2026-03-05T10:00:43,461 Created temporary directory: /tmp/pip-ephem-wheel-cache-s11ea55g 2026-03-05T10:00:43,463 Created temporary directory: /tmp/pip-build-tracker-snta1cbk 2026-03-05T10:00:43,464 Initialized build tracking at /tmp/pip-build-tracker-snta1cbk 2026-03-05T10:00:43,464 Created build tracker: /tmp/pip-build-tracker-snta1cbk 2026-03-05T10:00:43,465 Entered build tracker: /tmp/pip-build-tracker-snta1cbk 2026-03-05T10:00:43,465 Created temporary directory: /tmp/pip-wheel-sbg2yfr7 2026-03-05T10:00:43,468 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 2026-03-05T10:00:43,471 Created temporary directory: /tmp/pip-ephem-wheel-cache-t4ggebbg 2026-03-05T10:00:43,493 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-03-05T10:00:43,496 2 location(s) to search for versions of kssdutils: 2026-03-05T10:00:43,496 * https://pypi.org/simple/kssdutils/ 2026-03-05T10:00:43,496 * https://www.piwheels.org/simple/kssdutils/ 2026-03-05T10:00:43,497 Fetching project page and analyzing links: https://pypi.org/simple/kssdutils/ 2026-03-05T10:00:43,498 Getting page https://pypi.org/simple/kssdutils/ 2026-03-05T10:00:43,499 Found index url https://pypi.org/simple 2026-03-05T10:00:43,710 Fetched page https://pypi.org/simple/kssdutils/ as application/vnd.pypi.simple.v1+json 2026-03-05T10:00:43,714 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 2026-03-05T10:00:43,714 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 2026-03-05T10:00:43,715 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 2026-03-05T10:00:43,716 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 2026-03-05T10:00:43,717 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 2026-03-05T10:00:43,717 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 2026-03-05T10:00:43,718 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 2026-03-05T10:00:43,719 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 2026-03-05T10:00:43,720 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 2026-03-05T10:00:43,720 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 2026-03-05T10:00:43,721 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 2026-03-05T10:00:43,721 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 2026-03-05T10:00:43,722 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 2026-03-05T10:00:43,723 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 2026-03-05T10:00:43,724 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdutils/ 2026-03-05T10:00:43,724 Getting page https://www.piwheels.org/simple/kssdutils/ 2026-03-05T10:00:43,725 Found index url https://www.piwheels.org/simple 2026-03-05T10:00:43,878 Fetched page https://www.piwheels.org/simple/kssdutils/ as text/html 2026-03-05T10:00:43,891 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.7-cp311-cp311-linux_armv6l.whl#sha256=5beb32a7772765a880c50ab75f1b8a504d6c960523a444ea7829d7fef3671c4c (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T10:00:43,892 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.7-cp311-cp311-linux_armv7l.whl#sha256=5beb32a7772765a880c50ab75f1b8a504d6c960523a444ea7829d7fef3671c4c (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T10:00:43,892 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.7-cp39-cp39-linux_armv6l.whl#sha256=bea859a11c139a17abe9233844b7d680aab56d553fc883a214cb8aea8147aa7c (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T10:00:43,893 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.7-cp39-cp39-linux_armv7l.whl#sha256=bea859a11c139a17abe9233844b7d680aab56d553fc883a214cb8aea8147aa7c (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T10:00:43,894 Skipping link: No binaries permitted for kssdutils: 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https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.2-cp39-cp39-linux_armv7l.whl#sha256=e7719ceb9b4ce3c5cfbfa12e1b4e8d314e117ca845fd6bedcafe8abadb5ca1f3 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T10:00:43,903 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.0-cp311-cp311-linux_armv6l.whl#sha256=0c8e77f57ec908176d8961c597a98abc9259dee9141399da1712be9b1d560bc8 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T10:00:43,903 Skipping link: No binaries permitted for kssdutils: https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.1.0-cp311-cp311-linux_armv7l.whl#sha256=0c8e77f57ec908176d8961c597a98abc9259dee9141399da1712be9b1d560bc8 (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T10:00:43,904 Skipping link: No binaries permitted for kssdutils: 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https://archive1.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp311-cp311-linux_armv7l.whl#sha256=85c10f6c3223fb99e39dfddbef722fd2913bd5c63f089283ce23dae20c6a4a4d (from https://www.piwheels.org/simple/kssdutils/) 2026-03-05T10:00:43,913 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/) 2026-03-05T10:00:43,913 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/) 2026-03-05T10:00:43,914 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/) 2026-03-05T10:00:43,914 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/) 2026-03-05T10:00:43,915 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/) 2026-03-05T10:00:43,915 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/) 2026-03-05T10:00:43,916 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/) 2026-03-05T10:00:43,916 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/) 2026-03-05T10:00:43,917 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/) 2026-03-05T10:00:43,917 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/) 2026-03-05T10:00:43,918 Skipping link: not a file: https://www.piwheels.org/simple/kssdutils/ 2026-03-05T10:00:43,919 Skipping link: not a file: https://pypi.org/simple/kssdutils/ 2026-03-05T10:00:43,939 Given no hashes to check 1 links for project 'kssdutils': discarding no candidates 2026-03-05T10:00:43,957 Collecting kssdutils==1.1.8 2026-03-05T10:00:43,960 Created temporary directory: /tmp/pip-unpack-9bhuqk4o 2026-03-05T10:00:44,093 Downloading kssdutils-1.1.8.tar.gz (44 kB) 2026-03-05T10:00:44,199 Added kssdutils==1.1.8 from https://files.pythonhosted.org/packages/a8/d7/8426d81d46965dcb35320a45f5b457453be5160b18551902b31860952f69/kssdutils-1.1.8.tar.gz to build tracker '/tmp/pip-build-tracker-snta1cbk' 2026-03-05T10:00:44,201 Running setup.py (path:/tmp/pip-wheel-sbg2yfr7/kssdutils_3373d07c1832455a8962e1639badedb5/setup.py) egg_info for package kssdutils 2026-03-05T10:00:44,201 Created temporary directory: /tmp/pip-pip-egg-info-vb5f_5uz 2026-03-05T10:00:44,202 Preparing metadata (setup.py): started 2026-03-05T10:00:44,203 Running command python setup.py egg_info 2026-03-05T10:00:45,082 running egg_info 2026-03-05T10:00:45,109 creating /tmp/pip-pip-egg-info-vb5f_5uz/kssdutils.egg-info 2026-03-05T10:00:45,110 writing /tmp/pip-pip-egg-info-vb5f_5uz/kssdutils.egg-info/PKG-INFO 2026-03-05T10:00:45,114 writing