2026-03-06T09:13:04,534 Created temporary directory: /tmp/pip-ephem-wheel-cache-qbuzhv_u 2026-03-06T09:13:04,535 Created temporary directory: /tmp/pip-build-tracker-ll0vs543 2026-03-06T09:13:04,536 Initialized build tracking at /tmp/pip-build-tracker-ll0vs543 2026-03-06T09:13:04,536 Created build tracker: /tmp/pip-build-tracker-ll0vs543 2026-03-06T09:13:04,537 Entered build tracker: /tmp/pip-build-tracker-ll0vs543 2026-03-06T09:13:04,538 Created temporary directory: /tmp/pip-wheel-ol02ijeb 2026-03-06T09:13:04,540 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 2026-03-06T09:13:04,543 Created temporary directory: /tmp/pip-ephem-wheel-cache-enzmdtro 2026-03-06T09:13:04,564 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-03-06T09:13:04,568 2 location(s) to search for versions of kssdutils: 2026-03-06T09:13:04,568 * https://pypi.org/simple/kssdutils/ 2026-03-06T09:13:04,568 * https://www.piwheels.org/simple/kssdutils/ 2026-03-06T09:13:04,568 Fetching project page and analyzing links: https://pypi.org/simple/kssdutils/ 2026-03-06T09:13:04,569 Getting page https://pypi.org/simple/kssdutils/ 2026-03-06T09:13:04,571 Found index url https://pypi.org/simple 2026-03-06T09:13:04,778 Fetched page https://pypi.org/simple/kssdutils/ as application/vnd.pypi.simple.v1+json 2026-03-06T09:13:04,782 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 2026-03-06T09:13:04,783 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 2026-03-06T09:13:04,783 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 2026-03-06T09:13:04,784 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 2026-03-06T09:13:04,785 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 2026-03-06T09:13:04,785 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 2026-03-06T09:13:04,786 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 2026-03-06T09:13:04,787 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 2026-03-06T09:13:04,787 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 2026-03-06T09:13:04,788 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 2026-03-06T09:13:04,788 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 2026-03-06T09:13:04,789 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 2026-03-06T09:13:04,790 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 2026-03-06T09:13:04,790 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 2026-03-06T09:13:04,791 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 2026-03-06T09:13:04,791 Found link https://files.pythonhosted.org/packages/bd/e0/d7aec62c770afea4b416e12c6e0afcb31d4d07c6a9320c903e87821c1512/kssdutils-1.2.0.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.2.0 2026-03-06T09:13:04,792 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdutils/ 2026-03-06T09:13:04,793 Getting page https://www.piwheels.org/simple/kssdutils/ 2026-03-06T09:13:04,794 Found index url https://www.piwheels.org/simple 2026-03-06T09:13:04,948 Fetched page https://www.piwheels.org/simple/kssdutils/ as text/html 2026-03-06T09:13:04,963 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.1.9-cp311-cp311-linux_armv6l.whl#sha256=4170c6f7b1539a2959a5c83dab6344741df3727fe6cd0c2f5f067e5bc498d13f (from https://www.piwheels.org/simple/kssdutils/) 2026-03-06T09:13:04,963 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.1.9-cp311-cp311-linux_armv7l.whl#sha256=4170c6f7b1539a2959a5c83dab6344741df3727fe6cd0c2f5f067e5bc498d13f (from https://www.piwheels.org/simple/kssdutils/) 2026-03-06T09:13:04,964 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/) 2026-03-06T09:13:04,965 Skipping link: No binaries permitted for kssdutils: 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https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.6-cp39-cp39-linux_armv6l.whl#sha256=bfe64af80d2aab63dccf6fb0418e3b806f4ee1b2fcff0eab77094040d2b6dca5 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-06T09:13:04,984 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.6-cp39-cp39-linux_armv7l.whl#sha256=bfe64af80d2aab63dccf6fb0418e3b806f4ee1b2fcff0eab77094040d2b6dca5 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-06T09:13:04,984 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.5-cp311-cp311-linux_armv6l.whl#sha256=29ec8af3f080743643fee31ce978f3d65a6d90b950248e2ed6827316567aaa62 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-06T09:13:04,985 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.5-cp311-cp311-linux_armv7l.whl#sha256=29ec8af3f080743643fee31ce978f3d65a6d90b950248e2ed6827316567aaa62 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-06T09:13:04,986 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.5-cp39-cp39-linux_armv6l.whl#sha256=fb21de5c7d85619ac9cc1fafe3280f0130178032b169f1cf7ceac0cb6326d42e (from https://www.piwheels.org/simple/kssdutils/) 2026-03-06T09:13:04,986 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.5-cp39-cp39-linux_armv7l.whl#sha256=fb21de5c7d85619ac9cc1fafe3280f0130178032b169f1cf7ceac0cb6326d42e (from https://www.piwheels.org/simple/kssdutils/) 2026-03-06T09:13:04,986 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/) 2026-03-06T09:13:04,987 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/) 2026-03-06T09:13:04,987 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/) 2026-03-06T09:13:04,988 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/) 2026-03-06T09:13:04,988 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/) 2026-03-06T09:13:04,989 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/) 2026-03-06T09:13:04,990 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/) 2026-03-06T09:13:04,990 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/) 2026-03-06T09:13:04,991 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/) 2026-03-06T09:13:04,991 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/) 2026-03-06T09:13:04,992 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/) 2026-03-06T09:13:04,993 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/) 2026-03-06T09:13:04,993 Skipping link: not a file: https://www.piwheels.org/simple/kssdutils/ 2026-03-06T09:13:04,994 Skipping link: not a file: https://pypi.org/simple/kssdutils/ 2026-03-06T09:13:05,015 Given no hashes to check 1 links for project 'kssdutils': discarding no candidates 2026-03-06T09:13:05,033 Collecting kssdutils==1.2.0 2026-03-06T09:13:05,035 Created temporary directory: /tmp/pip-unpack-augl0e9i 2026-03-06T09:13:05,167 Downloading kssdutils-1.2.0.tar.gz (45 kB) 2026-03-06T09:13:05,277 Added kssdutils==1.2.0 from https://files.pythonhosted.org/packages/bd/e0/d7aec62c770afea4b416e12c6e0afcb31d4d07c6a9320c903e87821c1512/kssdutils-1.