2024-12-17T10:03:16,385 Disabling truststore because Python version isn't 3.10+ 2024-12-17T10:03:16,935 Created temporary directory: /tmp/pip-build-tracker-guvqi24m 2024-12-17T10:03:16,936 Initialized build tracking at /tmp/pip-build-tracker-guvqi24m 2024-12-17T10:03:16,936 Created build tracker: /tmp/pip-build-tracker-guvqi24m 2024-12-17T10:03:16,936 Entered build tracker: /tmp/pip-build-tracker-guvqi24m 2024-12-17T10:03:16,937 Created temporary directory: /tmp/pip-wheel-torbba1x 2024-12-17T10:03:16,942 Created temporary directory: /tmp/pip-ephem-wheel-cache-vay16w3r 2024-12-17T10:03:16,989 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-12-17T10:03:16,992 2 location(s) to search for versions of kssdutils: 2024-12-17T10:03:16,992 * https://pypi.org/simple/kssdutils/ 2024-12-17T10:03:16,992 * https://www.piwheels.org/simple/kssdutils/ 2024-12-17T10:03:16,995 Fetching project page and analyzing links: https://pypi.org/simple/kssdutils/ 2024-12-17T10:03:16,995 Getting page https://pypi.org/simple/kssdutils/ 2024-12-17T10:03:16,997 Found index url https://pypi.org/simple/ 2024-12-17T10:03:17,020 Fetched page https://pypi.org/simple/kssdutils/ as application/vnd.pypi.simple.v1+json 2024-12-17T10:03:17,022 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 2024-12-17T10:03:17,023 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 2024-12-17T10:03:17,023 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 2024-12-17T10:03:17,024 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 2024-12-17T10:03:17,024 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 2024-12-17T10:03:17,025 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 2024-12-17T10:03:17,025 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdutils/ 2024-12-17T10:03:17,025 Getting page https://www.piwheels.org/simple/kssdutils/ 2024-12-17T10:03:17,027 Found index url https://www.piwheels.org/simple/ 2024-12-17T10:03:17,064 Fetched page https://www.piwheels.org/simple/kssdutils/ as text/html 2024-12-17T10:03:17,073 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.6-cp311-cp311-linux_armv6l.whl#sha256=24cea74c37c72ec3f541e6eca026f6a906455d0e0160dc7d0f4526ab89a58125 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,073 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.6-cp311-cp311-linux_armv7l.whl#sha256=24cea74c37c72ec3f541e6eca026f6a906455d0e0160dc7d0f4526ab89a58125 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,073 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.5-cp311-cp311-linux_armv6l.whl#sha256=29ec8af3f080743643fee31ce978f3d65a6d90b950248e2ed6827316567aaa62 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,074 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.5-cp311-cp311-linux_armv7l.whl#sha256=29ec8af3f080743643fee31ce978f3d65a6d90b950248e2ed6827316567aaa62 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,074 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.5-cp39-cp39-linux_armv6l.whl#sha256=fb21de5c7d85619ac9cc1fafe3280f0130178032b169f1cf7ceac0cb6326d42e (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,074 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.5-cp39-cp39-linux_armv7l.whl#sha256=fb21de5c7d85619ac9cc1fafe3280f0130178032b169f1cf7ceac0cb6326d42e (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,075 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp311-cp311-linux_armv6l.whl#sha256=85c10f6c3223fb99e39dfddbef722fd2913bd5c63f089283ce23dae20c6a4a4d (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,075 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp311-cp311-linux_armv7l.whl#sha256=85c10f6c3223fb99e39dfddbef722fd2913bd5c63f089283ce23dae20c6a4a4d (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,075 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp39-cp39-linux_armv6l.whl#sha256=809195defd92c452797e9a87d99cfa8217c9ca4800c4a57d3e669846368160b1 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,076 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp39-cp39-linux_armv7l.whl#sha256=809195defd92c452797e9a87d99cfa8217c9ca4800c4a57d3e669846368160b1 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,076 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp311-cp311-linux_armv6l.whl#sha256=88788d94e7e118cfdf4e2cb04c558d2032ffa4f9352b663efd1a76f098c9f31d (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,076 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp311-cp311-linux_armv7l.whl#sha256=88788d94e7e118cfdf4e2cb04c558d2032ffa4f9352b663efd1a76f098c9f31d (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,076 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp39-cp39-linux_armv6l.whl#sha256=29a695a62aae6fa18fcad3ae6bfc6bbe19f545f66740fde177ddbf23efa45d15 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,077 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp39-cp39-linux_armv7l.whl#sha256=29a695a62aae6fa18fcad3ae6bfc6bbe19f545f66740fde177ddbf23efa45d15 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,077 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp311-cp311-linux_armv6l.whl#sha256=e93f43f34a8ab412f6a0c97bc930a5c9c72997258d109e3f069a56b6270ff331 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,077 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp311-cp311-linux_armv7l.whl#sha256=e93f43f34a8ab412f6a0c97bc930a5c9c72997258d109e3f069a56b6270ff331 