2025-09-18T02:13:46,577 Created temporary directory: /tmp/pip-ephem-wheel-cache-gz1_7aon 2025-09-18T02:13:46,582 Created temporary directory: /tmp/pip-build-tracker-ii8ic59h 2025-09-18T02:13:46,583 Initialized build tracking at /tmp/pip-build-tracker-ii8ic59h 2025-09-18T02:13:46,584 Created build tracker: /tmp/pip-build-tracker-ii8ic59h 2025-09-18T02:13:46,585 Entered build tracker: /tmp/pip-build-tracker-ii8ic59h 2025-09-18T02:13:46,587 Created temporary directory: /tmp/pip-wheel-4s7i62e5 2025-09-18T02:13:46,590 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 2025-09-18T02:13:46,593 Created temporary directory: /tmp/pip-ephem-wheel-cache-w9tcrahu 2025-09-18T02:13:46,616 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-18T02:13:46,619 2 location(s) to search for versions of kssdutils: 2025-09-18T02:13:46,619 * https://pypi.org/simple/kssdutils/ 2025-09-18T02:13:46,619 * https://www.piwheels.org/simple/kssdutils/ 2025-09-18T02:13:46,620 Fetching project page and analyzing links: https://pypi.org/simple/kssdutils/ 2025-09-18T02:13:46,621 Getting page https://pypi.org/simple/kssdutils/ 2025-09-18T02:13:46,623 Found index url https://pypi.org/simple 2025-09-18T02:13:46,843 Fetched page https://pypi.org/simple/kssdutils/ as application/vnd.pypi.simple.v1+json 2025-09-18T02:13:46,846 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 2025-09-18T02:13:46,847 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 2025-09-18T02:13:46,848 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 2025-09-18T02:13:46,849 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 2025-09-18T02:13:46,849 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 2025-09-18T02:13:46,850 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 2025-09-18T02:13:46,851 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 2025-09-18T02:13:46,852 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 2025-09-18T02:13:46,853 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 2025-09-18T02:13:46,854 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 2025-09-18T02:13:46,854 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 2025-09-18T02:13:46,855 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 2025-09-18T02:13:46,857 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 2025-09-18T02:13:46,857 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdutils/ 2025-09-18T02:13:46,858 Getting page https://www.piwheels.org/simple/kssdutils/ 2025-09-18T02:13:46,859 Found index url https://www.piwheels.org/simple 2025-09-18T02:13:47,023 Fetched page https://www.piwheels.org/simple/kssdutils/ as text/html 2025-09-18T02:13:47,035 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.5-cp311-cp311-linux_armv6l.whl#sha256=954571c31f45999b6eeb2cc007104d4a864f065c6aac3ff584a2e5d01fe7d22f (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,036 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.5-cp311-cp311-linux_armv7l.whl#sha256=954571c31f45999b6eeb2cc007104d4a864f065c6aac3ff584a2e5d01fe7d22f (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,037 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.1.5-cp39-cp39-linux_armv6l.whl#sha256=109623235074cfc937bce9a38d6d20bcf42003659045c0bda63bb091408c003d (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,037 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.1.5-cp39-cp39-linux_armv7l.whl#sha256=109623235074cfc937bce9a38d6d20bcf42003659045c0bda63bb091408c003d (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,038 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.4-cp311-cp311-linux_armv6l.whl#sha256=887ef39ec2c7cd34700ce800859855937714cdcebb02dcbd1c99aa7266df6c1b (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,038 Skipping link: No binaries permitted for kssdutils: 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https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.0-cp311-cp311-linux_armv7l.whl#sha256=0c8e77f57ec908176d8961c597a98abc9259dee9141399da1712be9b1d560bc8 (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,045 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.1.0-cp39-cp39-linux_armv6l.whl#sha256=8a0994f4f968bd25192b59f99dc7d482fae725cc841190d55a79c2ec3c47e0cd (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,046 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.1.0-cp39-cp39-linux_armv7l.whl#sha256=8a0994f4f968bd25192b59f99dc7d482fae725cc841190d55a79c2ec3c47e0cd (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,046 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.7-cp311-cp311-linux_armv6l.whl#sha256=c45bd36d62b251ee659d4aeaaca8255ff10d29d84edaf2551a0fed903f1a5fe3 (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,047 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.7-cp311-cp311-linux_armv7l.whl#sha256=c45bd36d62b251ee659d4aeaaca8255ff10d29d84edaf2551a0fed903f1a5fe3 (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,048 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.7-cp39-cp39-linux_armv6l.whl#sha256=fcc578373bf2b252b22da188e4ca939bebcc53786b1f302a901a5cf261df624e (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,048 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.7-cp39-cp39-linux_armv7l.whl#sha256=fcc578373bf2b252b22da188e4ca939bebcc53786b1f302a901a5cf261df624e (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,049 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.6-cp311-cp311-linux_armv6l.whl#sha256=24cea74c37c72ec3f541e6eca026f6a906455d0e0160dc7d0f4526ab89a58125 (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,049 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.6-cp311-cp311-linux_armv7l.whl#sha256=24cea74c37c72ec3f541e6eca026f6a906455d0e0160dc7d0f4526ab89a58125 (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,050 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.6-cp39-cp39-linux_armv6l.whl#sha256=bfe64af80d2aab63dccf6fb0418e3b806f4ee1b2fcff0eab77094040d2b6dca5 (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,050 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/) 2025-09-18T02:13:47,051 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/) 2025-09-18T02:13:47,051 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/) 2025-09-18T02:13:47,051 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/) 2025-09-18T02:13:47,052 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/) 2025-09-18T02:13:47,052 Skipping link: No binaries permitted for kssdutils: 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https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp39-cp39-linux_armv6l.whl#sha256=29a695a62aae6fa18fcad3ae6bfc6bbe19f545f66740fde177ddbf23efa45d15 (from https://www.piwheels.org/simple/kssdutils/) 2025-09-18T02:13:47,056 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/) 2025-09-18T02:13:47,057 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/) 2025-09-18T02:13:47,057 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/) 2025-09-18T02:13:47,058 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/) 2025-09-18T02:13:47,058 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/) 2025-09-18T02:13:47,059 Skipping link: not a file: https://www.piwheels.org/simple/kssdutils/ 