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-ll0vs543' 2026-03-06T09:13:05,278 Running setup.py (path:/tmp/pip-wheel-ol02ijeb/kssdutils_2a4657aca31e4c348af0a9556574b6e0/setup.py) egg_info for package kssdutils 2026-03-06T09:13:05,279 Created temporary directory: /tmp/pip-pip-egg-info-np2idbj4 2026-03-06T09:13:05,280 Preparing metadata (setup.py): started 2026-03-06T09:13:05,281 Running command python setup.py egg_info 2026-03-06T09:13:06,143 running egg_info 2026-03-06T09:13:06,169 creating /tmp/pip-pip-egg-info-np2idbj4/kssdutils.egg-info 2026-03-06T09:13:06,170 writing /tmp/pip-pip-egg-info-np2idbj4/kssdutils.egg-info/PKG-INFO 2026-03-06T09:13:06,174 writing dependency_links to /tmp/pip-pip-egg-info-np2idbj4/kssdutils.egg-info/dependency_links.txt 2026-03-06T09:13:06,176 writing top-level names to /tmp/pip-pip-egg-info-np2idbj4/kssdutils.egg-info/top_level.txt 2026-03-06T09:13:06,177 writing manifest file '/tmp/pip-pip-egg-info-np2idbj4/kssdutils.egg-info/SOURCES.txt' 2026-03-06T09:13:06,261 reading manifest file '/tmp/pip-pip-egg-info-np2idbj4/kssdutils.egg-info/SOURCES.txt' 2026-03-06T09:13:06,263 reading manifest template 'MANIFEST.in' 2026-03-06T09:13:06,271 writing manifest file '/tmp/pip-pip-egg-info-np2idbj4/kssdutils.egg-info/SOURCES.txt' 2026-03-06T09:13:06,378 Preparing metadata (setup.py): finished with status 'done' 2026-03-06T09:13:06,382 Source in /tmp/pip-wheel-ol02ijeb/kssdutils_2a4657aca31e4c348af0a9556574b6e0 has version 1.2.0, which satisfies requirement kssdutils==1.2.0 from https://files.pythonhosted.org/packages/bd/e0/d7aec62c770afea4b416e12c6e0afcb31d4d07c6a9320c903e87821c1512/kssdutils-1.2.0.tar.gz 2026-03-06T09:13:06,383 Removed kssdutils==1.2.0 from https://files.pythonhosted.org/packages/bd/e0/d7aec62c770afea4b416e12c6e0afcb31d4d07c6a9320c903e87821c1512/kssdutils-1.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-ll0vs543' 2026-03-06T09:13:06,387 Created temporary directory: /tmp/pip-unpack-vk9uq56o 2026-03-06T09:13:06,387 Building wheels for collected packages: kssdutils 2026-03-06T09:13:06,392 Created temporary directory: /tmp/pip-wheel-027zqubc 2026-03-06T09:13:06,392 Building wheel for kssdutils (setup.py): started 2026-03-06T09:13:06,394 Destination directory: /tmp/pip-wheel-027zqubc 2026-03-06T09:13:06,394 Running command python setup.py bdist_wheel 2026-03-06T09:13:07,230 running bdist_wheel 2026-03-06T09:13:07,335 running build 2026-03-06T09:13:07,335 running build_py 2026-03-06T09:13:07,367 creating build/lib.linux-armv7l-cpython-311 2026-03-06T09:13:07,369 copying kssdutils.py -> build/lib.linux-armv7l-cpython-311 2026-03-06T09:13:07,371 running egg_info 2026-03-06T09:13:07,399 writing kssdutils.egg-info/PKG-INFO 2026-03-06T09:13:07,401 writing dependency_links to kssdutils.egg-info/dependency_links.txt 2026-03-06T09:13:07,404 writing top-level names to kssdutils.egg-info/top_level.txt 2026-03-06T09:13:07,433 reading manifest file 'kssdutils.egg-info/SOURCES.txt' 2026-03-06T09:13:07,436 reading manifest template 'MANIFEST.in' 2026-03-06T09:13:07,444 writing manifest file 'kssdutils.egg-info/SOURCES.txt' 2026-03-06T09:13:07,445 running build_ext 2026-03-06T09:13:07,986 building 'kssdtool' extension 2026-03-06T09:13:07,987 creating build/temp.linux-armv7l-cpython-311 2026-03-06T09:13:07,989 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 2026-03-06T09:13:08,166 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2026-03-06T09:13:08,167 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-03-06T09:13:08,167 109 | for (unsigned int i = 0; i < comp_num; i++) { 2026-03-06T09:13:08,168 | ^ 2026-03-06T09:13:08,171 co2mco.c: In function ‘co2unitllmco’: 2026-03-06T09:13:08,172 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-03-06T09:13:08,172 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2026-03-06T09:13:08,173 | ^ 2026-03-06T09:13:08,877 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 2026-03-06T09:13:09,256 command_composite.c: In function ‘get_species_abundance’: 2026-03-06T09:13:09,257 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2026-03-06T09:13:09,257 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2026-03-06T09:13:09,258 | ^~ 2026-03-06T09:13:09,259 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2026-03-06T09:13:09,259 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2026-03-06T09:13:09,260 | ^~ 2026-03-06T09:13:09,261 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:09,261 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-03-06T09:13:09,262 | ^ 2026-03-06T09:13:09,263 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:09,263 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-03-06T09:13:09,264 | ^~~~~~~~~~ 2026-03-06T09:13:09,264 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-06T09:13:09,265 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-03-06T09:13:09,266 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:09,266 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:09,267 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-03-06T09:13:09,268 | ^ 2026-03-06T09:13:09,268 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:09,269 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-03-06T09:13:09,269 | ^~~~~~~~~~ 2026-03-06T09:13:09,270 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-06T09:13:09,270 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-03-06T09:13:09,271 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:09,272 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:09,272 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-03-06T09:13:09,273 | ^ 2026-03-06T09:13:09,273 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:09,274 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-03-06T09:13:09,274 | ^~~~~~~~~~ 2026-03-06T09:13:09,275 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-06T09:13:09,275 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-03-06T09:13:09,276 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:09,276 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:09,277 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-03-06T09:13:09,278 | ^ 2026-03-06T09:13:09,279 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:09,279 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-03-06T09:13:09,280 | ^~~~~~~~~~ 2026-03-06T09:13:09,280 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-06T09:13:09,281 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-03-06T09:13:09,282 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:09,282 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:09,283 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-03-06T09:13:09,284 | ^ 2026-03-06T09:13:09,284 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:09,285 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-03-06T09:13:09,285 | ^~~~~~~~~~~~ 2026-03-06T09:13:09,286 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2026-03-06T09:13:09,287 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-03-06T09:13:09,287 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:09,523 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 2026-03-06T09:13:09,757 command_dist.c: In function ‘mco_cbd_co_dist’: 2026-03-06T09:13:09,758 command_dist.c:664:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-06T09:13:09,759 664 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-06T09:13:09,759 | ~~^ 2026-03-06T09:13:09,760 | | 2026-03-06T09:13:09,760 | long unsigned int 2026-03-06T09:13:09,763 | %u 2026-03-06T09:13:09,764 665 