ^ 2026-03-05T13:52:32,924 command_dist.c: In function ‘mco_co_dist_core’: 2026-03-05T13:52:32,925 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-03-05T13:52:32,925 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2026-03-05T13:52:32,926 | ^ 2026-03-05T13:52:32,927 command_dist.c: In function ‘koc_dist_print_nobin’: 2026-03-05T13:52:32,928 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-05T13:52:32,928 1239 | for (int rid = 0; rid < ref_num; rid++) 2026-03-05T13:52:32,929 | ^ 2026-03-05T13:52:32,930 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-05T13:52:32,930 1245 | for (int rid = 0; rid < ref_num; rid++) { 2026-03-05T13:52:32,931 | ^ 2026-03-05T13:52:32,936 command_dist.c: In function ‘dist_print_nobin’: 2026-03-05T13:52:32,938 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-05T13:52:32,938 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2026-03-05T13:52:32,939 | ^ 2026-03-05T13:52:32,941 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-05T13:52:32,941 1356 | for (int rid = 0; rid < ref_num; rid++) { 2026-03-05T13:52:32,942 | ^ 2026-03-05T13:52:32,943 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-05T13:52:32,944 1382 | for (int rid = 0; rid < ref_num; rid++) 2026-03-05T13:52:32,944 | ^ 2026-03-05T13:52:33,303 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2026-03-05T13:52:33,304 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2026-03-05T13:52:33,305 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2026-03-05T13:52:33,305 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:33,306 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2026-03-05T13:52:33,307 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2026-03-05T13:52:33,307 | ^~~~~~~~~~~~ 2026-03-05T13:52:34,138 command_dist.c: In function ‘get_dim_shuffle’: 2026-03-05T13:52:34,139 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2026-03-05T13:52:34,140 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2026-03-05T13:52:34,140 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:34,141 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2026-03-05T13:52:34,142 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2026-03-05T13:52:34,142 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,039 command_dist.c: In function ‘mco_cbd_co_dist’: 2026-03-05T13:52:35,040 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:35,041 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T13:52:35,041 | ^~ ~~~~~~~~~ 2026-03-05T13:52:35,042 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-03-05T13:52:35,042 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T13:52:35,043 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,044 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T13:52:35,044 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T13:52:35,045 | ^~~~~~~~~~~~~~~ 2026-03-05T13:52:35,046 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-03-05T13:52:35,046 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T13:52:35,047 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,047 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T13:52:35,047 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T13:52:35,048 | ^~~~~~~~~~~ 2026-03-05T13:52:35,048 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:35,049 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T13:52:35,050 | ^~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,050 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2026-03-05T13:52:35,051 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T13:52:35,051 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,052 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T13:52:35,052 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T13:52:35,053 | ^~~~~ 2026-03-05T13:52:35,054 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:35,055 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T13:52:35,055 | ^~~~~~~~~~~ 2026-03-05T13:52:35,056 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-05T13:52:35,057 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T13:52:35,057 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,290 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2026-03-05T13:52:35,291 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:35,292 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T13:52:35,292 | ^~ ~~~~~~~~~ 2026-03-05T13:52:35,293 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-03-05T13:52:35,294 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T13:52:35,294 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,295 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T13:52:35,295 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T13:52:35,296 | ^~~~~~~~~~~~~~~ 2026-03-05T13:52:35,296 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-03-05T13:52:35,297 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T13:52:35,298 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,298 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T13:52:35,299 823 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-05T13:52:35,299 | ^~~~~~~~~~~~~ 2026-03-05T13:52:35,300 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-03-05T13:52:35,301 823 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-05T13:52:35,301 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,302 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:35,302 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-03-05T13:52:35,303 | ^ 2026-03-05T13:52:35,304 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2026-03-05T13:52:35,304 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-03-05T13:52:35,305 | ^~~~~~~~~~ 2026-03-05T13:52:35,305 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2026-03-05T13:52:35,306 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-03-05T13:52:35,306 