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,078 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp39-cp39-linux_armv6l.whl#sha256=0d9c0566cba326dbedbea1c1ea643cc81efe1b0b47b292f956e933d1a9fedb35 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,078 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp39-cp39-linux_armv7l.whl#sha256=0d9c0566cba326dbedbea1c1ea643cc81efe1b0b47b292f956e933d1a9fedb35 (from https://www.piwheels.org/simple/kssdutils/) 2024-12-17T10:03:17,078 Skipping link: not a file: https://www.piwheels.org/simple/kssdutils/ 2024-12-17T10:03:17,079 Skipping link: not a file: https://pypi.org/simple/kssdutils/ 2024-12-17T10:03:17,103 Given no hashes to check 1 links for project 'kssdutils': discarding no candidates 2024-12-17T10:03:17,105 Collecting kssdutils==1.0.6 2024-12-17T10:03:17,108 Created temporary directory: /tmp/pip-unpack-3kpyj4ed 2024-12-17T10:03:17,149 Downloading kssdutils-1.0.6.tar.gz (44 kB) 2024-12-17T10:03:17,228 Added kssdutils==1.0.6 from https://files.pythonhosted.org/packages/aa/08/08fa5f76478fd3dbe9534ad21332b5dc03826197935c2b696e189af49f0b/kssdutils-1.0.6.tar.gz to build tracker '/tmp/pip-build-tracker-guvqi24m' 2024-12-17T10:03:17,231 Running setup.py (path:/tmp/pip-wheel-torbba1x/kssdutils_282dd1ec980f45c2a308f28b0129f229/setup.py) egg_info for package kssdutils 2024-12-17T10:03:17,231 Created temporary directory: /tmp/pip-pip-egg-info-px3cf7mh 2024-12-17T10:03:17,232 Preparing metadata (setup.py): started 2024-12-17T10:03:17,233 Running command python setup.py egg_info 2024-12-17T10:03:18,411 running egg_info 2024-12-17T10:03:18,451 creating /tmp/pip-pip-egg-info-px3cf7mh/kssdutils.egg-info 2024-12-17T10:03:18,452 writing /tmp/pip-pip-egg-info-px3cf7mh/kssdutils.egg-info/PKG-INFO 2024-12-17T10:03:18,455 writing dependency_links to /tmp/pip-pip-egg-info-px3cf7mh/kssdutils.egg-info/dependency_links.txt 2024-12-17T10:03:18,458 writing top-level names to /tmp/pip-pip-egg-info-px3cf7mh/kssdutils.egg-info/top_level.txt 2024-12-17T10:03:18,459 writing manifest file '/tmp/pip-pip-egg-info-px3cf7mh/kssdutils.egg-info/SOURCES.txt' 2024-12-17T10:03:18,597 reading manifest file '/tmp/pip-pip-egg-info-px3cf7mh/kssdutils.egg-info/SOURCES.txt' 2024-12-17T10:03:18,598 reading manifest template 'MANIFEST.in' 2024-12-17T10:03:18,607 writing manifest file '/tmp/pip-pip-egg-info-px3cf7mh/kssdutils.egg-info/SOURCES.txt' 2024-12-17T10:03:18,696 Preparing metadata (setup.py): finished with status 'done' 2024-12-17T10:03:18,700 Source in /tmp/pip-wheel-torbba1x/kssdutils_282dd1ec980f45c2a308f28b0129f229 has version 1.0.6, which satisfies requirement kssdutils==1.0.6 from https://files.pythonhosted.org/packages/aa/08/08fa5f76478fd3dbe9534ad21332b5dc03826197935c2b696e189af49f0b/kssdutils-1.0.6.tar.gz 2024-12-17T10:03:18,701 Removed kssdutils==1.0.6 from https://files.pythonhosted.org/packages/aa/08/08fa5f76478fd3dbe9534ad21332b5dc03826197935c2b696e189af49f0b/kssdutils-1.0.6.tar.gz from build tracker '/tmp/pip-build-tracker-guvqi24m' 2024-12-17T10:03:18,706 Created temporary directory: /tmp/pip-unpack-f67g972r 2024-12-17T10:03:18,707 Created temporary directory: /tmp/pip-unpack-f84nj7tt 2024-12-17T10:03:18,707 Building wheels for collected packages: kssdutils 2024-12-17T10:03:18,711 Created temporary directory: /tmp/pip-wheel-_tbx7rys 2024-12-17T10:03:18,711 Building wheel for kssdutils (setup.py): started 2024-12-17T10:03:18,712 Destination directory: /tmp/pip-wheel-_tbx7rys 2024-12-17T10:03:18,712 Running command python setup.py bdist_wheel 2024-12-17T10:03:20,010 running bdist_wheel 2024-12-17T10:03:20,185 running build 2024-12-17T10:03:20,186 running build_py 2024-12-17T10:03:20,223 creating build/lib.linux-armv7l-cpython-39 2024-12-17T10:03:20,225 copying kssdutils.py -> build/lib.linux-armv7l-cpython-39 2024-12-17T10:03:20,228 running egg_info 2024-12-17T10:03:20,266 writing kssdutils.egg-info/PKG-INFO 2024-12-17T10:03:20,269 writing dependency_links to kssdutils.egg-info/dependency_links.txt 2024-12-17T10:03:20,271 writing top-level names to kssdutils.egg-info/top_level.txt 2024-12-17T10:03:20,310 reading manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-12-17T10:03:20,314 reading manifest template 'MANIFEST.in' 2024-12-17T10:03:20,324 writing manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-12-17T10:03:20,326 running build_ext 2024-12-17T10:03:20,814 building 'kssdtool' extension 2024-12-17T10:03:20,815 creating build/temp.linux-armv7l-cpython-39 2024-12-17T10:03:20,817 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c co2mco.c -o build/temp.linux-armv7l-cpython-39/co2mco.o -fopenmp 2024-12-17T10:03:20,978 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-12-17T10:03:20,979 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-12-17T10:03:20,979 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-12-17T10:03:20,979 | ^ 2024-12-17T10:03:20,982 co2mco.c: In function ‘co2unitllmco’: 2024-12-17T10:03:20,983 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-12-17T10:03:20,983 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-12-17T10:03:20,983 | ^ 2024-12-17T10:03:21,597 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_composite.c -o build/temp.linux-armv7l-cpython-39/command_composite.o -fopenmp 2024-12-17T10:03:21,896 