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-06T09:13:09,764 | ~~~~~~~ 2026-03-06T09:13:09,765 | | 2026-03-06T09:13:09,765 | size_t {aka unsigned int} 2026-03-06T09:13:09,766 command_dist.c:664:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-06T09:13:09,766 664 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-06T09:13:09,767 | ~~^ 2026-03-06T09:13:09,768 | | 2026-03-06T09:13:09,768 | long unsigned int 2026-03-06T09:13:09,769 | %u 2026-03-06T09:13:09,769 665 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-06T09:13:09,770 666 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-06T09:13:09,771 | ~~~~~~~~~ 2026-03-06T09:13:09,771 | | 2026-03-06T09:13:09,772 | size_t {aka unsigned int} 2026-03-06T09:13:09,773 command_dist.c:664:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-03-06T09:13:09,774 664 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-06T09:13:09,774 | ~~^ 2026-03-06T09:13:09,775 | | 2026-03-06T09:13:09,776 | long unsigned int 2026-03-06T09:13:09,776 | %u 2026-03-06T09:13:09,777 665 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-06T09:13:09,777 666 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-06T09:13:09,778 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:09,779 | | 2026-03-06T09:13:09,779 | unsigned int 2026-03-06T09:13:09,780 command_dist.c:702:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-03-06T09:13:09,780 702 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2026-03-06T09:13:09,781 | ^ 2026-03-06T09:13:09,782 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2026-03-06T09:13:09,782 command_dist.c:850:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-06T09:13:09,782 850 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-03-06T09:13:09,783 | ~~^ ~~~~~~~ 2026-03-06T09:13:09,783 | | | 2026-03-06T09:13:09,784 | long unsigned int size_t {aka unsigned int} 2026-03-06T09:13:09,784 | %u 2026-03-06T09:13:09,785 command_dist.c:850:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-06T09:13:09,785 850 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-03-06T09:13:09,786 | ~~^ 2026-03-06T09:13:09,786 | | 2026-03-06T09:13:09,787 | long unsigned int 2026-03-06T09:13:09,787 | %u 2026-03-06T09:13:09,788 851 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2026-03-06T09:13:09,788 | ~~~~~~~~~ 2026-03-06T09:13:09,789 | | 2026-03-06T09:13:09,789 | size_t {aka unsigned int} 2026-03-06T09:13:09,790 command_dist.c:850:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-03-06T09:13:09,791 850 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-03-06T09:13:09,792 | ~~^ 2026-03-06T09:13:09,792 | | 2026-03-06T09:13:09,793 | long unsigned int 2026-03-06T09:13:09,793 | %u 2026-03-06T09:13:09,794 851 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2026-03-06T09:13:09,795 852 | (size_t) b * unitsz_distf_mapped); 2026-03-06T09:13:09,795 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:09,796 | | 2026-03-06T09:13:09,797 | unsigned int 2026-03-06T09:13:09,797 command_dist.c:797:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2026-03-06T09:13:09,798 797 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2026-03-06T09:13:09,799 | ^~~~~~~ 2026-03-06T09:13:09,800 command_dist.c:796:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2026-03-06T09:13:09,800 796 | struct stat cbd_fcode_stat; 2026-03-06T09:13:09,801 | ^~~~~~~~~~~~~~ 2026-03-06T09:13:09,801 command_dist.c:795:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2026-03-06T09:13:09,801 795 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2026-03-06T09:13:09,802 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:09,802 command_dist.c:795:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2026-03-06T09:13:09,803 795 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2026-03-06T09:13:09,803 | ^~~~~~~~~~~~~~~~~ 2026-03-06T09:13:09,803 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2026-03-06T09:13:09,804 command_dist.c:1005:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-06T09:13:09,804 1005 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-06T09:13:09,805 | ~~^ 2026-03-06T09:13:09,805 | | 2026-03-06T09:13:09,805 | long unsigned int 2026-03-06T09:13:09,806 | %u 2026-03-06T09:13:09,806 1006 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-06T09:13:09,807 | ~~~~~~~ 2026-03-06T09:13:09,807 | | 2026-03-06T09:13:09,807 | size_t {aka unsigned int} 2026-03-06T09:13:09,808 command_dist.c:1005:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-06T09:13:09,809 1005 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-06T09:13:09,810 | ~~^ 2026-03-06T09:13:09,810 | | 2026-03-06T09:13:09,811 | long unsigned int 2026-03-06T09:13:09,811 | %u 2026-03-06T09:13:09,812 1006 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-06T09:13:09,813 1007 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-06T09:13:09,813 | ~~~~~~~~~ 2026-03-06T09:13:09,814 | | 2026-03-06T09:13:09,815 | size_t {aka unsigned int} 2026-03-06T09:13:09,815 command_dist.c:1005:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-03-06T09:13:09,816 1005 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-06T09:13:09,816 | ~~^ 2026-03-06T09:13:09,817 | | 2026-03-06T09:13:09,818 | long unsigned int 2026-03-06T09:13:09,818 | %u 2026-03-06T09:13:09,819 1006 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-06T09:13:09,820 1007 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-06T09:13:09,821 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:09,821 | | 2026-03-06T09:13:09,822 | unsigned int 2026-03-06T09:13:09,822 command_dist.c:1021:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2026-03-06T09:13:09,823 1021 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2026-03-06T09:13:09,823 | ^ 2026-03-06T09:13:09,824 command_dist.c: In function ‘mco_co_dist_core’: 2026-03-06T09:13:09,824 command_dist.c:1103:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-03-06T09:13:09,825 1103 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2026-03-06T09:13:09,825 | ^ 2026-03-06T09:13:09,828 command_dist.c: In function ‘koc_dist_print_nobin’: 2026-03-06T09:13:09,830 command_dist.c:1226:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-06T09:13:09,830 1226 | for (int rid = 0; rid < ref_num; rid++) 2026-03-06T09:13:09,831 | ^ 2026-03-06T09:13:09,832 command_dist.c:1232:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-06T09:13:09,833 1232 | for (int rid = 0; rid < ref_num; rid++) { 2026-03-06T09:13:09,834 | ^ 2026-03-06T09:13:09,839 command_dist.c: In function ‘dist_print_nobin’: 2026-03-06T09:13:09,841 command_dist.c:1322:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-06T09:13:09,841 1322 | if ((N_max > NREF) || (N_max > ref_num)) { 2026-03-06T09:13:09,842 | ^ 2026-03-06T09:13:09,844 command_dist.c:1343:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-06T09:13:09,845 1343 | for (int rid = 0; rid < ref_num; rid++) { 2026-03-06T09:13:09,846 | ^ 2026-03-06T09:13:09,847 command_dist.c:1369:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-06T09:13:09,848 1369 | for (int rid = 0; rid < ref_num; rid++) 2026-03-06T09:13:09,848 | ^ 