2025-09-18T02:13:47,059 Skipping link: not a file: https://pypi.org/simple/kssdutils/ 2025-09-18T02:13:47,080 Given no hashes to check 1 links for project 'kssdutils': discarding no candidates 2025-09-18T02:13:47,098 Collecting kssdutils==1.1.7 2025-09-18T02:13:47,100 Created temporary directory: /tmp/pip-unpack-9m0fxk73 2025-09-18T02:13:47,323 Downloading kssdutils-1.1.7.tar.gz (47 kB) 2025-09-18T02:13:47,437 Added kssdutils==1.1.7 from https://files.pythonhosted.org/packages/c3/44/c52bfc36ee73ebbc978099403a176e76446f23b1691c9df71bd38bbe6430/kssdutils-1.1.7.tar.gz to build tracker '/tmp/pip-build-tracker-ii8ic59h' 2025-09-18T02:13:47,438 Running setup.py (path:/tmp/pip-wheel-4s7i62e5/kssdutils_8aadbefaf8004d4c813157d6a1d66fb3/setup.py) egg_info for package kssdutils 2025-09-18T02:13:47,439 Created temporary directory: /tmp/pip-pip-egg-info-yl586cy_ 2025-09-18T02:13:47,440 Preparing metadata (setup.py): started 2025-09-18T02:13:47,441 Running command python setup.py egg_info 2025-09-18T02:13:48,292 running egg_info 2025-09-18T02:13:48,319 creating /tmp/pip-pip-egg-info-yl586cy_/kssdutils.egg-info 2025-09-18T02:13:48,320 writing /tmp/pip-pip-egg-info-yl586cy_/kssdutils.egg-info/PKG-INFO 2025-09-18T02:13:48,323 writing dependency_links to /tmp/pip-pip-egg-info-yl586cy_/kssdutils.egg-info/dependency_links.txt 2025-09-18T02:13:48,325 writing requirements to /tmp/pip-pip-egg-info-yl586cy_/kssdutils.egg-info/requires.txt 2025-09-18T02:13:48,326 writing top-level names to /tmp/pip-pip-egg-info-yl586cy_/kssdutils.egg-info/top_level.txt 2025-09-18T02:13:48,327 writing manifest file '/tmp/pip-pip-egg-info-yl586cy_/kssdutils.egg-info/SOURCES.txt' 2025-09-18T02:13:48,436 reading manifest file '/tmp/pip-pip-egg-info-yl586cy_/kssdutils.egg-info/SOURCES.txt' 2025-09-18T02:13:48,438 reading manifest template 'MANIFEST.in' 2025-09-18T02:13:48,446 writing manifest file '/tmp/pip-pip-egg-info-yl586cy_/kssdutils.egg-info/SOURCES.txt' 2025-09-18T02:13:48,551 Preparing metadata (setup.py): finished with status 'done' 2025-09-18T02:13:48,555 Source in /tmp/pip-wheel-4s7i62e5/kssdutils_8aadbefaf8004d4c813157d6a1d66fb3 has version 1.1.7, which satisfies requirement kssdutils==1.1.7 from https://files.pythonhosted.org/packages/c3/44/c52bfc36ee73ebbc978099403a176e76446f23b1691c9df71bd38bbe6430/kssdutils-1.1.7.tar.gz 2025-09-18T02:13:48,556 Removed kssdutils==1.1.7 from https://files.pythonhosted.org/packages/c3/44/c52bfc36ee73ebbc978099403a176e76446f23b1691c9df71bd38bbe6430/kssdutils-1.1.7.tar.gz from build tracker '/tmp/pip-build-tracker-ii8ic59h' 2025-09-18T02:13:48,561 Created temporary directory: /tmp/pip-unpack-_u92hrxq 2025-09-18T02:13:48,562 Building wheels for collected packages: kssdutils 2025-09-18T02:13:48,567 Created temporary directory: /tmp/pip-wheel-i_klrhkh 2025-09-18T02:13:48,567 Building wheel for kssdutils (setup.py): started 2025-09-18T02:13:48,569 Destination directory: /tmp/pip-wheel-i_klrhkh 2025-09-18T02:13:48,569 Running command python setup.py bdist_wheel 2025-09-18T02:13:49,395 running bdist_wheel 2025-09-18T02:13:49,529 running build 2025-09-18T02:13:49,529 running build_py 2025-09-18T02:13:49,558 creating build/lib.linux-armv7l-cpython-311 2025-09-18T02:13:49,560 copying kssdutils.py -> build/lib.linux-armv7l-cpython-311 2025-09-18T02:13:49,563 running egg_info 2025-09-18T02:13:49,590 writing kssdutils.egg-info/PKG-INFO 2025-09-18T02:13:49,594 writing dependency_links to kssdutils.egg-info/dependency_links.txt 2025-09-18T02:13:49,596 writing requirements to kssdutils.egg-info/requires.txt 2025-09-18T02:13:49,597 writing top-level names to kssdutils.egg-info/top_level.txt 2025-09-18T02:13:49,627 reading manifest file 'kssdutils.egg-info/SOURCES.txt' 2025-09-18T02:13:49,630 reading manifest template 'MANIFEST.in' 2025-09-18T02:13:49,640 writing manifest file 'kssdutils.egg-info/SOURCES.txt' 2025-09-18T02:13:49,642 running build_ext 2025-09-18T02:13:50,163 building 'kssdtool' extension 2025-09-18T02:13:50,164 creating build/temp.linux-armv7l-cpython-311 2025-09-18T02:13:50,166 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c co2mco.c -o build/temp.linux-armv7l-cpython-311/co2mco.o -fopenmp 2025-09-18T02:13:50,346 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2025-09-18T02:13:50,347 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-18T02:13:50,349 109 | for (unsigned int i = 0; i < comp_num; i++) { 2025-09-18T02:13:50,351 | ^ 2025-09-18T02:13:50,352 co2mco.c: In function ‘co2unitllmco’: 2025-09-18T02:13:50,353 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-18T02:13:50,354 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2025-09-18T02:13:50,355 | ^ 2025-09-18T02:13:51,065 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_composite.c -o build/temp.linux-armv7l-cpython-311/command_composite.o -fopenmp 2025-09-18T02:13:51,441 command_composite.c: In function ‘get_species_abundance’: 2025-09-18T02:13:51,442 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2025-09-18T02:13:51,443 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2025-09-18T02:13:51,443 | ^~ 2025-09-18T02:13:51,444 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2025-09-18T02:13:51,445 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2025-09-18T02:13:51,445 | ^~ 2025-09-18T02:13:51,446 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:51,447 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-09-18T02:13:51,447 | ^ 2025-09-18T02:13:51,448 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:51,449 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-09-18T02:13:51,449 | ^~~~~~~~~~ 2025-09-18T02:13:51,450 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-09-18T02:13:51,451 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-09-18T02:13:51,451 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:51,452 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:51,452 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-09-18T02:13:51,453 | ^ 2025-09-18T02:13:51,454 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:51,454 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-09-18T02:13:51,454 | ^~~~~~~~~~ 2025-09-18T02:13:51,455 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-09-18T02:13:51,456 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-09-18T02:13:51,456 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:51,457 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:51,457 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-09-18T02:13:51,458 | ^ 2025-09-18T02:13:51,459 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:51,459 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-09-18T02:13:51,460 | ^~~~~~~~~~ 2025-09-18T02:13:51,460 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-09-18T02:13:51,461 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-09-18T02:13:51,461 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:51,462 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:51,462 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-09-18T02:13:51,463 | ^ 2025-09-18T02:13:51,464 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:51,464 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-09-18T02:13:51,465 | ^~~~~~~~~~ 