command_composite.c: In function ‘get_species_abundance’: 2024-12-17T10:03:21,897 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-12-17T10:03:21,897 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-12-17T10:03:21,897 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:21,898 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-12-17T10:03:21,898 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-12-17T10:03:21,898 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:21,899 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:21,899 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-12-17T10:03:21,899 | ^ 2024-12-17T10:03:21,900 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-12-17T10:03:21,900 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-12-17T10:03:21,900 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:21,900 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:21,901 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-12-17T10:03:21,901 | ^ 2024-12-17T10:03:21,901 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-12-17T10:03:21,901 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-12-17T10:03:21,901 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:21,902 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:21,902 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-12-17T10:03:21,902 | ^ 2024-12-17T10:03:21,902 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-12-17T10:03:21,902 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-12-17T10:03:21,902 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:21,903 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:21,903 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-12-17T10:03:21,903 | ^ 2024-12-17T10:03:21,903 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-12-17T10:03:21,903 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-12-17T10:03:21,904 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:21,904 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:21,904 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-12-17T10:03:21,904 | ^ 2024-12-17T10:03:21,904 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-12-17T10:03:21,905 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-12-17T10:03:21,905 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:22,141 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist.c -o build/temp.linux-armv7l-cpython-39/command_dist.o -fopenmp 2024-12-17T10:03:22,335 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-12-17T10:03:22,336 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=] 2024-12-17T10:03:22,336 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-17T10:03:22,336 | ~~^ 2024-12-17T10:03:22,336 | | 2024-12-17T10:03:22,337 | long unsigned int 2024-12-17T10:03:22,337 | %u 2024-12-17T10:03:22,337 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-17T10:03:22,337 | ~~~~~~~ 2024-12-17T10:03:22,337 | | 2024-12-17T10:03:22,337 | size_t {aka unsigned int} 2024-12-17T10:03:22,337 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=] 2024-12-17T10:03:22,337 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-17T10:03:22,338 | ~~^ 2024-12-17T10:03:22,338 | | 2024-12-17T10:03:22,338 | long unsigned int 2024-12-17T10:03:22,338 | %u 2024-12-17T10:03:22,338 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-17T10:03:22,338 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-12-17T10:03:22,338 | ~~~~~~~~~ 2024-12-17T10:03:22,338 | | 2024-12-17T10:03:22,339 | size_t {aka unsigned int} 2024-12-17T10:03:22,339 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-12-17T10:03:22,339 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-17T10:03:22,339 | ~~^ 2024-12-17T10:03:22,339 | | 2024-12-17T10:03:22,339 | long unsigned int 2024-12-17T10:03:22,339 | %u 2024-12-17T10:03:22,340 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-17T10:03:22,340 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-12-17T10:03:22,340 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:22,340 | | 2024-12-17T10:03:22,340 | unsigned int 2024-12-17T10:03:22,341 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-12-17T10:03:22,341 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-12-17T10:03:22,341 | ^ 2024-12-17T10:03:22,347 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-12-17T10:03:22,348 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=] 2024-12-17T10:03:22,348 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-12-17T10:03:22,348 | ~~^ ~~~~~~~ 2024-12-17T10:03:22,349 | | | 2024-12-17T10:03:22,349 | long unsigned int size_t {aka unsigned int} 2024-12-17T10:03:22,349 | %u 2024-12-17T10:03:22,350 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=] 2024-12-17T10:03:22,350 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-12-17T10:03:22,350 | ~~^ 2024-12-17T10:03:22,350 | | 2024-12-17T10:03:22,350 | long unsigned int 2024-12-17T10:03:22,350 | %u 2024-12-17T10:03:22,350 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-12-17T10:03:22,350 | ~~~~~~~~~ 2024-12-17T10:03:22,351 | | 2024-12-17T10:03:22,351 | size_t {aka unsigned int} 2024-12-17T10:03:22,351 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-12-17T10:03:22,351 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-12-17T10:03:22,351 | ~~^ 2024-12-17T10:03:22,352 | | 2024-12-17T10:03:22,352 | long unsigned int 2024-12-17T10:03:22,352 | %u 2024-12-17T10:03:22,352 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-12-17T10:03:22,352 865 | (size_t) b * unitsz_distf_mapped); 2024-12-17T10:03:22,352 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:22,352 | | 2024-12-17T10:03:22,352 | unsigned int 2024-12-17T10:03:22,353 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-12-17T10:03:22,353 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-12-17T10:03:22,354 | ^~~~~~~ 2024-12-17T10:03:22,354 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-12-17T10:03:22,354 809 | struct stat cbd_fcode_stat; 2024-12-17T10:03:22,354 | ^~~~~~~~~~~~~~ 2024-12-17T10:03:22,354 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-12-17T10:03:22,354 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-12-17T10:03:22,354 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:22,355 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-12-17T10:03:22,355 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-12-17T10:03:22,355 | ^~~~~~~~~~~~~~~~~ 2024-12-17T10:03:22,361 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-12-17T10:03:22,362 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=] 2024-12-17T10:03:22,362 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-17T10:03:22,362 | ~~^ 2024-12-17T10:03:22,362 | | 2024-12-17T10:03:22,362 | long unsigned int 2024-12-17T10:03:22,362 | %u 2024-12-17T10:03:22,363 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-17T10:03:22,363 | ~~~~~~~ 2024-12-17T10:03:22,363 | | 2024-12-17T10:03:22,363 | size_t {aka unsigned int} 2024-12-17T10:03:22,364 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=] 2024-12-17T10:03:22,364 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-17T10:03:22,364 | ~~^ 2024-12-17T10:03:22,364 | | 2024-12-17T10:03:22,364 | long unsigned int 2024-12-17T10:03:22,364 | %u 2024-12-17T10:03:22,364 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-17T10:03:22,364 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-12-17T10:03:22,365 | ~~~~~~~~~ 2024-12-17T10:03:22,365 | | 2024-12-17T10:03:22,365 | size_t {aka unsigned int} 2024-12-17T10:03:22,365 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-12-17T10:03:22,365 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-17T10:03:22,366 | ~~^ 2024-12-17T10:03:22,366 | | 2024-12-17T10:03:22,366 | long unsigned int 2024-12-17T10:03:22,366 | %u 2024-12-17T10:03:22,366 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-17T10:03:22,366 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-12-17T10:03:22,367 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:22,367 | | 2024-12-17T10:03:22,367 | unsigned int 2024-12-17T10:03:22,367 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-12-17T10:03:22,367 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-12-17T10:03:22,367 | ^ 2024-12-17T10:03:22,370 command_dist.c: In function ‘mco_co_dist_core’: 2024-12-17T10:03:22,371 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-12-17T10:03:22,371 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-12-17T10:03:22,371 | ^ 2024-12-17T10:03:22,377 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-12-17T10:03:22,377 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-17T10:03:22,378 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-12-17T10:03:22,378 | ^ 2024-12-17T10:03:22,379 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-17T10:03:22,379 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-12-17T10:03:22,379 | ^ 2024-12-17T10:03:22,384 command_dist.c: In function ‘dist_print_nobin’: 2024-12-17T10:03:22,385 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-17T10:03:22,385 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-12-17T10:03:22,385 | ^ 2024-12-17T10:03:22,387 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-17T10:03:22,387 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-12-17T10:03:22,387 | ^ 2024-12-17T10:03:22,389 command_dist.c:1380:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-17T10:03:22,389 1380 | for (int rid = 0; rid < ref_num; rid++) 2024-12-17T10:03:22,389 | ^ 2024-12-17T10:03:22,390 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-17T10:03:22,390 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-12-17T10:03:22,390 | ^ 2024-12-17T10:03:22,640 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-12-17T10:03:22,641 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-12-17T10:03:22,641 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-12-17T10:03:22,641 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:22,641 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-12-17T10:03:22,641 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-12-17T10:03:22,641 | ^~~~~~~~~~~~ 2024-12-17T10:03:23,363 command_dist.c: In function ‘get_dim_shuffle’: 2024-12-17T10:03:23,364 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-12-17T10:03:23,364 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-12-17T10:03:23,364 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:23,364 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-12-17T10:03:23,364 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-12-17T10:03:23,365 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,147 