dependency_links to /tmp/pip-pip-egg-info-vb5f_5uz/kssdutils.egg-info/dependency_links.txt 2026-03-05T10:00:45,116 writing top-level names to /tmp/pip-pip-egg-info-vb5f_5uz/kssdutils.egg-info/top_level.txt 2026-03-05T10:00:45,117 writing manifest file '/tmp/pip-pip-egg-info-vb5f_5uz/kssdutils.egg-info/SOURCES.txt' 2026-03-05T10:00:45,198 reading manifest file '/tmp/pip-pip-egg-info-vb5f_5uz/kssdutils.egg-info/SOURCES.txt' 2026-03-05T10:00:45,199 reading manifest template 'MANIFEST.in' 2026-03-05T10:00:45,207 writing manifest file '/tmp/pip-pip-egg-info-vb5f_5uz/kssdutils.egg-info/SOURCES.txt' 2026-03-05T10:00:45,313 Preparing metadata (setup.py): finished with status 'done' 2026-03-05T10:00:45,316 Source in /tmp/pip-wheel-sbg2yfr7/kssdutils_3373d07c1832455a8962e1639badedb5 has version 1.1.8, which satisfies requirement kssdutils==1.1.8 from https://files.pythonhosted.org/packages/a8/d7/8426d81d46965dcb35320a45f5b457453be5160b18551902b31860952f69/kssdutils-1.1.8.tar.gz 2026-03-05T10:00:45,317 Removed kssdutils==1.1.8 from https://files.pythonhosted.org/packages/a8/d7/8426d81d46965dcb35320a45f5b457453be5160b18551902b31860952f69/kssdutils-1.1.8.tar.gz from build tracker '/tmp/pip-build-tracker-snta1cbk' 2026-03-05T10:00:45,321 Created temporary directory: /tmp/pip-unpack-p8irr7qc 2026-03-05T10:00:45,321 Building wheels for collected packages: kssdutils 2026-03-05T10:00:45,325 Created temporary directory: /tmp/pip-wheel-t0w3zgky 2026-03-05T10:00:45,326 Building wheel for kssdutils (setup.py): started 2026-03-05T10:00:45,327 Destination directory: /tmp/pip-wheel-t0w3zgky 2026-03-05T10:00:45,328 Running command python setup.py bdist_wheel 2026-03-05T10:00:46,156 running bdist_wheel 2026-03-05T10:00:46,262 running build 2026-03-05T10:00:46,263 running build_ext 2026-03-05T10:00:46,807 building 'kssdtool' extension 2026-03-05T10:00:46,808 creating build/temp.linux-armv7l-cpython-311 2026-03-05T10:00:46,811 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 2026-03-05T10:00:46,986 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2026-03-05T10:00:46,987 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-03-05T10:00:46,987 109 | for (unsigned int i = 0; i < comp_num; i++) { 2026-03-05T10:00:46,988 | ^ 2026-03-05T10:00:46,990 co2mco.c: In function ‘co2unitllmco’: 2026-03-05T10:00:46,991 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2026-03-05T10:00:46,992 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2026-03-05T10:00:46,993 | ^ 2026-03-05T10:00:47,698 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_composite.c -o build/temp.linux-armv7l-cpython-311/command_composite.o -fopenmp 2026-03-05T10:00:48,077 command_composite.c: In function ‘get_species_abundance’: 2026-03-05T10:00:48,077 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2026-03-05T10:00:48,078 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2026-03-05T10:00:48,079 | ^~ 2026-03-05T10:00:48,079 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2026-03-05T10:00:48,080 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2026-03-05T10:00:48,081 | ^~ 2026-03-05T10:00:48,082 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:48,083 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-03-05T10:00:48,083 | ^ 2026-03-05T10:00:48,084 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:48,084 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-03-05T10:00:48,085 | ^~~~~~~~~~ 2026-03-05T10:00:48,085 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-05T10:00:48,086 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2026-03-05T10:00:48,086 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:48,087 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:48,088 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-03-05T10:00:48,088 | ^ 2026-03-05T10:00:48,089 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:48,089 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-03-05T10:00:48,090 | ^~~~~~~~~~ 2026-03-05T10:00:48,090 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-05T10:00:48,091 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2026-03-05T10:00:48,092 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:48,092 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:48,093 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-03-05T10:00:48,094 | ^ 2026-03-05T10:00:48,094 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:48,095 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-03-05T10:00:48,096 | ^~~~~~~~~~ 2026-03-05T10:00:48,097 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-05T10:00:48,097 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2026-03-05T10:00:48,098 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:48,099 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:48,099 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-03-05T10:00:48,100 | ^ 2026-03-05T10:00:48,100 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:48,101 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-03-05T10:00:48,102 | ^~~~~~~~~~ 2026-03-05T10:00:48,102 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2026-03-05T10:00:48,103 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2026-03-05T10:00:48,104 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:48,105 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:48,106 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-03-05T10:00:48,106 | ^ 2026-03-05T10:00:48,107 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:48,107 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-03-05T10:00:48,108 | ^~~~~~~~~~~~ 2026-03-05T10:00:48,108 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2026-03-05T10:00:48,108 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2026-03-05T10:00:48,109 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:48,337 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 2026-03-05T10:00:48,593 command_dist.c: In function ‘mco_cbd_co_dist’: 2026-03-05T10:00:48,595 command_dist.c:677:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-05T10:00:48,595 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T10:00:48,596 | ~~^ 2026-03-05T10:00:48,596 | | 2026-03-05T10:00:48,597 | long unsigned int 2026-03-05T10:00:48,597 | %u 2026-03-05T10:00:48,598 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T10:00:48,598 | ~~~~~~~ 2026-03-05T10:00:48,599 | | 2026-03-05T10:00:48,600 | size_t {aka unsigned int} 2026-03-05T10:00:48,600 command_dist.c:677:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-05T10:00:48,601 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T10:00:48,602 | ~~^ 2026-03-05T10:00:48,602 | | 2026-03-05T10:00:48,603 | long unsigned int 2026-03-05T10:00:48,604 | %u 2026-03-05T10:00:48,604 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T10:00:48,605 679 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-05T10:00:48,605 | ~~~~~~~~~ 2026-03-05T10:00:48,606 | | 