2026-03-06T09:13:10,208 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2026-03-06T09:13:10,208 command_dist.c:390:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2026-03-06T09:13:10,209 390 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2026-03-06T09:13:10,210 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:10,210 command_dist.c:362:40: note: ‘com_abund_fp’ was declared here 2026-03-06T09:13:10,211 362 | FILE *com_cofp, *indexfp, *com_abund_fp; 2026-03-06T09:13:10,212 | ^~~~~~~~~~~~ 2026-03-06T09:13:11,043 command_dist.c: In function ‘get_dim_shuffle’: 2026-03-06T09:13:11,044 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2026-03-06T09:13:11,045 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2026-03-06T09:13:11,046 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:11,046 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2026-03-06T09:13:11,047 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2026-03-06T09:13:11,048 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:11,944 command_dist.c: In function ‘mco_cbd_co_dist’: 2026-03-06T09:13:11,945 command_dist.c:583:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:11,946 583 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-06T09:13:11,946 | ^~ ~~~~~~~~~ 2026-03-06T09:13:11,947 command_dist.c:583:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-03-06T09:13:11,947 583 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-06T09:13:11,948 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:11,948 command_dist.c:612:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-06T09:13:11,949 612 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-06T09:13:11,949 | ^~~~~~~~~~~~~~~ 2026-03-06T09:13:11,950 command_dist.c:612:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-03-06T09:13:11,950 612 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-06T09:13:11,951 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:11,951 command_dist.c:668:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-06T09:13:11,952 668 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-06T09:13:11,952 | ^~~~~~~~~~~ 2026-03-06T09:13:11,953 command_dist.c:668:38: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:11,953 668 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-06T09:13:11,954 | ^~~~~~~~~~~~~~~~~ 2026-03-06T09:13:11,955 command_dist.c:668:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2026-03-06T09:13:11,955 668 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-06T09:13:11,956 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:11,957 command_dist.c:669:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-06T09:13:11,958 669 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-06T09:13:11,958 | ^~~~~ 2026-03-06T09:13:11,959 command_dist.c:669:32: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:11,960 669 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-06T09:13:11,960 | ^~~~~~~~~~~ 2026-03-06T09:13:11,961 command_dist.c:669:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-06T09:13:11,962 669 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-06T09:13:11,962 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,197 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2026-03-06T09:13:12,199 command_dist.c:750:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:12,199 750 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-06T09:13:12,200 | ^~ ~~~~~~~~~ 2026-03-06T09:13:12,201 command_dist.c:750:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-03-06T09:13:12,201 750 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-06T09:13:12,202 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,202 command_dist.c:777:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-06T09:13:12,202 777 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-06T09:13:12,203 | ^~~~~~~~~~~~~~~ 2026-03-06T09:13:12,203 command_dist.c:777:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-03-06T09:13:12,204 777 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-06T09:13:12,204 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,205 command_dist.c:810:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-06T09:13:12,205 810 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-06T09:13:12,206 | ^~~~~~~~~~~~~ 2026-03-06T09:13:12,206 command_dist.c:810:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-03-06T09:13:12,207 810 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-06T09:13:12,207 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,208 command_dist.c:836:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:12,208 836 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-03-06T09:13:12,209 | ^ 2026-03-06T09:13:12,209 command_dist.c:836:33: note: directive argument in the range [0, 536870912] 2026-03-06T09:13:12,210 836 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-03-06T09:13:12,211 | ^~~~~~~~~~ 2026-03-06T09:13:12,211 command_dist.c:836:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2026-03-06T09:13:12,212 836 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-03-06T09:13:12,212 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,213 command_dist.c:838:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:12,214 838 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-03-06T09:13:12,214 | ^ 2026-03-06T09:13:12,215 command_dist.c:838:28: note: directive argument in the range [0, 536870912] 2026-03-06T09:13:12,216 838 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-03-06T09:13:12,216 | ^~~~~~~~~~ 2026-03-06T09:13:12,217 command_dist.c:838:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2026-03-06T09:13:12,218 838 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-03-06T09:13:12,219 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,479 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2026-03-06T09:13:12,480 command_dist.c:914:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:12,481 914 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-06T09:13:12,482 | ^~ ~~~~~~~~~ 2026-03-06T09:13:12,482 command_dist.c:914:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-03-06T09:13:12,483 914 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-06T09:13:12,484 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,484 command_dist.c:943:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-06T09:13:12,484 943 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-06T09:13:12,485 | ^~~~~~~~~~~~~~~ 2026-03-06T09:13:12,485 command_dist.c:943:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-03-06T09:13:12,486 943 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-06T09:13:12,486 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,487 command_dist.c:977:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-06T09:13:12,487 977 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-06T09:13:12,487 | ^~~~~~~~~~~~~ 2026-03-06T09:13:12,488 command_dist.c:977:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-03-06T09:13:12,489 977 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-06T09:13:12,489 