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-12-17T10:03:24,147 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:24,147 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-17T10:03:24,147 | ^~ ~~~~~~~~~ 2024-12-17T10:03:24,148 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-12-17T10:03:24,148 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-17T10:03:24,148 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,148 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-17T10:03:24,148 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-17T10:03:24,149 | ^~~~~~~~~~~~~~~ 2024-12-17T10:03:24,149 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-12-17T10:03:24,149 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-17T10:03:24,149 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,150 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-17T10:03:24,150 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-12-17T10:03:24,150 | ^~~~~~~~~~~ 2024-12-17T10:03:24,150 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-12-17T10:03:24,151 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-12-17T10:03:24,151 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,151 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-17T10:03:24,151 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-12-17T10:03:24,151 | ^~~~~ 2024-12-17T10:03:24,151 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-12-17T10:03:24,152 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-12-17T10:03:24,152 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,357 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-12-17T10:03:24,358 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:24,358 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-17T10:03:24,358 | ^~ ~~~~~~~~~ 2024-12-17T10:03:24,359 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-12-17T10:03:24,359 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-17T10:03:24,359 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,359 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-17T10:03:24,360 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-17T10:03:24,360 | ^~~~~~~~~~~~~~~ 2024-12-17T10:03:24,360 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-12-17T10:03:24,360 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-17T10:03:24,360 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,361 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-17T10:03:24,361 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-12-17T10:03:24,361 | ^~~~~~~~~~~~~ 2024-12-17T10:03:24,361 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-12-17T10:03:24,361 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-12-17T10:03:24,361 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,362 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:24,362 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-12-17T10:03:24,363 | ^ 2024-12-17T10:03:24,363 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-12-17T10:03:24,363 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-12-17T10:03:24,363 | ^~~~~~~~~~ 2024-12-17T10:03:24,363 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-12-17T10:03:24,364 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-12-17T10:03:24,364 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,364 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:24,364 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-12-17T10:03:24,364 | ^ 2024-12-17T10:03:24,365 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-12-17T10:03:24,365 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-12-17T10:03:24,365 | ^~~~~~~~~~ 2024-12-17T10:03:24,365 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-12-17T10:03:24,365 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-12-17T10:03:24,365 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,602 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-12-17T10:03:24,602 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:24,603 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-17T10:03:24,603 | ^~ ~~~~~~~~~ 2024-12-17T10:03:24,603 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-12-17T10:03:24,603 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-17T10:03:24,603 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,604 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-17T10:03:24,604 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-17T10:03:24,604 | ^~~~~~~~~~~~~~~ 2024-12-17T10:03:24,605 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-12-17T10:03:24,605 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-17T10:03:24,605 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,606 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-17T10:03:24,606 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-12-17T10:03:24,606 | ^~~~~~~~~~~~~ 2024-12-17T10:03:24,606 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-12-17T10:03:24,606 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-12-17T10:03:24,606 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,608 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-17T10:03:24,608 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-12-17T10:03:24,608 | ^~~~~~~~~~~ 2024-12-17T10:03:24,608 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-12-17T10:03:24,608 