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,307 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:35,307 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-03-05T13:52:35,308 | ^ 2026-03-05T13:52:35,308 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2026-03-05T13:52:35,309 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-03-05T13:52:35,310 | ^~~~~~~~~~ 2026-03-05T13:52:35,310 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2026-03-05T13:52:35,311 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-03-05T13:52:35,312 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,570 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2026-03-05T13:52:35,572 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:35,572 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T13:52:35,573 | ^~ ~~~~~~~~~ 2026-03-05T13:52:35,574 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-03-05T13:52:35,574 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T13:52:35,575 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,576 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T13:52:35,576 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T13:52:35,577 | ^~~~~~~~~~~~~~~ 2026-03-05T13:52:35,577 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-03-05T13:52:35,578 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T13:52:35,578 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,579 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T13:52:35,580 990 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-05T13:52:35,580 | ^~~~~~~~~~~~~ 2026-03-05T13:52:35,581 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-03-05T13:52:35,582 990 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-05T13:52:35,583 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,583 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T13:52:35,583 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T13:52:35,584 | ^~~~~~~~~~~ 2026-03-05T13:52:35,584 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:35,585 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T13:52:35,585 | ^~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,585 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2026-03-05T13:52:35,586 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T13:52:35,587 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,587 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T13:52:35,588 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T13:52:35,588 | ^~~~~ 2026-03-05T13:52:35,589 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:35,589 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T13:52:35,590 | ^~~~~~~~~~~ 2026-03-05T13:52:35,591 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-05T13:52:35,592 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T13:52:35,592 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,862 command_dist.c: In function ‘combine_queries’: 2026-03-05T13:52:35,864 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T13:52:35,865 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2026-03-05T13:52:35,865 | ^ 2026-03-05T13:52:35,866 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T13:52:35,866 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2026-03-05T13:52:35,867 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,867 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T13:52:35,868 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2026-03-05T13:52:35,868 | ^ 2026-03-05T13:52:35,869 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T13:52:35,870 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2026-03-05T13:52:35,870 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:35,872 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:35,872 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2026-03-05T13:52:35,873 | ^~ ~~~~~~~~ 2026-03-05T13:52:35,874 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-03-05T13:52:35,874 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2026-03-05T13:52:35,875 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:36,356 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 2026-03-05T13:52:36,528 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_set.c -o build/temp.linux-armv7l-cpython-311/command_set.o -fopenmp 2026-03-05T13:52:36,695 command_set.c: In function ‘sketch_operate’: 2026-03-05T13:52:36,695 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-03-05T13:52:36,696 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2026-03-05T13:52:36,696 | ^ 2026-03-05T13:52:36,710 command_set.c: In function ‘combin_subset_pans’: 2026-03-05T13:52:36,710 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-03-05T13:52:36,711 457 | free(co_dstat_fpath); 2026-03-05T13:52:36,711 | ^~~~~~~~~~~~~~ 2026-03-05T13:52:36,712 In file included from kssdheaders/global_basic.h:159, 2026-03-05T13:52:36,712 from command_set.c:15: 2026-03-05T13:52:36,713 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2026-03-05T13:52:36,714 568 | extern void free (void *__ptr) __THROW; 2026-03-05T13:52:36,714 | ~~~~~~^~~~~ 2026-03-05T13:52:36,720 command_set.c: In function ‘grouping_genomes’: 2026-03-05T13:52:36,721 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-03-05T13:52:36,721 562 | free(co_dstat_fpath); 2026-03-05T13:52:36,722 | ^~~~~~~~~~~~~~ 2026-03-05T13:52:36,723 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2026-03-05T13:52:36,724 568 | extern void free (void *__ptr) __THROW; 2026-03-05T13:52:36,724 | ~~~~~~^~~~~ 2026-03-05T13:52:36,890 command_set.c: In function ‘sketch_union’: 2026-03-05T13:52:36,891 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T13:52:36,891 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:36,892 | ^ 2026-03-05T13:52:36,893 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T13:52:36,893 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:36,894 