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,490 command_dist.c:1009:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-06T09:13:12,491 1009 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-06T09:13:12,491 | ^~~~~~~~~~~ 2026-03-06T09:13:12,492 command_dist.c:1009:38: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:12,492 1009 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-06T09:13:12,493 | ^~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,494 command_dist.c:1009:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2026-03-06T09:13:12,494 1009 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-06T09:13:12,495 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,495 command_dist.c:1010:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-06T09:13:12,496 1010 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-06T09:13:12,496 | ^~~~~ 2026-03-06T09:13:12,497 command_dist.c:1010:32: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:12,498 1010 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-06T09:13:12,498 | ^~~~~~~~~~~ 2026-03-06T09:13:12,499 command_dist.c:1010:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-06T09:13:12,500 1010 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-06T09:13:12,500 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,771 command_dist.c: In function ‘combine_queries’: 2026-03-06T09:13:12,773 command_dist.c:1479:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-06T09:13:12,774 1479 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2026-03-06T09:13:12,774 | ^ 2026-03-06T09:13:12,775 command_dist.c:1479:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-06T09:13:12,776 1479 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2026-03-06T09:13:12,776 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,777 command_dist.c:1486:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-06T09:13:12,778 1486 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2026-03-06T09:13:12,778 | ^ 2026-03-06T09:13:12,779 command_dist.c:1486:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-06T09:13:12,779 1486 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2026-03-06T09:13:12,780 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:12,782 command_dist.c:1590:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:12,783 1590 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2026-03-06T09:13:12,783 | ^~ ~~~~~~~~ 2026-03-06T09:13:12,784 command_dist.c:1590:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-03-06T09:13:12,785 1590 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2026-03-06T09:13:12,786 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,289 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 2026-03-06T09:13:13,467 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 2026-03-06T09:13:13,638 command_set.c: In function ‘sketch_operate’: 2026-03-06T09:13:13,639 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-03-06T09:13:13,640 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2026-03-06T09:13:13,640 | ^ 2026-03-06T09:13:13,652 command_set.c: In function ‘combin_subset_pans’: 2026-03-06T09:13:13,653 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-03-06T09:13:13,653 457 | free(co_dstat_fpath); 2026-03-06T09:13:13,654 | ^~~~~~~~~~~~~~ 2026-03-06T09:13:13,655 In file included from kssdheaders/global_basic.h:159, 2026-03-06T09:13:13,656 from command_set.c:15: 2026-03-06T09:13:13,656 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2026-03-06T09:13:13,657 568 | extern void free (void *__ptr) __THROW; 2026-03-06T09:13:13,657 | ~~~~~~^~~~~ 2026-03-06T09:13:13,660 command_set.c: In function ‘grouping_genomes’: 2026-03-06T09:13:13,660 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-03-06T09:13:13,661 562 | free(co_dstat_fpath); 2026-03-06T09:13:13,662 | ^~~~~~~~~~~~~~ 2026-03-06T09:13:13,662 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2026-03-06T09:13:13,663 568 | extern void free (void *__ptr) __THROW; 2026-03-06T09:13:13,664 | ~~~~~~^~~~~ 2026-03-06T09:13:13,828 command_set.c: In function ‘sketch_union’: 2026-03-06T09:13:13,829 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-06T09:13:13,829 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:13,830 | ^ 2026-03-06T09:13:13,831 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-06T09:13:13,832 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:13,832 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,833 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:13,833 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-06T09:13:13,834 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:13,834 command_set.c:82:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:13,835 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-06T09:13:13,835 | ^~~~~~~~~~ 2026-03-06T09:13:13,836 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-06T09:13:13,837 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-06T09:13:13,837 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,838 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:13,838 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-03-06T09:13:13,839 | ^~ ~~~~~~~~~~ 2026-03-06T09:13:13,840 command_set.c:92:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:13,840 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-03-06T09:13:13,841 | ^~~~~~~~~~ 2026-03-06T09:13:13,842 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-06T09:13:13,842 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-03-06T09:13:13,843 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,963 command_set.c: In function ‘sketch_operate’: 2026-03-06T09:13:13,964 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:13,964 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-03-06T09:13:13,965 | ^~ ~~~~~~~~~~ 2026-03-06T09:13:13,966 command_set.c:153:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:13,966 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-03-06T09:13:13,967 | ^~~~~~~~~~ 2026-03-06T09:13:13,967 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-06T09:13:13,968 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-03-06T09:13:13,969 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,970 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:13,970 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-03-06T09:13:13,971 | ^~ ~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,972 command_set.c:155:29: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:13,972 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-03-06T09:13:13,973 | ^~~~~~~~~~ 2026-03-06T09:13:13,974 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2026-03-06T09:13:13,975 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-03-06T09:13:13,975 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,976 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:13,976 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-06T09:13:13,977 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:13,977 command_set.c:165:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:13,978 