2025-09-18T02:13:51,466 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2025-09-18T02:13:51,466 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-09-18T02:13:51,467 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:51,468 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:51,468 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-09-18T02:13:51,469 | ^ 2025-09-18T02:13:51,470 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:51,470 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-09-18T02:13:51,471 | ^~~~~~~~~~~~ 2025-09-18T02:13:51,472 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2025-09-18T02:13:51,472 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-09-18T02:13:51,473 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:51,698 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist.c -o build/temp.linux-armv7l-cpython-311/command_dist.o -fopenmp 2025-09-18T02:13:51,979 command_dist.c: In function ‘mco_cbd_co_dist’: 2025-09-18T02:13:51,980 command_dist.c:677:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-09-18T02:13:51,980 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-09-18T02:13:51,981 | ~~^ 2025-09-18T02:13:51,981 | | 2025-09-18T02:13:51,982 | long unsigned int 2025-09-18T02:13:51,982 | %u 2025-09-18T02:13:51,982 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-09-18T02:13:51,983 | ~~~~~~~ 2025-09-18T02:13:51,983 | | 2025-09-18T02:13:51,984 | size_t {aka unsigned int} 2025-09-18T02:13:51,984 command_dist.c:677:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-09-18T02:13:51,985 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-09-18T02:13:51,986 | ~~^ 2025-09-18T02:13:51,986 | | 2025-09-18T02:13:51,987 | long unsigned int 2025-09-18T02:13:51,987 | %u 2025-09-18T02:13:51,988 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-09-18T02:13:51,988 679 | maplength, (size_t) b * unitsz_distf_mapped); 2025-09-18T02:13:51,989 | ~~~~~~~~~ 2025-09-18T02:13:51,990 | | 2025-09-18T02:13:51,990 | size_t {aka unsigned int} 2025-09-18T02:13:51,991 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-09-18T02:13:51,991 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-09-18T02:13:51,992 | ~~^ 2025-09-18T02:13:51,993 | | 2025-09-18T02:13:51,993 | long unsigned int 2025-09-18T02:13:51,994 | %u 2025-09-18T02:13:51,994 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-09-18T02:13:51,995 679 | maplength, (size_t) b * unitsz_distf_mapped); 2025-09-18T02:13:51,995 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:51,996 | | 2025-09-18T02:13:51,996 | unsigned int 2025-09-18T02:13:51,997 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-18T02:13:51,997 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2025-09-18T02:13:51,998 | ^ 2025-09-18T02:13:51,998 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2025-09-18T02:13:51,999 command_dist.c:863:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-09-18T02:13:51,999 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-09-18T02:13:51,999 | ~~^ ~~~~~~~ 2025-09-18T02:13:52,000 | | | 2025-09-18T02:13:52,000 | long unsigned int size_t {aka unsigned int} 2025-09-18T02:13:52,001 | %u 2025-09-18T02:13:52,001 command_dist.c:863:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-09-18T02:13:52,002 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-09-18T02:13:52,002 | ~~^ 2025-09-18T02:13:52,002 | | 2025-09-18T02:13:52,003 | long unsigned int 2025-09-18T02:13:52,003 | %u 2025-09-18T02:13:52,004 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2025-09-18T02:13:52,005 | ~~~~~~~~~ 2025-09-18T02:13:52,005 | | 2025-09-18T02:13:52,006 | size_t {aka unsigned int} 2025-09-18T02:13:52,007 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-09-18T02:13:52,007 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-09-18T02:13:52,008 | ~~^ 2025-09-18T02:13:52,008 | | 2025-09-18T02:13:52,008 | long unsigned int 2025-09-18T02:13:52,009 | %u 2025-09-18T02:13:52,009 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2025-09-18T02:13:52,010 865 | (size_t) b * unitsz_distf_mapped); 2025-09-18T02:13:52,011 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:52,011 | | 2025-09-18T02:13:52,012 | unsigned int 2025-09-18T02:13:52,013 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2025-09-18T02:13:52,013 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2025-09-18T02:13:52,014 | ^~~~~~~ 2025-09-18T02:13:52,014 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2025-09-18T02:13:52,015 809 | struct stat cbd_fcode_stat; 2025-09-18T02:13:52,015 | ^~~~~~~~~~~~~~ 2025-09-18T02:13:52,016 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2025-09-18T02:13:52,016 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2025-09-18T02:13:52,017 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:52,018 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2025-09-18T02:13:52,018 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2025-09-18T02:13:52,019 | ^~~~~~~~~~~~~~~~~ 2025-09-18T02:13:52,019 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2025-09-18T02:13:52,020 command_dist.c:1018:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-09-18T02:13:52,021 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-09-18T02:13:52,021 | ~~^ 2025-09-18T02:13:52,022 | | 2025-09-18T02:13:52,022 | long unsigned int 2025-09-18T02:13:52,023 | %u 2025-09-18T02:13:52,023 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-09-18T02:13:52,023 | ~~~~~~~ 2025-09-18T02:13:52,024 | | 2025-09-18T02:13:52,024 | size_t {aka unsigned int} 2025-09-18T02:13:52,025 command_dist.c:1018:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-09-18T02:13:52,025 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-09-18T02:13:52,026 | ~~^ 2025-09-18T02:13:52,027 | | 2025-09-18T02:13:52,027 | long unsigned int 2025-09-18T02:13:52,028 | %u 2025-09-18T02:13:52,028 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-09-18T02:13:52,029 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2025-09-18T02:13:52,030 | ~~~~~~~~~ 2025-09-18T02:13:52,030 | | 2025-09-18T02:13:52,031 | size_t {aka unsigned int} 2025-09-18T02:13:52,031 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-09-18T02:13:52,032 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-09-18T02:13:52,033 | ~~^ 2025-09-18T02:13:52,033 | | 2025-09-18T02:13:52,034 | long unsigned int 2025-09-18T02:13:52,034 | %u 2025-09-18T02:13:52,035 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-09-18T02:13:52,036 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2025-09-18T02:13:52,036 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:52,037 | | 2025-09-18T02:13:52,037 | unsigned int 2025-09-18T02:13:52,038 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2025-09-18T02:13:52,038 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2025-09-18T02:13:52,039 | ^ 2025-09-18T02:13:52,040 command_dist.c: In function ‘mco_co_dist_core’: 2025-09-18T02:13:52,040 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-18T02:13:52,041 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2025-09-18T02:13:52,041 | ^ 2025-09-18T02:13:52,042 command_dist.c: In function ‘koc_dist_print_nobin’: 2025-09-18T02:13:52,043 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-18T02:13:52,044 