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:36,894 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:36,895 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T13:52:36,896 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:36,896 command_set.c:82:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:36,897 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T13:52:36,898 | ^~~~~~~~~~ 2026-03-05T13:52:36,898 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T13:52:36,899 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T13:52:36,900 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:36,901 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:36,901 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-03-05T13:52:36,901 | ^~ ~~~~~~~~~~ 2026-03-05T13:52:36,902 command_set.c:92:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:36,902 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-03-05T13:52:36,903 | ^~~~~~~~~~ 2026-03-05T13:52:36,903 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-05T13:52:36,904 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-03-05T13:52:36,904 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,029 command_set.c: In function ‘sketch_operate’: 2026-03-05T13:52:37,029 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,030 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-03-05T13:52:37,030 | ^~ ~~~~~~~~~~ 2026-03-05T13:52:37,031 command_set.c:153:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,031 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-03-05T13:52:37,032 | ^~~~~~~~~~ 2026-03-05T13:52:37,033 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-05T13:52:37,033 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-03-05T13:52:37,034 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,035 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,035 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-03-05T13:52:37,036 | ^~ ~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,036 command_set.c:155:29: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,037 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-03-05T13:52:37,038 | ^~~~~~~~~~ 2026-03-05T13:52:37,039 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2026-03-05T13:52:37,039 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-03-05T13:52:37,040 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,040 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,041 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T13:52:37,041 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:37,042 command_set.c:165:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,043 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T13:52:37,043 | ^~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,044 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T13:52:37,045 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T13:52:37,046 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,047 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,047 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T13:52:37,047 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:37,048 command_set.c:169:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,048 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T13:52:37,049 | ^~~~~~~~~~ 2026-03-05T13:52:37,049 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T13:52:37,050 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T13:52:37,050 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,051 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,051 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T13:52:37,052 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:37,052 command_set.c:174:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,053 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T13:52:37,053 | ^~~~~~~~~~ 2026-03-05T13:52:37,054 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T13:52:37,055 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T13:52:37,055 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,056 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,057 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T13:52:37,057 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:37,058 command_set.c:187:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,059 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T13:52:37,059 | ^~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,060 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T13:52:37,061 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T13:52:37,062 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,062 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T13:52:37,063 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:37,063 | ^ 2026-03-05T13:52:37,064 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T13:52:37,065 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:37,065 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,222 command_set.c: In function ‘uniq_sketch_union’: 2026-03-05T13:52:37,222 command_set.c:219:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T13:52:37,223 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2026-03-05T13:52:37,224 | ^ 2026-03-05T13:52:37,225 command_set.c:219:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2026-03-05T13:52:37,225 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2026-03-05T13:52:37,226 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,226 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T13:52:37,226 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:37,227 | ^ 2026-03-05T13:52:37,227 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T13:52:37,228 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:37,228 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,228 