2026-03-05T10:00:48,607 | size_t {aka unsigned int} 2026-03-05T10:00:48,607 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-03-05T10:00:48,608 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T10:00:48,609 | ~~^ 2026-03-05T10:00:48,609 | | 2026-03-05T10:00:48,610 | long unsigned int 2026-03-05T10:00:48,611 | %u 2026-03-05T10:00:48,611 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T10:00:48,612 679 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-05T10:00:48,612 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:48,613 | | 2026-03-05T10:00:48,613 | unsigned int 2026-03-05T10:00:48,614 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-03-05T10:00:48,614 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2026-03-05T10:00:48,615 | ^ 2026-03-05T10:00:48,615 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2026-03-05T10:00:48,617 command_dist.c:863:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-05T10:00:48,618 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-03-05T10:00:48,618 | ~~^ ~~~~~~~ 2026-03-05T10:00:48,619 | | | 2026-03-05T10:00:48,619 | long unsigned int size_t {aka unsigned int} 2026-03-05T10:00:48,620 | %u 2026-03-05T10:00:48,621 command_dist.c:863:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-05T10:00:48,621 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-03-05T10:00:48,622 | ~~^ 2026-03-05T10:00:48,622 | | 2026-03-05T10:00:48,623 | long unsigned int 2026-03-05T10:00:48,624 | %u 2026-03-05T10:00:48,625 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2026-03-05T10:00:48,625 | ~~~~~~~~~ 2026-03-05T10:00:48,626 | | 2026-03-05T10:00:48,626 | size_t {aka unsigned int} 2026-03-05T10:00:48,627 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-03-05T10:00:48,627 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2026-03-05T10:00:48,628 | ~~^ 2026-03-05T10:00:48,628 | | 2026-03-05T10:00:48,629 | long unsigned int 2026-03-05T10:00:48,629 | %u 2026-03-05T10:00:48,630 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2026-03-05T10:00:48,631 865 | (size_t) b * unitsz_distf_mapped); 2026-03-05T10:00:48,631 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:48,632 | | 2026-03-05T10:00:48,632 | unsigned int 2026-03-05T10:00:48,633 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2026-03-05T10:00:48,633 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2026-03-05T10:00:48,634 | ^~~~~~~ 2026-03-05T10:00:48,634 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2026-03-05T10:00:48,635 809 | struct stat cbd_fcode_stat; 2026-03-05T10:00:48,635 | ^~~~~~~~~~~~~~ 2026-03-05T10:00:48,636 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2026-03-05T10:00:48,636 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2026-03-05T10:00:48,637 | ^~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:48,637 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2026-03-05T10:00:48,638 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2026-03-05T10:00:48,639 | ^~~~~~~~~~~~~~~~~ 2026-03-05T10:00:48,640 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2026-03-05T10:00:48,642 command_dist.c:1018:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-05T10:00:48,643 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T10:00:48,643 | ~~^ 2026-03-05T10:00:48,644 | | 2026-03-05T10:00:48,644 | long unsigned int 2026-03-05T10:00:48,645 | %u 2026-03-05T10:00:48,645 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T10:00:48,646 | ~~~~~~~ 2026-03-05T10:00:48,647 | | 2026-03-05T10:00:48,647 | size_t {aka unsigned int} 2026-03-05T10:00:48,648 command_dist.c:1018:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-05T10:00:48,648 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T10:00:48,649 | ~~^ 2026-03-05T10:00:48,649 | | 2026-03-05T10:00:48,650 | long unsigned int 2026-03-05T10:00:48,650 | %u 2026-03-05T10:00:48,651 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T10:00:48,652 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-05T10:00:48,653 | ~~~~~~~~~ 2026-03-05T10:00:48,654 | | 2026-03-05T10:00:48,654 | size_t {aka unsigned int} 2026-03-05T10:00:48,655 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2026-03-05T10:00:48,655 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2026-03-05T10:00:48,656 | ~~^ 2026-03-05T10:00:48,656 | | 2026-03-05T10:00:48,657 | long unsigned int 2026-03-05T10:00:48,657 | %u 2026-03-05T10:00:48,658 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2026-03-05T10:00:48,658 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2026-03-05T10:00:48,659 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:48,659 | | 2026-03-05T10:00:48,660 | unsigned int 2026-03-05T10:00:48,660 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2026-03-05T10:00:48,661 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2026-03-05T10:00:48,662 | ^ 2026-03-05T10:00:48,662 command_dist.c: In function ‘mco_co_dist_core’: 2026-03-05T10:00:48,663 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-03-05T10:00:48,664 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2026-03-05T10:00:48,665 | ^ 2026-03-05T10:00:48,668 command_dist.c: In function ‘koc_dist_print_nobin’: 2026-03-05T10:00:48,670 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-05T10:00:48,670 1239 | for (int rid = 0; rid < ref_num; rid++) 2026-03-05T10:00:48,671 | ^ 2026-03-05T10:00:48,672 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-05T10:00:48,673 1245 | for (int rid = 0; rid < ref_num; rid++) { 2026-03-05T10:00:48,673 | ^ 2026-03-05T10:00:48,679 command_dist.c: In function ‘dist_print_nobin’: 2026-03-05T10:00:48,681 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-05T10:00:48,681 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2026-03-05T10:00:48,682 | ^ 2026-03-05T10:00:48,684 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-05T10:00:48,685 1356 | for (int rid = 0; rid < ref_num; rid++) { 2026-03-05T10:00:48,685 | ^ 2026-03-05T10:00:48,687 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2026-03-05T10:00:48,688 1382 | for (int rid = 0; rid < ref_num; rid++) 2026-03-05T10:00:48,689 | ^ 2026-03-05T10:00:49,050 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2026-03-05T10:00:49,051 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2026-03-05T10:00:49,051 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2026-03-05T10:00:49,052 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:49,052 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2026-03-05T10:00:49,053 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2026-03-05T10:00:49,053 | ^~~~~~~~~~~~ 2026-03-05T10:00:49,887 command_dist.c: In function ‘get_dim_shuffle’: 2026-03-05T10:00:49,888 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2026-03-05T10:00:49,889 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2026-03-05T10:00:49,889 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:49,890 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2026-03-05T10:00:49,890 