1239 | for (int rid = 0; rid < ref_num; rid++) 2025-09-18T02:13:52,044 | ^ 2025-09-18T02:13:52,045 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-18T02:13:52,046 1245 | for (int rid = 0; rid < ref_num; rid++) { 2025-09-18T02:13:52,046 | ^ 2025-09-18T02:13:52,052 command_dist.c: In function ‘dist_print_nobin’: 2025-09-18T02:13:52,053 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-18T02:13:52,054 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2025-09-18T02:13:52,054 | ^ 2025-09-18T02:13:52,056 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-18T02:13:52,057 1356 | for (int rid = 0; rid < ref_num; rid++) { 2025-09-18T02:13:52,058 | ^ 2025-09-18T02:13:52,059 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-18T02:13:52,059 1382 | for (int rid = 0; rid < ref_num; rid++) 2025-09-18T02:13:52,060 | ^ 2025-09-18T02:13:52,420 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2025-09-18T02:13:52,420 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-18T02:13:52,421 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2025-09-18T02:13:52,422 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:52,423 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2025-09-18T02:13:52,423 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2025-09-18T02:13:52,424 | ^~~~~~~~~~~~ 2025-09-18T02:13:53,291 command_dist.c: In function ‘get_dim_shuffle’: 2025-09-18T02:13:53,291 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2025-09-18T02:13:53,292 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2025-09-18T02:13:53,292 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:53,293 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2025-09-18T02:13:53,293 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2025-09-18T02:13:53,294 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,195 command_dist.c: In function ‘mco_cbd_co_dist’: 2025-09-18T02:13:54,196 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:54,196 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-09-18T02:13:54,197 | ^~ ~~~~~~~~~ 2025-09-18T02:13:54,197 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-09-18T02:13:54,197 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-09-18T02:13:54,198 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,199 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-09-18T02:13:54,199 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-09-18T02:13:54,200 | ^~~~~~~~~~~~~~~ 2025-09-18T02:13:54,200 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-09-18T02:13:54,201 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-09-18T02:13:54,201 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,202 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-09-18T02:13:54,202 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-09-18T02:13:54,203 | ^~~~~~~~~~~ 2025-09-18T02:13:54,203 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:54,204 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-09-18T02:13:54,204 | ^~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,205 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2025-09-18T02:13:54,205 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-09-18T02:13:54,206 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,207 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-09-18T02:13:54,207 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-09-18T02:13:54,208 | ^~~~~ 2025-09-18T02:13:54,208 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:54,209 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-09-18T02:13:54,210 | ^~~~~~~~~~~ 2025-09-18T02:13:54,210 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-09-18T02:13:54,211 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-09-18T02:13:54,212 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,446 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2025-09-18T02:13:54,447 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:54,447 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-09-18T02:13:54,448 | ^~ ~~~~~~~~~ 2025-09-18T02:13:54,448 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-09-18T02:13:54,448 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-09-18T02:13:54,449 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,449 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-09-18T02:13:54,450 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-09-18T02:13:54,450 | ^~~~~~~~~~~~~~~ 2025-09-18T02:13:54,451 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-09-18T02:13:54,451 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-09-18T02:13:54,452 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,452 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-09-18T02:13:54,453 823 | sprintf(distf, "%s/distance.out", distout_dir); 2025-09-18T02:13:54,453 | ^~~~~~~~~~~~~ 2025-09-18T02:13:54,454 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-09-18T02:13:54,454 823 | sprintf(distf, "%s/distance.out", distout_dir); 2025-09-18T02:13:54,455 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,455 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:54,456 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-09-18T02:13:54,456 | ^ 2025-09-18T02:13:54,457 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2025-09-18T02:13:54,457 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-09-18T02:13:54,458 | ^~~~~~~~~~ 2025-09-18T02:13:54,458 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2025-09-18T02:13:54,459 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-09-18T02:13:54,460 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,460 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:54,461 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-09-18T02:13:54,461 | ^ 2025-09-18T02:13:54,462 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2025-09-18T02:13:54,463 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-09-18T02:13:54,463 | ^~~~~~~~~~ 2025-09-18T02:13:54,464 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2025-09-18T02:13:54,465 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-09-18T02:13:54,465 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,732 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2025-09-18T02:13:54,733 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:54,734 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-09-18T02:13:54,734 | ^~ ~~~~~~~~~ 2025-09-18T02:13:54,734 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-09-18T02:13:54,735 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-09-18T02:13:54,735 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,736 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-09-18T02:13:54,736 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-09-18T02:13:54,737 | ^~~~~~~~~~~~~~~ 2025-09-18T02:13:54,737 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-09-18T02:13:54,738 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-09-18T02:13:54,738 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,738 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-09-18T02:13:54,739 990 | sprintf(distf, "%s/distance.out", distout_dir); 2025-09-18T02:13:54,740 | ^~~~~~~~~~~~~ 