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-12-17T10:03:24,609 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,609 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-17T10:03:24,609 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-12-17T10:03:24,609 | ^~~~~ 2024-12-17T10:03:24,610 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-12-17T10:03:24,610 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-12-17T10:03:24,610 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,857 command_dist.c: In function ‘combine_queries’: 2024-12-17T10:03:24,858 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-17T10:03:24,858 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-12-17T10:03:24,859 | ^ 2024-12-17T10:03:24,859 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-17T10:03:24,859 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-12-17T10:03:24,860 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,860 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-17T10:03:24,861 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-12-17T10:03:24,861 | ^ 2024-12-17T10:03:24,861 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-17T10:03:24,862 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-12-17T10:03:24,862 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:24,864 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:24,864 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-12-17T10:03:24,864 | ^~ ~~~~~~~~ 2024-12-17T10:03:24,865 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-12-17T10:03:24,865 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-12-17T10:03:24,865 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,340 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o -fopenmp 2024-12-17T10:03:25,515 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_set.c -o build/temp.linux-armv7l-cpython-39/command_set.o -fopenmp 2024-12-17T10:03:25,694 command_set.c: In function ‘sketch_operate’: 2024-12-17T10:03:25,695 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-12-17T10:03:25,695 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-12-17T10:03:25,695 | ^ 2024-12-17T10:03:25,705 command_set.c: In function ‘combin_subset_pans’: 2024-12-17T10:03:25,705 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-12-17T10:03:25,705 457 | free(co_dstat_fpath); 2024-12-17T10:03:25,706 | ^~~~~~~~~~~~~~ 2024-12-17T10:03:25,706 In file included from kssdheaders/global_basic.h:159, 2024-12-17T10:03:25,706 from command_set.c:15: 2024-12-17T10:03:25,706 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-12-17T10:03:25,706 565 | extern void free (void *__ptr) __THROW; 2024-12-17T10:03:25,706 | ~~~~~~^~~~~ 2024-12-17T10:03:25,710 command_set.c: In function ‘grouping_genomes’: 2024-12-17T10:03:25,711 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-12-17T10:03:25,711 562 | free(co_dstat_fpath); 2024-12-17T10:03:25,711 | ^~~~~~~~~~~~~~ 2024-12-17T10:03:25,711 In file included from kssdheaders/global_basic.h:159, 2024-12-17T10:03:25,711 from command_set.c:15: 2024-12-17T10:03:25,711 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-12-17T10:03:25,711 565 | extern void free (void *__ptr) __THROW; 2024-12-17T10:03:25,712 | ~~~~~~^~~~~ 2024-12-17T10:03:25,826 command_set.c: In function ‘sketch_union’: 2024-12-17T10:03:25,827 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-17T10:03:25,827 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:25,827 | ^ 2024-12-17T10:03:25,827 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-17T10:03:25,827 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:25,827 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,828 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:25,828 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-12-17T10:03:25,828 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:25,828 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-17T10:03:25,828 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-12-17T10:03:25,828 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,828 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:25,829 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-12-17T10:03:25,829 | ^~ ~~~~~~~~~~ 2024-12-17T10:03:25,829 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-12-17T10:03:25,829 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-12-17T10:03:25,829 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,940 command_set.c: In function ‘sketch_operate’: 2024-12-17T10:03:25,940 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:25,941 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-12-17T10:03:25,941 | ^~ ~~~~~~~~~~ 2024-12-17T10:03:25,941 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-12-17T10:03:25,941 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-12-17T10:03:25,941 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,941 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:25,941 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-12-17T10:03:25,942 | ^~ ~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,942 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-12-17T10:03:25,942 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-12-17T10:03:25,942 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,942 