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2026-03-05T10:00:49,891 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:50,789 command_dist.c: In function ‘mco_cbd_co_dist’: 2026-03-05T10:00:50,790 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:50,791 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T10:00:50,791 | ^~ ~~~~~~~~~ 2026-03-05T10:00:50,792 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-03-05T10:00:50,792 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T10:00:50,793 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:50,794 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T10:00:50,794 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T10:00:50,795 | ^~~~~~~~~~~~~~~ 2026-03-05T10:00:50,796 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-03-05T10:00:50,796 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T10:00:50,797 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:50,797 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T10:00:50,798 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T10:00:50,799 | ^~~~~~~~~~~ 2026-03-05T10:00:50,799 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:50,800 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T10:00:50,800 | ^~~~~~~~~~~~~~~~~ 2026-03-05T10:00:50,801 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2026-03-05T10:00:50,802 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T10:00:50,803 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:50,803 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T10:00:50,804 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T10:00:50,805 | ^~~~~ 2026-03-05T10:00:50,806 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:50,806 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T10:00:50,807 | ^~~~~~~~~~~ 2026-03-05T10:00:50,807 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-05T10:00:50,808 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T10:00:50,808 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,040 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2026-03-05T10:00:51,041 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:51,042 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T10:00:51,043 | ^~ ~~~~~~~~~ 2026-03-05T10:00:51,044 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-03-05T10:00:51,044 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T10:00:51,045 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,045 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T10:00:51,046 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T10:00:51,046 | ^~~~~~~~~~~~~~~ 2026-03-05T10:00:51,047 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-03-05T10:00:51,048 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T10:00:51,049 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,050 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T10:00:51,051 823 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-05T10:00:51,052 | ^~~~~~~~~~~~~ 2026-03-05T10:00:51,054 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-03-05T10:00:51,055 823 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-05T10:00:51,056 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,057 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:51,058 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-03-05T10:00:51,058 | ^ 2026-03-05T10:00:51,060 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2026-03-05T10:00:51,060 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-03-05T10:00:51,061 | ^~~~~~~~~~ 2026-03-05T10:00:51,062 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2026-03-05T10:00:51,062 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2026-03-05T10:00:51,064 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,064 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:51,065 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-03-05T10:00:51,067 | ^ 2026-03-05T10:00:51,068 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2026-03-05T10:00:51,069 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-03-05T10:00:51,070 | ^~~~~~~~~~ 2026-03-05T10:00:51,071 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2026-03-05T10:00:51,073 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2026-03-05T10:00:51,074 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,320 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2026-03-05T10:00:51,321 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:51,322 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T10:00:51,322 | ^~ ~~~~~~~~~ 2026-03-05T10:00:51,323 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2026-03-05T10:00:51,323 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2026-03-05T10:00:51,324 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,325 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T10:00:51,325 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T10:00:51,326 | ^~~~~~~~~~~~~~~ 2026-03-05T10:00:51,327 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2026-03-05T10:00:51,328 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2026-03-05T10:00:51,330 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,330 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T10:00:51,331 990 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-05T10:00:51,332 | ^~~~~~~~~~~~~ 2026-03-05T10:00:51,332 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-03-05T10:00:51,333 990 | sprintf(distf, "%s/distance.out", distout_dir); 2026-03-05T10:00:51,334 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,335 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T10:00:51,337 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T10:00:51,337 | ^~~~~~~~~~~ 2026-03-05T10:00:51,339 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:51,339 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T10:00:51,341 | ^~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,342 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2026-03-05T10:00:51,344 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2026-03-05T10:00:51,345 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,346 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2026-03-05T10:00:51,346 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T10:00:51,347 | ^~~~~ 2026-03-05T10:00:51,348 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:51,349 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T10:00:51,350 | ^~~~~~~~~~~ 2026-03-05T10:00:51,351 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-05T10:00:51,352 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2026-03-05T10:00:51,352 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,611 command_dist.c: In function ‘combine_queries’: 2026-03-05T10:00:51,612 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T10:00:51,614 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2026-03-05T10:00:51,615 | ^ 2026-03-05T10:00:51,615 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T10:00:51,616 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2026-03-05T10:00:51,616 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,617 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T10:00:51,618 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2026-03-05T10:00:51,619 | ^ 2026-03-05T10:00:51,620 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T10:00:51,621 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2026-03-05T10:00:51,622 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:51,623 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:51,624 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2026-03-05T10:00:51,625 | ^~ ~~~~~~~~ 2026-03-05T10:00:51,625 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2026-03-05T10:00:51,626 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2026-03-05T10:00:51,627 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,107 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 2026-03-05T10:00:52,286 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 2026-03-05T10:00:52,463 command_set.c: In function ‘sketch_operate’: 2026-03-05T10:00:52,463 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2026-03-05T10:00:52,464 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2026-03-05T10:00:52,465 | ^ 2026-03-05T10:00:52,476 command_set.c: In function ‘combin_subset_pans’: 2026-03-05T10:00:52,477 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-03-05T10:00:52,478 457 | free(co_dstat_fpath); 2026-03-05T10:00:52,478 | ^~~~~~~~~~~~~~ 2026-03-05T10:00:52,479 In file included from kssdheaders/global_basic.h:159, 2026-03-05T10:00:52,480 from command_set.c:15: 2026-03-05T10:00:52,481 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2026-03-05T10:00:52,481 568 | extern void free (void *__ptr) __THROW; 2026-03-05T10:00:52,482 | ~~~~~~^~~~~ 2026-03-05T10:00:52,484 command_set.c: In function ‘grouping_genomes’: 2026-03-05T10:00:52,484 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2026-03-05T10:00:52,485 562 | free(co_dstat_fpath); 2026-03-05T10:00:52,485 | ^~~~~~~~~~~~~~ 2026-03-05T10:00:52,486 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2026-03-05T10:00:52,487 568 | extern void free (void *__ptr) __THROW; 2026-03-05T10:00:52,487 | ~~~~~~^~~~~ 2026-03-05T10:00:52,652 command_set.c: In function ‘sketch_union’: 2026-03-05T10:00:52,653 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T10:00:52,653 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:52,654 | ^ 2026-03-05T10:00:52,654 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T10:00:52,655 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:52,656 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,656 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:52,657 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T10:00:52,658 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:52,659 command_set.c:82:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:52,659 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T10:00:52,660 | ^~~~~~~~~~ 2026-03-05T10:00:52,661 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T10:00:52,662 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T10:00:52,662 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,663 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:52,664 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-03-05T10:00:52,664 | ^~ ~~~~~~~~~~ 2026-03-05T10:00:52,665 command_set.c:92:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:52,666 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-03-05T10:00:52,666 | ^~~~~~~~~~ 2026-03-05T10:00:52,667 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-05T10:00:52,667 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2026-03-05T10:00:52,668 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,784 command_set.c: In function ‘sketch_operate’: 2026-03-05T10:00:52,785 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:52,786 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-03-05T10:00:52,786 | ^~ ~~~~~~~~~~ 2026-03-05T10:00:52,787 command_set.c:153:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:52,788 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-03-05T10:00:52,788 | ^~~~~~~~~~ 2026-03-05T10:00:52,789 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2026-03-05T10:00:52,789 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2026-03-05T10:00:52,790 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,790 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:52,791 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-03-05T10:00:52,791 | ^~ ~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,792 command_set.c:155:29: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:52,792 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-03-05T10:00:52,793 | ^~~~~~~~~~ 2026-03-05T10:00:52,794 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2026-03-05T10:00:52,794 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2026-03-05T10:00:52,795 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,795 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:52,796 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T10:00:52,796 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:52,797 command_set.c:165:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:52,798 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T10:00:52,799 | ^~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,799 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T10:00:52,800 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T10:00:52,801 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,801 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:52,802 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T10:00:52,803 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:52,803 command_set.c:169:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:52,804 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T10:00:52,804 | ^~~~~~~~~~ 2026-03-05T10:00:52,805 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T10:00:52,806 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2026-03-05T10:00:52,806 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,807 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:52,808 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T10:00:52,808 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:52,809 command_set.c:174:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:52,810 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T10:00:52,810 | ^~~~~~~~~~ 2026-03-05T10:00:52,811 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T10:00:52,811 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T10:00:52,812 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,813 