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,229 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T13:52:37,229 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:37,230 command_set.c:247:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,230 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T13:52:37,231 | ^~~~~~~~~~ 2026-03-05T13:52:37,231 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T13:52:37,232 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T13:52:37,233 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,233 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,234 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-03-05T13:52:37,235 | ^~ ~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,236 command_set.c:259:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,236 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-03-05T13:52:37,237 | ^~~~~~~~~~ 2026-03-05T13:52:37,238 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2026-03-05T13:52:37,238 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-03-05T13:52:37,239 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,376 command_set.c: In function ‘combin_pans’: 2026-03-05T13:52:37,377 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,377 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T13:52:37,378 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:37,379 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2026-03-05T13:52:37,379 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T13:52:37,380 | ^~~~~~~~~~ 2026-03-05T13:52:37,380 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2026-03-05T13:52:37,381 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T13:52:37,381 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,382 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,383 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T13:52:37,383 | ^~ ~~~~~~~~~~ 2026-03-05T13:52:37,384 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2026-03-05T13:52:37,384 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T13:52:37,385 | ^~~~~~~~~~ 2026-03-05T13:52:37,385 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2026-03-05T13:52:37,385 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T13:52:37,386 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,386 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T13:52:37,387 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:37,387 | ^ 2026-03-05T13:52:37,388 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T13:52:37,388 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:37,389 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,600 command_set.c: In function ‘combin_subset_pans’: 2026-03-05T13:52:37,601 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,601 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T13:52:37,602 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:37,603 command_set.c:469:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,603 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T13:52:37,604 | ^~~~~~~~~~ 2026-03-05T13:52:37,604 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T13:52:37,605 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T13:52:37,606 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,606 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,607 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T13:52:37,607 | ^~ ~~~~~~~~~~ 2026-03-05T13:52:37,608 command_set.c:475:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,609 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T13:52:37,609 | ^~~~~~~~~~ 2026-03-05T13:52:37,610 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T13:52:37,610 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T13:52:37,611 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,611 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,612 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T13:52:37,612 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:37,613 command_set.c:481:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,613 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T13:52:37,614 | ^~~~~~~~~~ 2026-03-05T13:52:37,615 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T13:52:37,615 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T13:52:37,616 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,616 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,617 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T13:52:37,617 | ^~ ~~~~~~~~~~ 2026-03-05T13:52:37,617 command_set.c:512:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,618 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T13:52:37,618 | ^~~~~~~~~~ 2026-03-05T13:52:37,619 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T13:52:37,619 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T13:52:37,619 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,620 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T13:52:37,621 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:37,621 | ^ 2026-03-05T13:52:37,622 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T13:52:37,622 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:37,623 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,855 command_set.c: In function ‘grouping_genomes’: 2026-03-05T13:52:37,856 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,857 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T13:52:37,858 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:37,858 command_set.c:574:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,859 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T13:52:37,859 | ^~~~~~~~~~ 2026-03-05T13:52:37,860 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T13:52:37,861 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T13:52:37,861 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,862 