2025-09-18T02:13:54,740 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-09-18T02:13:54,740 990 | sprintf(distf, "%s/distance.out", distout_dir); 2025-09-18T02:13:54,741 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,742 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-09-18T02:13:54,742 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-09-18T02:13:54,742 | ^~~~~~~~~~~ 2025-09-18T02:13:54,743 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:54,743 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-09-18T02:13:54,744 | ^~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,744 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2025-09-18T02:13:54,745 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-09-18T02:13:54,745 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:54,746 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-09-18T02:13:54,746 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-09-18T02:13:54,747 | ^~~~~ 2025-09-18T02:13:54,747 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:54,748 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-09-18T02:13:54,748 | ^~~~~~~~~~~ 2025-09-18T02:13:54,749 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-09-18T02:13:54,749 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-09-18T02:13:54,750 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:55,022 command_dist.c: In function ‘combine_queries’: 2025-09-18T02:13:55,023 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-09-18T02:13:55,024 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2025-09-18T02:13:55,024 | ^ 2025-09-18T02:13:55,025 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-09-18T02:13:55,025 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2025-09-18T02:13:55,026 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:55,027 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-09-18T02:13:55,027 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2025-09-18T02:13:55,028 | ^ 2025-09-18T02:13:55,028 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-09-18T02:13:55,029 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2025-09-18T02:13:55,029 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:55,031 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:55,032 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2025-09-18T02:13:55,032 | ^~ ~~~~~~~~ 2025-09-18T02:13:55,033 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-09-18T02:13:55,033 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2025-09-18T02:13:55,034 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:55,533 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o -fopenmp 2025-09-18T02:13:55,725 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_set.c -o build/temp.linux-armv7l-cpython-311/command_set.o -fopenmp 2025-09-18T02:13:55,925 command_set.c: In function ‘sketch_operate’: 2025-09-18T02:13:55,925 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-18T02:13:55,926 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2025-09-18T02:13:55,927 | ^ 2025-09-18T02:13:55,938 command_set.c: In function ‘combin_subset_pans’: 2025-09-18T02:13:55,939 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2025-09-18T02:13:55,939 457 | free(co_dstat_fpath); 2025-09-18T02:13:55,940 | ^~~~~~~~~~~~~~ 2025-09-18T02:13:55,941 In file included from kssdheaders/global_basic.h:159, 2025-09-18T02:13:55,941 from command_set.c:15: 2025-09-18T02:13:55,942 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2025-09-18T02:13:55,942 568 | extern void free (void *__ptr) __THROW; 2025-09-18T02:13:55,943 | ~~~~~~^~~~~ 2025-09-18T02:13:55,946 command_set.c: In function ‘grouping_genomes’: 2025-09-18T02:13:55,946 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2025-09-18T02:13:55,947 562 | free(co_dstat_fpath); 2025-09-18T02:13:55,947 | ^~~~~~~~~~~~~~ 2025-09-18T02:13:55,948 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2025-09-18T02:13:55,948 568 | extern void free (void *__ptr) __THROW; 2025-09-18T02:13:55,949 | ~~~~~~^~~~~ 2025-09-18T02:13:56,114 command_set.c: In function ‘sketch_union’: 2025-09-18T02:13:56,115 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-09-18T02:13:56,115 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:56,116 | ^ 2025-09-18T02:13:56,116 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-09-18T02:13:56,117 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:56,117 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,118 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,118 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-09-18T02:13:56,119 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:56,119 command_set.c:82:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,120 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-09-18T02:13:56,120 | ^~~~~~~~~~ 2025-09-18T02:13:56,121 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-09-18T02:13:56,121 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-09-18T02:13:56,122 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,123 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,123 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-09-18T02:13:56,124 | ^~ ~~~~~~~~~~ 2025-09-18T02:13:56,124 command_set.c:92:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,125 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-09-18T02:13:56,126 | ^~~~~~~~~~ 2025-09-18T02:13:56,126 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-09-18T02:13:56,127 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-09-18T02:13:56,127 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,245 command_set.c: In function ‘sketch_operate’: 2025-09-18T02:13:56,246 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,246 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-09-18T02:13:56,247 | ^~ ~~~~~~~~~~ 2025-09-18T02:13:56,247 command_set.c:153:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,248 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-09-18T02:13:56,248 | ^~~~~~~~~~ 2025-09-18T02:13:56,249 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-09-18T02:13:56,249 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-09-18T02:13:56,250 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,251 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,251 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-09-18T02:13:56,252 | ^~ ~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,252 command_set.c:155:29: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,253 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-09-18T02:13:56,254 | ^~~~~~~~~~ 2025-09-18T02:13:56,254 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2025-09-18T02:13:56,255 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-09-18T02:13:56,255 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,256 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,256 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-09-18T02:13:56,257 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:56,257 command_set.c:165:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,258 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-09-18T02:13:56,258 | ^~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,259 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-09-18T02:13:56,260 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-09-18T02:13:56,260 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,261 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,261 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-09-18T02:13:56,262 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:56,262 command_set.c:169:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,263 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-09-18T02:13:56,264 | ^~~~~~~~~~ 2025-09-18T02:13:56,264 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-09-18T02:13:56,265 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-09-18T02:13:56,265 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,266 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,266 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-09-18T02:13:56,267 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:56,268 command_set.c:174:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,268 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-09-18T02:13:56,269 | ^~~~~~~~~~ 2025-09-18T02:13:56,269 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-09-18T02:13:56,270 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-09-18T02:13:56,271 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,271 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,272 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-09-18T02:13:56,272 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:56,273 command_set.c:187:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,273 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-09-18T02:13:56,274 | ^~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,274 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-09-18T02:13:56,275 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-09-18T02:13:56,275 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,276 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-09-18T02:13:56,277 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:56,277 | ^ 2025-09-18T02:13:56,278 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-09-18T02:13:56,278 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:56,279 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,419 command_set.c: In function ‘uniq_sketch_union’: 2025-09-18T02:13:56,420 command_set.c:219:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-09-18T02:13:56,420 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2025-09-18T02:13:56,421 | ^ 2025-09-18T02:13:56,422 command_set.c:219:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2025-09-18T02:13:56,422 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2025-09-18T02:13:56,423 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,423 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-09-18T02:13:56,424 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:56,425 | ^ 2025-09-18T02:13:56,425 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-09-18T02:13:56,426 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:56,427 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,427 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,428 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-09-18T02:13:56,428 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:56,429 command_set.c:247:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,430 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-09-18T02:13:56,430 | ^~~~~~~~~~ 2025-09-18T02:13:56,431 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-09-18T02:13:56,431 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-09-18T02:13:56,432 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,433 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,433 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-09-18T02:13:56,434 | ^~ ~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,435 command_set.c:259:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,435 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-09-18T02:13:56,436 | ^~~~~~~~~~ 2025-09-18T02:13:56,436 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2025-09-18T02:13:56,437 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-09-18T02:13:56,437 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,565 command_set.c: In function ‘combin_pans’: 2025-09-18T02:13:56,565 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,566 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-09-18T02:13:56,566 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:56,567 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2025-09-18T02:13:56,567 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-09-18T02:13:56,568 | ^~~~~~~~~~ 2025-09-18T02:13:56,568 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2025-09-18T02:13:56,569 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-09-18T02:13:56,569 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,570 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,570 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-09-18T02:13:56,571 | ^~ ~~~~~~~~~~ 2025-09-18T02:13:56,572 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2025-09-18T02:13:56,572 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-09-18T02:13:56,573 | ^~~~~~~~~~ 2025-09-18T02:13:56,573 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2025-09-18T02:13:56,574 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-09-18T02:13:56,575 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,575 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-09-18T02:13:56,576 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:56,576 | ^ 2025-09-18T02:13:56,577 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-09-18T02:13:56,577 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:56,578 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,782 command_set.c: In function ‘combin_subset_pans’: 2025-09-18T02:13:56,783 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,783 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-09-18T02:13:56,784 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:56,784 command_set.c:469:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,785 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-09-18T02:13:56,785 | ^~~~~~~~~~ 2025-09-18T02:13:56,786 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-09-18T02:13:56,786 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-09-18T02:13:56,787 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,787 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,787 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-09-18T02:13:56,788 | ^~ ~~~~~~~~~~ 2025-09-18T02:13:56,788 command_set.c:475:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,789 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-09-18T02:13:56,789 | ^~~~~~~~~~ 2025-09-18T02:13:56,789 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-09-18T02:13:56,790 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-09-18T02:13:56,790 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,791 