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-06T09:13:13,978 | ^~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,979 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-06T09:13:13,979 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-06T09:13:13,980 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,980 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:13,981 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-06T09:13:13,982 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:13,982 command_set.c:169:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:13,983 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-06T09:13:13,983 | ^~~~~~~~~~ 2026-03-06T09:13:13,984 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-06T09:13:13,984 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-06T09:13:13,985 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,986 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:13,986 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-03-06T09:13:13,987 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:13,988 command_set.c:174:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:13,988 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-03-06T09:13:13,989 | ^~~~~~~~~~ 2026-03-06T09:13:13,990 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-06T09:13:13,990 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-03-06T09:13:13,991 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,992 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:13,992 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-03-06T09:13:13,993 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:13,994 command_set.c:187:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:13,995 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-03-06T09:13:13,996 | ^~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,997 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-06T09:13:13,997 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-03-06T09:13:13,998 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:13,998 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-06T09:13:13,999 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:13,999 | ^ 2026-03-06T09:13:14,000 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-06T09:13:14,000 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:14,001 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,138 command_set.c: In function ‘uniq_sketch_union’: 2026-03-06T09:13:14,138 command_set.c:219:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-06T09:13:14,139 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2026-03-06T09:13:14,139 | ^ 2026-03-06T09:13:14,140 command_set.c:219:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2026-03-06T09:13:14,140 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2026-03-06T09:13:14,141 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,142 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-06T09:13:14,142 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:14,143 | ^ 2026-03-06T09:13:14,143 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-06T09:13:14,144 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:14,145 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,145 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,146 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-06T09:13:14,147 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:14,147 command_set.c:247:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:14,148 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-06T09:13:14,149 | ^~~~~~~~~~ 2026-03-06T09:13:14,150 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-06T09:13:14,150 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-06T09:13:14,151 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,152 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,152 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-03-06T09:13:14,153 | ^~ ~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,153 command_set.c:259:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:14,154 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-03-06T09:13:14,155 | ^~~~~~~~~~ 2026-03-06T09:13:14,155 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2026-03-06T09:13:14,156 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-03-06T09:13:14,157 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,283 command_set.c: In function ‘combin_pans’: 2026-03-06T09:13:14,284 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,284 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-06T09:13:14,285 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:14,285 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2026-03-06T09:13:14,286 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-06T09:13:14,286 | ^~~~~~~~~~ 2026-03-06T09:13:14,287 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2026-03-06T09:13:14,287 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-06T09:13:14,288 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,288 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,289 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-06T09:13:14,290 | ^~ ~~~~~~~~~~ 2026-03-06T09:13:14,290 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2026-03-06T09:13:14,291 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-06T09:13:14,291 | ^~~~~~~~~~ 2026-03-06T09:13:14,292 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2026-03-06T09:13:14,292 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-06T09:13:14,293 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,294 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-06T09:13:14,294 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:14,295 | ^ 2026-03-06T09:13:14,296 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-06T09:13:14,296 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:14,297 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,500 command_set.c: In function ‘combin_subset_pans’: 2026-03-06T09:13:14,501 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,502 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-06T09:13:14,502 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:14,503 command_set.c:469:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:14,503 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-06T09:13:14,504 | ^~~~~~~~~~ 2026-03-06T09:13:14,504 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-06T09:13:14,505 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-06T09:13:14,505 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,506 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,507 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-06T09:13:14,507 | ^~ ~~~~~~~~~~ 2026-03-06T09:13:14,508 command_set.c:475:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:14,509 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-06T09:13:14,509 | ^~~~~~~~~~ 2026-03-06T09:13:14,510 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-06T09:13:14,510 