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,862 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T13:52:37,863 | ^~ ~~~~~~~~~~ 2026-03-05T13:52:37,863 command_set.c:580:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,864 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T13:52:37,864 | ^~~~~~~~~~ 2026-03-05T13:52:37,865 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T13:52:37,866 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T13:52:37,866 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,867 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,867 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T13:52:37,868 | ^~ ~~~~~~~~~~~ 2026-03-05T13:52:37,869 command_set.c:612:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,869 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T13:52:37,869 | ^~~~~~~~~~ 2026-03-05T13:52:37,870 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T13:52:37,870 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T13:52:37,871 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,872 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T13:52:37,872 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T13:52:37,873 | ^~ ~~~~~~~~~~ 2026-03-05T13:52:37,873 command_set.c:634:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T13:52:37,874 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T13:52:37,874 | ^~~~~~~~~~ 2026-03-05T13:52:37,874 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T13:52:37,875 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T13:52:37,875 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:37,876 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T13:52:37,877 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:37,877 | ^ 2026-03-05T13:52:37,878 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T13:52:37,879 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T13:52:37,879 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T13:52:38,162 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 2026-03-05T13:52:38,474 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 2026-03-05T13:52:38,639 global_basic.c: In function ‘organize_infile_list’: 2026-03-05T13:52:38,640 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2026-03-05T13:52:38,641 195 | while (isspace(*buf)) buf++; 2026-03-05T13:52:38,641 | ^~~~~~~ 2026-03-05T13:52:38,642 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2026-03-05T13:52:38,643 34 | #include 2026-03-05T13:52:38,643 +++ |+#include 2026-03-05T13:52:38,644 35 | 2026-03-05T13:52:38,645 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=] 2026-03-05T13:52:38,645 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2026-03-05T13:52:38,646 | ~~^ 2026-03-05T13:52:38,647 | | 2026-03-05T13:52:38,648 | long unsigned int 2026-03-05T13:52:38,649 | %u 2026-03-05T13:52:38,649 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2026-03-05T13:52:38,650 | ~~~~~~~~~~~ 2026-03-05T13:52:38,650 | | 2026-03-05T13:52:38,652 | size_t {aka unsigned int} 2026-03-05T13:52:38,652 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=] 2026-03-05T13:52:38,653 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2026-03-05T13:52:38,654 | ~~^ 2026-03-05T13:52:38,654 | | 2026-03-05T13:52:38,655 | long unsigned int 2026-03-05T13:52:38,655 | %u 2026-03-05T13:52:38,656 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2026-03-05T13:52:38,657 | ~~~~~~~~~~~ 2026-03-05T13:52:38,657 | | 2026-03-05T13:52:38,658 | size_t {aka unsigned int} 2026-03-05T13:52:39,438 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 2026-03-05T13:52:39,613 iseq2comem.c: In function ‘reads2mco’: 2026-03-05T13:52:39,614 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,614 156 | if (base > TL) { 2026-03-05T13:52:39,615 | ^ 2026-03-05T13:52:39,616 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,616 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T13:52:39,617 | ^~ 2026-03-05T13:52:39,618 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,619 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T13:52:39,619 | ^ 2026-03-05T13:52:39,620 iseq2comem.c: In function ‘fasta2co’: 2026-03-05T13:52:39,621 iseq2comem.c:213:69: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T13:52:39,621 213 | if ((infp = popen(fas_fname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2026-03-05T13:52:39,622 | ^~~~~~~~~~~~~~~ 2026-03-05T13:52:39,623 iseq2comem.c:219:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T13:52:39,623 219 | if ((infp = popen(seqfname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2026-03-05T13:52:39,624 | ^~~~~~~~~~~~~~~ 2026-03-05T13:52:39,625 iseq2comem.c:261:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,626 261 | if (base > TL) { 2026-03-05T13:52:39,626 | ^ 2026-03-05T13:52:39,627 iseq2comem.c:265:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,627 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T13:52:39,627 | ^~ 2026-03-05T13:52:39,628 iseq2comem.c:265:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,628 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T13:52:39,629 | ^ 2026-03-05T13:52:39,629 iseq2comem.c: In function ‘fastq2co’: 2026-03-05T13:52:39,630 iseq2comem.c:295:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2026-03-05T13:52:39,630 295 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2026-03-05T13:52:39,631 | ^~ 2026-03-05T13:52:39,631 iseq2comem.c:307:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T13:52:39,632 307 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2026-03-05T13:52:39,632 | ^~~~~~~~~~~~~~~ 2026-03-05T13:52:39,633 iseq2comem.c:313:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T13:52:39,634 313 | if ((infp = popen(seqfname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2026-03-05T13:52:39,634 | ^~~~~~~~~~~~~~~ 2026-03-05T13:52:39,635 