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,791 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-09-18T02:13:56,792 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:56,792 command_set.c:481:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,793 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-09-18T02:13:56,793 | ^~~~~~~~~~ 2025-09-18T02:13:56,794 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-09-18T02:13:56,795 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-09-18T02:13:56,795 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,796 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:56,796 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-09-18T02:13:56,797 | ^~ ~~~~~~~~~~ 2025-09-18T02:13:56,797 command_set.c:512:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:56,798 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-09-18T02:13:56,799 | ^~~~~~~~~~ 2025-09-18T02:13:56,799 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-09-18T02:13:56,800 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-09-18T02:13:56,800 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:56,801 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-09-18T02:13:56,801 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:56,802 | ^ 2025-09-18T02:13:56,802 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-09-18T02:13:56,803 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:56,804 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:57,028 command_set.c: In function ‘grouping_genomes’: 2025-09-18T02:13:57,029 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:57,029 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-09-18T02:13:57,030 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:57,030 command_set.c:574:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:57,031 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-09-18T02:13:57,031 | ^~~~~~~~~~ 2025-09-18T02:13:57,032 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-09-18T02:13:57,032 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-09-18T02:13:57,032 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:57,033 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:57,033 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-09-18T02:13:57,034 | ^~ ~~~~~~~~~~ 2025-09-18T02:13:57,034 command_set.c:580:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:57,035 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-09-18T02:13:57,035 | ^~~~~~~~~~ 2025-09-18T02:13:57,036 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-09-18T02:13:57,036 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-09-18T02:13:57,037 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:57,037 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:57,038 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-09-18T02:13:57,038 | ^~ ~~~~~~~~~~~ 2025-09-18T02:13:57,039 command_set.c:612:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:57,039 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-09-18T02:13:57,040 | ^~~~~~~~~~ 2025-09-18T02:13:57,040 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-09-18T02:13:57,041 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-09-18T02:13:57,042 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:57,042 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-09-18T02:13:57,043 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-09-18T02:13:57,044 | ^~ ~~~~~~~~~~ 2025-09-18T02:13:57,044 command_set.c:634:25: note: directive argument in the range [-2147483644, 2147483646] 2025-09-18T02:13:57,045 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-09-18T02:13:57,046 | ^~~~~~~~~~ 2025-09-18T02:13:57,046 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-09-18T02:13:57,047 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-09-18T02:13:57,047 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:57,048 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-09-18T02:13:57,049 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:57,049 | ^ 2025-09-18T02:13:57,050 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-09-18T02:13:57,050 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-09-18T02:13:57,051 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-18T02:13:57,323 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-311/command_shuffle.o -fopenmp 2025-09-18T02:13:57,637 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c global_basic.c -o build/temp.linux-armv7l-cpython-311/global_basic.o -fopenmp 2025-09-18T02:13:57,802 global_basic.c: In function ‘organize_infile_list’: 2025-09-18T02:13:57,802 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2025-09-18T02:13:57,803 195 | while (isspace(*buf)) buf++; 2025-09-18T02:13:57,803 | ^~~~~~~ 2025-09-18T02:13:57,804 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2025-09-18T02:13:57,804 34 | #include 2025-09-18T02:13:57,805 +++ |+#include 2025-09-18T02:13:57,805 35 | 2025-09-18T02:13:57,806 global_basic.c:201:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-09-18T02:13:57,806 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2025-09-18T02:13:57,807 | ~~^ 2025-09-18T02:13:57,807 | | 2025-09-18T02:13:57,808 | long unsigned int 2025-09-18T02:13:57,808 | %u 2025-09-18T02:13:57,809 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2025-09-18T02:13:57,810 | ~~~~~~~~~~~ 2025-09-18T02:13:57,810 | | 2025-09-18T02:13:57,811 | size_t {aka unsigned int} 2025-09-18T02:13:57,811 global_basic.c:233:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-09-18T02:13:57,812 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2025-09-18T02:13:57,812 | ~~^ 2025-09-18T02:13:57,813 | | 2025-09-18T02:13:57,813 | long unsigned int 2025-09-18T02:13:57,814 | %u 2025-09-18T02:13:57,815 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2025-09-18T02:13:57,815 | ~~~~~~~~~~~ 2025-09-18T02:13:57,816 | | 2025-09-18T02:13:57,816 | size_t {aka unsigned int} 2025-09-18T02:13:58,601 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-311/iseq2comem.o -fopenmp 2025-09-18T02:13:58,779 iseq2comem.c: In function ‘reads2mco’: 2025-09-18T02:13:58,780 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,781 156 | if (base > TL) { 2025-09-18T02:13:58,781 | ^ 2025-09-18T02:13:58,782 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,782 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-09-18T02:13:58,782 | ^~ 2025-09-18T02:13:58,783 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,783 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-09-18T02:13:58,784 | ^ 2025-09-18T02:13:58,785 iseq2comem.c: In function ‘fasta2co’: 2025-09-18T02:13:58,786 iseq2comem.c:213:69: warning: too many arguments for format [-Wformat-extra-args] 2025-09-18T02:13:58,786 213 | if ((infp = popen(fas_fname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2025-09-18T02:13:58,787 | ^~~~~~~~~~~~~~~ 2025-09-18T02:13:58,787 iseq2comem.c:219:68: warning: too many arguments for format [-Wformat-extra-args] 2025-09-18T02:13:58,788 219 | if ((infp = fopen(seqfname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2025-09-18T02:13:58,789 | ^~~~~~~~~~~~~~~ 2025-09-18T02:13:58,790 iseq2comem.c:261:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,791 