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-06T09:13:14,511 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,511 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,512 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-06T09:13:14,512 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:14,513 command_set.c:481:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:14,513 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-06T09:13:14,514 | ^~~~~~~~~~ 2026-03-06T09:13:14,514 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-06T09:13:14,515 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-06T09:13:14,515 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,516 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,517 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-06T09:13:14,518 | ^~ ~~~~~~~~~~ 2026-03-06T09:13:14,518 command_set.c:512:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:14,519 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-06T09:13:14,519 | ^~~~~~~~~~ 2026-03-06T09:13:14,520 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-06T09:13:14,521 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-06T09:13:14,522 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,522 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-06T09:13:14,523 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:14,524 | ^ 2026-03-06T09:13:14,525 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-06T09:13:14,525 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:14,526 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,746 command_set.c: In function ‘grouping_genomes’: 2026-03-06T09:13:14,747 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,747 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-06T09:13:14,748 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:14,749 command_set.c:574:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:14,749 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-06T09:13:14,750 | ^~~~~~~~~~ 2026-03-06T09:13:14,750 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-06T09:13:14,751 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-06T09:13:14,752 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,753 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,753 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-06T09:13:14,753 | ^~ ~~~~~~~~~~ 2026-03-06T09:13:14,754 command_set.c:580:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:14,754 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-06T09:13:14,755 | ^~~~~~~~~~ 2026-03-06T09:13:14,755 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-06T09:13:14,755 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-06T09:13:14,756 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,756 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,757 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-06T09:13:14,757 | ^~ ~~~~~~~~~~~ 2026-03-06T09:13:14,758 command_set.c:612:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:14,758 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-06T09:13:14,759 | ^~~~~~~~~~ 2026-03-06T09:13:14,760 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-06T09:13:14,760 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-06T09:13:14,761 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,762 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-06T09:13:14,762 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-06T09:13:14,763 | ^~ ~~~~~~~~~~ 2026-03-06T09:13:14,764 command_set.c:634:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-06T09:13:14,765 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-06T09:13:14,765 | ^~~~~~~~~~ 2026-03-06T09:13:14,766 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-06T09:13:14,767 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-06T09:13:14,768 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:14,768 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-06T09:13:14,769 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:14,769 | ^ 2026-03-06T09:13:14,770 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-06T09:13:14,770 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-06T09:13:14,771 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-06T09:13:15,041 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 2026-03-06T09:13:15,356 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 global_basic.c -o build/temp.linux-armv7l-cpython-311/global_basic.o -fopenmp 2026-03-06T09:13:15,560 global_basic.c: In function ‘organize_infile_list’: 2026-03-06T09:13:15,561 global_basic.c:186:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2026-03-06T09:13:15,562 186 | while (isspace(*buf)) buf++; 2026-03-06T09:13:15,563 | ^~~~~~~ 2026-03-06T09:13:15,564 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2026-03-06T09:13:15,564 34 | #include 2026-03-06T09:13:15,565 +++ |+#include 2026-03-06T09:13:15,565 35 | 2026-03-06T09:13:15,566 global_basic.c:192:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-06T09:13:15,566 192 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2026-03-06T09:13:15,567 | ~~^ 2026-03-06T09:13:15,567 | | 2026-03-06T09:13:15,568 | long unsigned int 2026-03-06T09:13:15,568 | %u 2026-03-06T09:13:15,569 193 | list_path, file_num, buf, strlen(buf), PATHLEN); 2026-03-06T09:13:15,569 | ~~~~~~~~~~~ 2026-03-06T09:13:15,570 | | 2026-03-06T09:13:15,571 | size_t {aka unsigned int} 2026-03-06T09:13:15,571 global_basic.c:224:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-06T09:13:15,572 224 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2026-03-06T09:13:15,573 | ~~^ 2026-03-06T09:13:15,574 | | 2026-03-06T09:13:15,574 | long unsigned int 2026-03-06T09:13:15,575 | %u 2026-03-06T09:13:15,576 225 | list_path, file_num, buf, strlen(buf), PATHLEN); 2026-03-06T09:13:15,576 | ~~~~~~~~~~~ 2026-03-06T09:13:15,577 | | 2026-03-06T09:13:15,578 | size_t {aka unsigned int} 2026-03-06T09:13:16,329 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 2026-03-06T09:13:16,508 iseq2comem.c: In function ‘reads2mco’: 2026-03-06T09:13:16,509 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,510 156 | if (base > TL) { 2026-03-06T09:13:16,510 | ^ 2026-03-06T09:13:16,511 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,512 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-06T09:13:16,513 | ^~ 2026-03-06T09:13:16,513 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,514 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-06T09:13:16,514 | ^ 2026-03-06T09:13:16,515 iseq2comem.c: In function ‘fasta2co’: 2026-03-06T09:13:16,516 iseq2comem.c:213:69: warning: too many arguments for format [-Wformat-extra-args] 2026-03-06T09:13:16,516 213 | if ((infp = popen(fas_fname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2026-03-06T09:13:16,517 | ^~~~~~~~~~~~~~~ 2026-03-06T09:13:16,517 iseq2comem.c:219:69: warning: too many arguments for format [-Wformat-extra-args] 2026-03-06T09:13:16,518 219 | if ((infp = popen(fas_fname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2026-03-06T09:13:16,518 | ^~~~~~~~~~~~~~~ 2026-03-06T09:13:16,519 iseq2comem.c:261:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,519 261 | if (base > TL) { 2026-03-06T09:13:16,520 | ^ 2026-03-06T09:13:16,521 iseq2comem.c:265:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,521 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-06T09:13:16,522 | ^~ 2026-03-06T09:13:16,523 iseq2comem.c:265:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,524 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-06T09:13:16,524 | ^ 2026-03-06T09:13:16,525 iseq2comem.c: In function ‘fastq2co’: 2026-03-06T09:13:16,526 iseq2comem.c:295:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2026-03-06T09:13:16,527 295 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2026-03-06T09:13:16,527 | ^~ 2026-03-06T09:13:16,528 iseq2comem.c:307:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-06T09:13:16,528 307 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2026-03-06T09:13:16,529 | ^~~~~~~~~~~~~~~ 2026-03-06T09:13:16,530 iseq2comem.c:313:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-06T09:13:16,530 313 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2026-03-06T09:13:16,531 | ^~~~~~~~~~~~~~~ 2026-03-06T09:13:16,532 iseq2comem.c:352:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,532 352 | if (base > TL) { 2026-03-06T09:13:16,533 | ^ 2026-03-06T09:13:16,534 iseq2comem.c:356:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,535 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-06T09:13:16,536 | ^~ 2026-03-06T09:13:16,536 iseq2comem.c:356:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,537 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-06T09:13:16,538 | ^ 2026-03-06T09:13:16,538 iseq2comem.c:375:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,539 375 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2026-03-06T09:13:16,539 | ^ 2026-03-06T09:13:16,539 iseq2comem.c: In function ‘fastq2koc’: 2026-03-06T09:13:16,540 iseq2comem.c:403:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-06T09:13:16,541 403 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2026-03-06T09:13:16,541 | ^~~~~~~~~~~~~~~~ 2026-03-06T09:13:16,543 iseq2comem.c:409:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-06T09:13:16,543 409 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2026-03-06T09:13:16,544 | ^~~~~~~~~~~~~~~~ 2026-03-06T09:13:16,544 iseq2comem.c:448:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,545 448 | if (base > TL) { 2026-03-06T09:13:16,546 | ^ 2026-03-06T09:13:16,546 iseq2comem.c:452:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,547 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-06T09:13:16,548 | ^~ 2026-03-06T09:13:16,549 iseq2comem.c:452:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,549 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-06T09:13:16,550 | ^ 2026-03-06T09:13:16,551 iseq2comem.c: In function ‘mt_shortreads2koc’: 2026-03-06T09:13:16,551 iseq2comem.c:628:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,552 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-06T09:13:16,553 | ^~ 2026-03-06T09:13:16,553 iseq2comem.c:628:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-06T09:13:16,554 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-06T09:13:16,555 | ^ 2026-03-06T09:13:17,933 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 2026-03-06T09:13:17,988 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 2026-03-06T09:13:18,113 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 2026-03-06T09:13:18,543 pykssd.c: In function ‘py_dist_dispatch’: 2026-03-06T09:13:18,543 pykssd.c:436:13: warning: unused variable ‘state1’ [-Wunused-variable] 2026-03-06T09:13:18,544 436 | int state1 = dist_dispatch(&dist_opt_val1); 2026-03-06T09:13:18,544 | ^~~~~~ 2026-03-06T09:13:18,545 pykssd.c:501:13: warning: unused variable ‘state2’ [-Wunused-variable] 2026-03-06T09:13:18,545 501 | int state2 = dist_dispatch(&dist_opt_val2); 2026-03-06T09:13:18,546 | ^~~~~~ 2026-03-06T09:13:18,547 pykssd.c:635:13: warning: unused variable ‘state4’ [-Wunused-variable] 2026-03-06T09:13:18,548 635 | int state4 = dist_dispatch(&dist_opt_val4); 2026-03-06T09:13:18,548 | ^~~~~~ 2026-03-06T09:13:19,318 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 2026-03-06T09:13:19,492 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-03-06T09:13:19,492 !! 2026-03-06T09:13:19,493 ******************************************************************************** 2026-03-06T09:13:19,494 Please avoid running ``setup.py`` directly. 2026-03-06T09:13:19,495 Instead, use pypa/build, pypa/installer or other 2026-03-06T09:13:19,495 standards-based tools. 2026-03-06T09:13:19,496 This deprecation is overdue, please update your project and remove deprecated 2026-03-06T09:13:19,497 calls to avoid build errors in the future. 2026-03-06T09:13:19,498 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-03-06T09:13:19,499 ******************************************************************************** 2026-03-06T09:13:19,500 !! 2026-03-06T09:13:19,501 self.initialize_options() 2026-03-06T09:13:19,520 installing to build/bdist.linux-armv7l/wheel 2026-03-06T09:13:19,521 running install 2026-03-06T09:13:19,545 running install_lib 2026-03-06T09:13:19,575 creating build/bdist.linux-armv7l/wheel 2026-03-06T09:13:19,578 copying build/lib.linux-armv7l-cpython-311/kssdtool.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2026-03-06T09:13:19,625 copying build/lib.linux-armv7l-cpython-311/kssdutils.py -> build/bdist.linux-armv7l/wheel/. 2026-03-06T09:13:19,628 running install_egg_info 2026-03-06T09:13:19,663 Copying kssdutils.egg-info to build/bdist.linux-armv7l/wheel/./kssdutils-1.2.0-py3.11.egg-info 2026-03-06T09:13:19,673 running install_scripts 2026-03-06T09:13:19,719 creating build/bdist.linux-armv7l/wheel/kssdutils-1.2.0.dist-info/WHEEL 2026-03-06T09:13:19,722 creating '/tmp/pip-wheel-027zqubc/kssdutils-1.2.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-03-06T09:13:19,805 adding 'kssdtool.cpython-311-arm-linux-gnueabihf.so' 2026-03-06T09:13:19,810 adding 'kssdutils.py' 2026-03-06T09:13:19,812 adding 'kssdutils-1.2.0.dist-info/METADATA' 2026-03-06T09:13:19,814 adding 'kssdutils-1.2.0.dist-info/WHEEL' 2026-03-06T09:13:19,815 adding 'kssdutils-1.2.0.dist-info/dependency_links.txt' 2026-03-06T09:13:19,817 adding 'kssdutils-1.2.0.dist-info/top_level.txt' 2026-03-06T09:13:19,818 adding 'kssdutils-1.2.0.dist-info/RECORD' 2026-03-06T09:13:19,822 removing build/bdist.linux-armv7l/wheel 2026-03-06T09:13:19,999 Building wheel for kssdutils (setup.py): finished with status 'done' 2026-03-06T09:13:20,004 Created wheel for kssdutils: filename=kssdutils-1.2.0-cp311-cp311-linux_armv7l.whl size=180841 sha256=f4620cb11cd680f7dcbbd7744c03dee2183ec0a4c4c6abd29bc599c70af26d1d 2026-03-06T09:13:20,005 Stored in directory: /tmp/pip-ephem-wheel-cache-enzmdtro/wheels/48/c3/03/ca99b28637ecc50e618b963bae2fc94d597b9b9f312de721d5 2026-03-06T09:13:20,014 Successfully built kssdutils 2026-03-06T09:13:20,024 Removed build tracker: '/tmp/pip-build-tracker-ll0vs543'