iseq2comem.c:352:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,636 352 | if (base > TL) { 2026-03-05T13:52:39,636 | ^ 2026-03-05T13:52:39,637 iseq2comem.c:356:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,638 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T13:52:39,639 | ^~ 2026-03-05T13:52:39,639 iseq2comem.c:356:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,640 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T13:52:39,641 | ^ 2026-03-05T13:52:39,641 iseq2comem.c:375:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,642 375 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2026-03-05T13:52:39,643 | ^ 2026-03-05T13:52:39,643 iseq2comem.c: In function ‘fastq2koc’: 2026-03-05T13:52:39,644 iseq2comem.c:403:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T13:52:39,645 403 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2026-03-05T13:52:39,645 | ^~~~~~~~~~~~~~~~ 2026-03-05T13:52:39,646 iseq2comem.c:409:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T13:52:39,647 409 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2026-03-05T13:52:39,648 | ^~~~~~~~~~~~~~~~ 2026-03-05T13:52:39,648 iseq2comem.c:448:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,649 448 | if (base > TL) { 2026-03-05T13:52:39,650 | ^ 2026-03-05T13:52:39,651 iseq2comem.c:452:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,651 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T13:52:39,652 | ^~ 2026-03-05T13:52:39,652 iseq2comem.c:452:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,653 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T13:52:39,653 | ^ 2026-03-05T13:52:39,654 iseq2comem.c: In function ‘mt_shortreads2koc’: 2026-03-05T13:52:39,654 iseq2comem.c:628:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,655 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T13:52:39,655 | ^~ 2026-03-05T13:52:39,656 iseq2comem.c:628:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T13:52:39,657 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T13:52:39,657 | ^ 2026-03-05T13:52:41,031 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 2026-03-05T13:52:41,085 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 2026-03-05T13:52:41,210 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 2026-03-05T13:52:41,600 pykssd.c: In function ‘py_dist_dispatch’: 2026-03-05T13:52:41,600 pykssd.c:339:13: warning: unused variable ‘state1’ [-Wunused-variable] 2026-03-05T13:52:41,601 339 | int state1 = dist_dispatch(&dist_opt_val1); 2026-03-05T13:52:41,602 | ^~~~~~ 2026-03-05T13:52:41,602 pykssd.c:404:13: warning: unused variable ‘state2’ [-Wunused-variable] 2026-03-05T13:52:41,603 404 | int state2 = dist_dispatch(&dist_opt_val2); 2026-03-05T13:52:41,604 | ^~~~~~ 2026-03-05T13:52:41,605 pykssd.c:538:13: warning: unused variable ‘state4’ [-Wunused-variable] 2026-03-05T13:52:41,606 538 | int state4 = dist_dispatch(&dist_opt_val4); 2026-03-05T13:52:41,606 | ^~~~~~ 2026-03-05T13:52:42,255 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/kssdtool.cpython-311-arm-linux-gnueabihf.so -fopenmp 2026-03-05T13:52:42,446 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-03-05T13:52:42,447 !! 2026-03-05T13:52:42,448 ******************************************************************************** 2026-03-05T13:52:42,448 Please avoid running ``setup.py`` directly. 2026-03-05T13:52:42,449 Instead, use pypa/build, pypa/installer or other 2026-03-05T13:52:42,449 standards-based tools. 2026-03-05T13:52:42,450 This deprecation is overdue, please update your project and remove deprecated 2026-03-05T13:52:42,451 calls to avoid build errors in the future. 2026-03-05T13:52:42,452 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-03-05T13:52:42,452 ******************************************************************************** 2026-03-05T13:52:42,453 !! 2026-03-05T13:52:42,454 self.initialize_options() 2026-03-05T13:52:42,474 installing to build/bdist.linux-armv7l/wheel 2026-03-05T13:52:42,475 running install 2026-03-05T13:52:42,499 running install_lib 2026-03-05T13:52:42,526 creating build/bdist.linux-armv7l/wheel 2026-03-05T13:52:42,527 copying build/lib.linux-armv7l-cpython-311/kssdutils.py -> build/bdist.linux-armv7l/wheel/. 2026-03-05T13:52:42,530 copying build/lib.linux-armv7l-cpython-311/kssdtool.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2026-03-05T13:52:42,537 running install_egg_info 2026-03-05T13:52:42,571 Copying kssdutils.egg-info to build/bdist.linux-armv7l/wheel/./kssdutils-1.1.9-py3.11.egg-info 2026-03-05T13:52:42,581 running install_scripts 2026-03-05T13:52:42,626 creating build/bdist.linux-armv7l/wheel/kssdutils-1.1.9.dist-info/WHEEL 2026-03-05T13:52:42,629 creating '/tmp/pip-wheel-z4w0apcq/kssdutils-1.1.9-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-03-05T13:52:42,712 adding 'kssdtool.cpython-311-arm-linux-gnueabihf.so' 2026-03-05T13:52:42,716 adding 'kssdutils.py' 2026-03-05T13:52:42,718 adding 'kssdutils-1.1.9.dist-info/METADATA' 2026-03-05T13:52:42,719 adding 'kssdutils-1.1.9.dist-info/WHEEL' 2026-03-05T13:52:42,720 adding 'kssdutils-1.1.9.dist-info/dependency_links.txt' 2026-03-05T13:52:42,721 adding 'kssdutils-1.1.9.dist-info/top_level.txt' 2026-03-05T13:52:42,722 adding 'kssdutils-1.1.9.dist-info/RECORD' 2026-03-05T13:52:42,725 removing build/bdist.linux-armv7l/wheel 2026-03-05T13:52:42,880 Building wheel for kssdutils (setup.py): finished with status 'done' 2026-03-05T13:52:42,884 Created wheel for kssdutils: filename=kssdutils-1.1.9-cp311-cp311-linux_armv7l.whl size=179671 sha256=4170c6f7b1539a2959a5c83dab6344741df3727fe6cd0c2f5f067e5bc498d13f 2026-03-05T13:52:42,885 Stored in directory: /tmp/pip-ephem-wheel-cache-anzk74zv/wheels/fe/41/88/9b09a051a95d144d89307c6cc8fa78d26e983e11bf5f647e93 2026-03-05T13:52:42,894 Successfully built kssdutils 2026-03-05T13:52:42,903 Removed build tracker: '/tmp/pip-build-tracker-2a_sr__3'