261 | if (base > TL) { 2025-09-18T02:13:58,791 | ^ 2025-09-18T02:13:58,792 iseq2comem.c:265:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,792 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-09-18T02:13:58,793 | ^~ 2025-09-18T02:13:58,793 iseq2comem.c:265:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,794 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-09-18T02:13:58,794 | ^ 2025-09-18T02:13:58,795 iseq2comem.c: In function ‘fastq2co’: 2025-09-18T02:13:58,796 iseq2comem.c:295:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2025-09-18T02:13:58,796 295 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2025-09-18T02:13:58,797 | ^~ 2025-09-18T02:13:58,798 iseq2comem.c:307:68: warning: too many arguments for format [-Wformat-extra-args] 2025-09-18T02:13:58,798 307 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2025-09-18T02:13:58,799 | ^~~~~~~~~~~~~~~ 2025-09-18T02:13:58,799 iseq2comem.c:313:68: warning: too many arguments for format [-Wformat-extra-args] 2025-09-18T02:13:58,800 313 | if ((infp = fopen(seqfname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2025-09-18T02:13:58,800 | ^~~~~~~~~~~~~~~ 2025-09-18T02:13:58,803 iseq2comem.c:352:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,803 352 | if (base > TL) { 2025-09-18T02:13:58,804 | ^ 2025-09-18T02:13:58,804 iseq2comem.c:356:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,805 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-09-18T02:13:58,805 | ^~ 2025-09-18T02:13:58,805 iseq2comem.c:356:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,806 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-09-18T02:13:58,807 | ^ 2025-09-18T02:13:58,808 iseq2comem.c:375:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,809 375 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2025-09-18T02:13:58,809 | ^ 2025-09-18T02:13:58,811 iseq2comem.c: In function ‘fastq2koc’: 2025-09-18T02:13:58,811 iseq2comem.c:403:68: warning: too many arguments for format [-Wformat-extra-args] 2025-09-18T02:13:58,812 403 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2025-09-18T02:13:58,812 | ^~~~~~~~~~~~~~~~ 2025-09-18T02:13:58,813 iseq2comem.c:409:68: warning: too many arguments for format [-Wformat-extra-args] 2025-09-18T02:13:58,813 409 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2025-09-18T02:13:58,814 | ^~~~~~~~~~~~~~~~ 2025-09-18T02:13:58,815 iseq2comem.c:448:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,816 448 | if (base > TL) { 2025-09-18T02:13:58,816 | ^ 2025-09-18T02:13:58,817 iseq2comem.c:452:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,817 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-09-18T02:13:58,818 | ^~ 2025-09-18T02:13:58,819 iseq2comem.c:452:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,819 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-09-18T02:13:58,820 | ^ 2025-09-18T02:13:58,827 iseq2comem.c: In function ‘mt_shortreads2koc’: 2025-09-18T02:13:58,828 iseq2comem.c:628:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,828 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-09-18T02:13:58,829 | ^~ 2025-09-18T02:13:58,830 iseq2comem.c:628:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-18T02:13:58,830 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-09-18T02:13:58,831 | ^ 2025-09-18T02:14:00,223 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2025-09-18T02:14:00,277 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mytime.c -o build/temp.linux-armv7l-cpython-311/mytime.o -fopenmp 2025-09-18T02:14:00,405 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c pykssd.c -o build/temp.linux-armv7l-cpython-311/pykssd.o -fopenmp 2025-09-18T02:14:00,787 pykssd.c: In function ‘py_dist_dispatch’: 2025-09-18T02:14:00,788 pykssd.c:339:13: warning: unused variable ‘state1’ [-Wunused-variable] 2025-09-18T02:14:00,788 339 | int state1 = dist_dispatch(&dist_opt_val1); 2025-09-18T02:14:00,789 | ^~~~~~ 2025-09-18T02:14:00,790 pykssd.c:404:13: warning: unused variable ‘state2’ [-Wunused-variable] 2025-09-18T02:14:00,791 404 | int state2 = dist_dispatch(&dist_opt_val2); 2025-09-18T02:14:00,791 | ^~~~~~ 2025-09-18T02:14:00,793 pykssd.c:538:13: warning: unused variable ‘state4’ [-Wunused-variable] 2025-09-18T02:14:00,794 538 | int state4 = dist_dispatch(&dist_opt_val4); 2025-09-18T02:14:00,794 | ^~~~~~ 2025-09-18T02:14:01,443 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 2025-09-18T02:14:01,622 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-18T02:14:01,623 !! 2025-09-18T02:14:01,624 ******************************************************************************** 2025-09-18T02:14:01,625 Please avoid running ``setup.py`` directly. 2025-09-18T02:14:01,625 Instead, use pypa/build, pypa/installer or other 2025-09-18T02:14:01,626 standards-based tools. 2025-09-18T02:14:01,627 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-18T02:14:01,627 or your builds will no longer be supported. 2025-09-18T02:14:01,628 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-18T02:14:01,629 ******************************************************************************** 2025-09-18T02:14:01,630 !! 2025-09-18T02:14:01,631 self.initialize_options() 2025-09-18T02:14:01,650 installing to build/bdist.linux-armv7l/wheel 2025-09-18T02:14:01,651 running install 2025-09-18T02:14:01,674 running install_lib 2025-09-18T02:14:01,702 creating build/bdist.linux-armv7l/wheel 2025-09-18T02:14:01,704 copying build/lib.linux-armv7l-cpython-311/kssdutils.py -> build/bdist.linux-armv7l/wheel/. 2025-09-18T02:14:01,706 copying build/lib.linux-armv7l-cpython-311/kssdtool.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-09-18T02:14:01,717 running install_egg_info 2025-09-18T02:14:01,751 Copying kssdutils.egg-info to build/bdist.linux-armv7l/wheel/./kssdutils-1.1.7-py3.11.egg-info 2025-09-18T02:14:01,764 running install_scripts 2025-09-18T02:14:01,814 creating build/bdist.linux-armv7l/wheel/kssdutils-1.1.7.dist-info/WHEEL 2025-09-18T02:14:01,817 creating '/tmp/pip-wheel-i_klrhkh/kssdutils-1.1.7-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-18T02:14:01,900 adding 'kssdtool.cpython-311-arm-linux-gnueabihf.so' 2025-09-18T02:14:01,905 adding 'kssdutils.py' 2025-09-18T02:14:01,907 adding 'kssdutils-1.1.7.dist-info/METADATA' 2025-09-18T02:14:01,908 adding 'kssdutils-1.1.7.dist-info/WHEEL' 2025-09-18T02:14:01,909 adding 'kssdutils-1.1.7.dist-info/dependency_links.txt' 2025-09-18T02:14:01,910 adding 'kssdutils-1.1.7.dist-info/top_level.txt' 2025-09-18T02:14:01,911 adding 'kssdutils-1.1.7.dist-info/RECORD' 2025-09-18T02:14:01,913 removing build/bdist.linux-armv7l/wheel 2025-09-18T02:14:02,062 Building wheel for kssdutils (setup.py): finished with status 'done' 2025-09-18T02:14:02,067 Created wheel for kssdutils: filename=kssdutils-1.1.7-cp311-cp311-linux_armv7l.whl size=181635 sha256=5beb32a7772765a880c50ab75f1b8a504d6c960523a444ea7829d7fef3671c4c 2025-09-18T02:14:02,068 Stored in directory: /tmp/pip-ephem-wheel-cache-w9tcrahu/wheels/45/77/d9/03f97ba9494437a01d35aed46b73f8730e07238975cec8297d 2025-09-18T02:14:02,077 Successfully built kssdutils 2025-09-18T02:14:02,086 Removed build tracker: '/tmp/pip-build-tracker-ii8ic59h'