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:52,813 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T10:00:52,814 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:52,814 command_set.c:187:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:52,815 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T10:00:52,815 | ^~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,816 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T10:00:52,816 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2026-03-05T10:00:52,817 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,817 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T10:00:52,818 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:52,818 | ^ 2026-03-05T10:00:52,819 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T10:00:52,820 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:52,820 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,959 command_set.c: In function ‘uniq_sketch_union’: 2026-03-05T10:00:52,960 command_set.c:219:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T10:00:52,960 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2026-03-05T10:00:52,961 | ^ 2026-03-05T10:00:52,962 command_set.c:219:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2026-03-05T10:00:52,962 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2026-03-05T10:00:52,963 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,964 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T10:00:52,964 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:52,965 | ^ 2026-03-05T10:00:52,966 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T10:00:52,966 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:52,967 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,968 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:52,968 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T10:00:52,969 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:52,970 command_set.c:247:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:52,970 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T10:00:52,971 | ^~~~~~~~~~ 2026-03-05T10:00:52,972 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T10:00:52,972 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2026-03-05T10:00:52,973 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,974 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:52,974 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-03-05T10:00:52,975 | ^~ ~~~~~~~~~~~~~~~ 2026-03-05T10:00:52,975 command_set.c:259:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:52,975 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-03-05T10:00:52,976 | ^~~~~~~~~~ 2026-03-05T10:00:52,976 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2026-03-05T10:00:52,977 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2026-03-05T10:00:52,977 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,105 command_set.c: In function ‘combin_pans’: 2026-03-05T10:00:53,106 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:53,106 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T10:00:53,107 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:53,107 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2026-03-05T10:00:53,108 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T10:00:53,109 | ^~~~~~~~~~ 2026-03-05T10:00:53,109 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2026-03-05T10:00:53,110 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T10:00:53,111 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,111 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:53,112 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T10:00:53,113 | ^~ ~~~~~~~~~~ 2026-03-05T10:00:53,114 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2026-03-05T10:00:53,114 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T10:00:53,115 | ^~~~~~~~~~ 2026-03-05T10:00:53,116 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2026-03-05T10:00:53,116 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T10:00:53,117 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,117 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T10:00:53,118 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:53,119 | ^ 2026-03-05T10:00:53,119 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T10:00:53,120 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:53,121 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,323 command_set.c: In function ‘combin_subset_pans’: 2026-03-05T10:00:53,324 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:53,325 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T10:00:53,325 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:53,325 command_set.c:469:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:53,326 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T10:00:53,326 | ^~~~~~~~~~ 2026-03-05T10:00:53,327 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T10:00:53,327 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T10:00:53,327 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,328 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:53,328 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T10:00:53,329 | ^~ ~~~~~~~~~~ 2026-03-05T10:00:53,329 command_set.c:475:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:53,330 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T10:00:53,330 | ^~~~~~~~~~ 2026-03-05T10:00:53,330 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T10:00:53,331 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T10:00:53,331 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,332 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:53,333 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T10:00:53,334 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:53,334 command_set.c:481:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:53,335 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T10:00:53,336 | ^~~~~~~~~~ 2026-03-05T10:00:53,337 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T10:00:53,338 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T10:00:53,338 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,339 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:53,340 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T10:00:53,340 | ^~ ~~~~~~~~~~ 2026-03-05T10:00:53,341 command_set.c:512:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:53,342 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T10:00:53,342 | ^~~~~~~~~~ 2026-03-05T10:00:53,343 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T10:00:53,344 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T10:00:53,345 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,346 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T10:00:53,347 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:53,348 | ^ 2026-03-05T10:00:53,348 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T10:00:53,349 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:53,349 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,568 command_set.c: In function ‘grouping_genomes’: 2026-03-05T10:00:53,569 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:53,570 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T10:00:53,570 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:53,571 command_set.c:574:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:53,571 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T10:00:53,571 | ^~~~~~~~~~ 2026-03-05T10:00:53,572 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T10:00:53,572 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2026-03-05T10:00:53,573 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,573 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:53,574 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T10:00:53,574 | ^~ ~~~~~~~~~~ 2026-03-05T10:00:53,575 command_set.c:580:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:53,575 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T10:00:53,576 | ^~~~~~~~~~ 2026-03-05T10:00:53,577 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T10:00:53,578 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2026-03-05T10:00:53,578 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,579 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:53,579 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T10:00:53,580 | ^~ ~~~~~~~~~~~ 2026-03-05T10:00:53,581 command_set.c:612:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:53,582 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T10:00:53,582 | ^~~~~~~~~~ 2026-03-05T10:00:53,583 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2026-03-05T10:00:53,583 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2026-03-05T10:00:53,584 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,585 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2026-03-05T10:00:53,585 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T10:00:53,586 | ^~ ~~~~~~~~~~ 2026-03-05T10:00:53,587 command_set.c:634:25: note: directive argument in the range [-2147483644, 2147483646] 2026-03-05T10:00:53,587 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T10:00:53,588 | ^~~~~~~~~~ 2026-03-05T10:00:53,589 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2026-03-05T10:00:53,590 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2026-03-05T10:00:53,590 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,591 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2026-03-05T10:00:53,591 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:53,592 | ^ 2026-03-05T10:00:53,592 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2026-03-05T10:00:53,593 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2026-03-05T10:00:53,594 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-03-05T10:00:53,927 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 2026-03-05T10:00:54,240 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 2026-03-05T10:00:54,441 global_basic.c: In function ‘organize_infile_list’: 2026-03-05T10:00:54,441 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2026-03-05T10:00:54,442 195 | while (isspace(*buf)) buf++; 2026-03-05T10:00:54,443 | ^~~~~~~ 2026-03-05T10:00:54,443 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2026-03-05T10:00:54,444 34 | #include 2026-03-05T10:00:54,444 +++ |+#include 2026-03-05T10:00:54,444 35 | 2026-03-05T10:00:54,445 global_basic.c:201:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-05T10:00:54,446 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2026-03-05T10:00:54,446 | ~~^ 2026-03-05T10:00:54,447 | | 2026-03-05T10:00:54,448 | long unsigned int 2026-03-05T10:00:54,448 | %u 2026-03-05T10:00:54,449 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2026-03-05T10:00:54,450 | ~~~~~~~~~~~ 2026-03-05T10:00:54,450 | | 2026-03-05T10:00:54,451 | size_t {aka unsigned int} 2026-03-05T10:00:54,451 global_basic.c:233:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2026-03-05T10:00:54,452 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2026-03-05T10:00:54,453 | ~~^ 2026-03-05T10:00:54,453 | | 2026-03-05T10:00:54,454 | long unsigned int 2026-03-05T10:00:54,454 | %u 2026-03-05T10:00:54,455 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2026-03-05T10:00:54,456 | ~~~~~~~~~~~ 2026-03-05T10:00:54,456 | | 2026-03-05T10:00:54,457 | size_t {aka unsigned int} 2026-03-05T10:00:55,205 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 2026-03-05T10:00:55,384 iseq2comem.c: In function ‘reads2mco’: 2026-03-05T10:00:55,385 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,385 156 | if (base > TL) { 2026-03-05T10:00:55,386 | ^ 2026-03-05T10:00:55,386 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,387 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T10:00:55,387 | ^~ 2026-03-05T10:00:55,388 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,388 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T10:00:55,389 | ^ 2026-03-05T10:00:55,391 iseq2comem.c: In function ‘fasta2co’: 2026-03-05T10:00:55,391 iseq2comem.c:213:69: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T10:00:55,392 213 | if ((infp = popen(fas_fname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2026-03-05T10:00:55,393 | ^~~~~~~~~~~~~~~ 2026-03-05T10:00:55,393 iseq2comem.c:219:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T10:00:55,394 219 | if ((infp = popen(seqfname, "r")) == NULL) fprintf(stderr, "fasta2co():%s", fas_fname, "\n"); 2026-03-05T10:00:55,394 | ^~~~~~~~~~~~~~~ 2026-03-05T10:00:55,396 iseq2comem.c:261:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,396 261 | if (base > TL) { 2026-03-05T10:00:55,397 | ^ 2026-03-05T10:00:55,398 iseq2comem.c:265:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,398 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T10:00:55,399 | ^~ 2026-03-05T10:00:55,400 iseq2comem.c:265:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,400 265 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T10:00:55,401 | ^ 2026-03-05T10:00:55,402 iseq2comem.c: In function ‘fastq2co’: 2026-03-05T10:00:55,402 iseq2comem.c:295:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2026-03-05T10:00:55,403 295 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2026-03-05T10:00:55,404 | ^~ 2026-03-05T10:00:55,404 iseq2comem.c:307:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T10:00:55,405 307 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2026-03-05T10:00:55,406 | ^~~~~~~~~~~~~~~ 2026-03-05T10:00:55,407 iseq2comem.c:313:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T10:00:55,407 313 | if ((infp = popen(seqfname, "r")) == NULL) fprintf(stderr, "fastq2co():%s", fq_fname, "\n"); 2026-03-05T10:00:55,408 | ^~~~~~~~~~~~~~~ 2026-03-05T10:00:55,410 iseq2comem.c:352:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,411 352 | if (base > TL) { 2026-03-05T10:00:55,411 | ^ 2026-03-05T10:00:55,412 iseq2comem.c:356:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,412 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T10:00:55,413 | ^~ 2026-03-05T10:00:55,413 iseq2comem.c:356:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,414 356 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T10:00:55,414 | ^ 2026-03-05T10:00:55,416 iseq2comem.c:375:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,416 375 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2026-03-05T10:00:55,417 | ^ 2026-03-05T10:00:55,418 iseq2comem.c: In function ‘fastq2koc’: 2026-03-05T10:00:55,419 iseq2comem.c:403:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T10:00:55,420 403 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2026-03-05T10:00:55,420 | ^~~~~~~~~~~~~~~~ 2026-03-05T10:00:55,421 iseq2comem.c:409:68: warning: too many arguments for format [-Wformat-extra-args] 2026-03-05T10:00:55,422 409 | if ((infp = popen(fq_fname, "r")) == NULL) fprintf(stderr, "fastq2koc():%s", fq_fname, "\n"); 2026-03-05T10:00:55,423 | ^~~~~~~~~~~~~~~~ 2026-03-05T10:00:55,423 iseq2comem.c:448:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,424 448 | if (base > TL) { 2026-03-05T10:00:55,425 | ^ 2026-03-05T10:00:55,425 iseq2comem.c:452:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,426 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T10:00:55,426 | ^~ 2026-03-05T10:00:55,427 iseq2comem.c:452:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,428 452 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T10:00:55,428 | ^ 2026-03-05T10:00:55,435 iseq2comem.c: In function ‘mt_shortreads2koc’: 2026-03-05T10:00:55,436 iseq2comem.c:628:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,437 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T10:00:55,438 | ^~ 2026-03-05T10:00:55,439 iseq2comem.c:628:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2026-03-05T10:00:55,439 628 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2026-03-05T10:00:55,441 | ^ 2026-03-05T10:00:56,821 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 2026-03-05T10:00:56,875 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 2026-03-05T10:00:57,007 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 2026-03-05T10:00:57,399 pykssd.c: In function ‘py_dist_dispatch’: 2026-03-05T10:00:57,400 pykssd.c:339:13: warning: unused variable ‘state1’ [-Wunused-variable] 2026-03-05T10:00:57,400 339 | int state1 = dist_dispatch(&dist_opt_val1); 2026-03-05T10:00:57,401 | ^~~~~~ 2026-03-05T10:00:57,402 pykssd.c:404:13: warning: unused variable ‘state2’ [-Wunused-variable] 2026-03-05T10:00:57,402 404 | int state2 = dist_dispatch(&dist_opt_val2); 2026-03-05T10:00:57,403 | ^~~~~~ 2026-03-05T10:00:57,404 pykssd.c:538:13: warning: unused variable ‘state4’ [-Wunused-variable] 2026-03-05T10:00:57,404 538 | int state4 = dist_dispatch(&dist_opt_val4); 2026-03-05T10:00:57,405 | ^~~~~~ 2026-03-05T10:00:58,054 creating build/lib.linux-armv7l-cpython-311 2026-03-05T10:00:58,055 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 2026-03-05T10:00:58,206 running build_scripts 2026-03-05T10:00:58,206 creating build/scripts-3.11 2026-03-05T10:00:58,208 copying kssdutils.py -> build/scripts-3.11 2026-03-05T10:00:58,210 changing mode of build/scripts-3.11/kssdutils.py from 644 to 755 2026-03-05T10:00:58,237 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-03-05T10:00:58,238 !! 2026-03-05T10:00:58,239 ******************************************************************************** 2026-03-05T10:00:58,240 Please avoid running ``setup.py`` directly. 2026-03-05T10:00:58,240 Instead, use pypa/build, pypa/installer or other 2026-03-05T10:00:58,241 standards-based tools. 2026-03-05T10:00:58,242 This deprecation is overdue, please update your project and remove deprecated 2026-03-05T10:00:58,243 calls to avoid build errors in the future. 2026-03-05T10:00:58,244 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-03-05T10:00:58,244 ******************************************************************************** 2026-03-05T10:00:58,245 !! 2026-03-05T10:00:58,246 self.initialize_options() 2026-03-05T10:00:58,264 installing to build/bdist.linux-armv7l/wheel 2026-03-05T10:00:58,265 running install 2026-03-05T10:00:58,288 running install_lib 2026-03-05T10:00:58,314 creating build/bdist.linux-armv7l/wheel 2026-03-05T10:00:58,316 copying build/lib.linux-armv7l-cpython-311/kssdtool.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2026-03-05T10:00:58,323 running install_egg_info 2026-03-05T10:00:58,356 running egg_info 2026-03-05T10:00:58,383 writing kssdutils.egg-info/PKG-INFO 2026-03-05T10:00:58,386 writing dependency_links to kssdutils.egg-info/dependency_links.txt 2026-03-05T10:00:58,388 writing top-level names to kssdutils.egg-info/top_level.txt 2026-03-05T10:00:58,416 reading manifest file 'kssdutils.egg-info/SOURCES.txt' 2026-03-05T10:00:58,420 reading manifest template 'MANIFEST.in' 2026-03-05T10:00:58,427 writing manifest file 'kssdutils.egg-info/SOURCES.txt' 2026-03-05T10:00:58,429 Copying kssdutils.egg-info to build/bdist.linux-armv7l/wheel/./kssdutils-1.1.8-py3.11.egg-info 2026-03-05T10:00:58,437 running install_scripts 2026-03-05T10:00:58,438 creating build/bdist.linux-armv7l/wheel/kssdutils-1.1.8.data/scripts 2026-03-05T10:00:58,440 copying build/scripts-3.11/kssdutils.py -> build/bdist.linux-armv7l/wheel/kssdutils-1.1.8.data/scripts 2026-03-05T10:00:58,442 changing mode of build/bdist.linux-armv7l/wheel/kssdutils-1.1.8.data/scripts/kssdutils.py to 755 2026-03-05T10:00:58,487 creating build/bdist.linux-armv7l/wheel/kssdutils-1.1.8.dist-info/WHEEL 2026-03-05T10:00:58,489 creating '/tmp/pip-wheel-t0w3zgky/kssdutils-1.1.8-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-03-05T10:00:58,573 adding 'kssdtool.cpython-311-arm-linux-gnueabihf.so' 2026-03-05T10:00:58,578 adding 'kssdutils-1.1.8.data/scripts/kssdutils.py' 2026-03-05T10:00:58,580 adding 'kssdutils-1.1.8.dist-info/METADATA' 2026-03-05T10:00:58,581 adding 'kssdutils-1.1.8.dist-info/WHEEL' 2026-03-05T10:00:58,582 adding 'kssdutils-1.1.8.dist-info/dependency_links.txt' 2026-03-05T10:00:58,583 adding 'kssdutils-1.1.8.dist-info/top_level.txt' 2026-03-05T10:00:58,584 adding 'kssdutils-1.1.8.dist-info/RECORD' 2026-03-05T10:00:58,588 removing build/bdist.linux-armv7l/wheel 2026-03-05T10:00:58,742 Building wheel for kssdutils (setup.py): finished with status 'done' 2026-03-05T10:00:58,747 Created wheel for kssdutils: filename=kssdutils-1.1.8-cp311-cp311-linux_armv7l.whl size=179717 sha256=1ca8d1a14ea2253a85ab097f8a97a065c394460f12019e954e44a8de87f5392c 2026-03-05T10:00:58,748 Stored in directory: /tmp/pip-ephem-wheel-cache-t4ggebbg/wheels/ef/1c/cb/0cdfaaeb13f843f4b5a917c84195b3693f56dd19d1a762de93 2026-03-05T10:00:58,756 Successfully built kssdutils 2026-03-05T10:00:58,765 Removed build tracker: '/tmp/pip-build-tracker-snta1cbk'