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:25,942 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-12-17T10:03:25,942 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:25,943 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-17T10:03:25,943 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-12-17T10:03:25,943 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,943 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:25,943 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-12-17T10:03:25,943 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:25,943 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-17T10:03:25,943 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-12-17T10:03:25,944 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,944 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:25,944 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-12-17T10:03:25,944 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:25,944 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-17T10:03:25,944 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-12-17T10:03:25,944 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,945 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:25,945 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-12-17T10:03:25,945 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:25,945 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-17T10:03:25,945 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-12-17T10:03:25,945 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:25,945 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-17T10:03:25,945 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:25,946 | ^ 2024-12-17T10:03:25,946 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-17T10:03:25,946 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:25,946 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,093 command_set.c: In function ‘uniq_sketch_union’: 2024-12-17T10:03:26,093 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-17T10:03:26,094 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:26,094 | ^ 2024-12-17T10:03:26,094 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-17T10:03:26,094 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:26,094 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,094 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,094 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-12-17T10:03:26,095 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:26,095 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-17T10:03:26,095 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-12-17T10:03:26,095 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,095 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,095 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-12-17T10:03:26,095 | ^~ ~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,096 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-12-17T10:03:26,096 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-12-17T10:03:26,096 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,220 command_set.c: In function ‘combin_pans’: 2024-12-17T10:03:26,220 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,220 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-17T10:03:26,220 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:26,221 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2024-12-17T10:03:26,221 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-17T10:03:26,221 | ^~~~~~~~~~ 2024-12-17T10:03:26,221 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-12-17T10:03:26,221 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-17T10:03:26,221 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,221 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,222 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-17T10:03:26,222 | ^~ ~~~~~~~~~~ 2024-12-17T10:03:26,222 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2024-12-17T10:03:26,222 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-17T10:03:26,222 | ^~~~~~~~~~ 2024-12-17T10:03:26,222 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-12-17T10:03:26,222 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-17T10:03:26,222 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,223 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-17T10:03:26,223 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:26,223 | ^ 2024-12-17T10:03:26,223 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-17T10:03:26,223 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:26,223 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,409 command_set.c: In function ‘combin_subset_pans’: 2024-12-17T10:03:26,410 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,410 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-12-17T10:03:26,410 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:26,410 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-17T10:03:26,410 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-12-17T10:03:26,410 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,410 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,411 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-12-17T10:03:26,411 | ^~ ~~~~~~~~~~ 2024-12-17T10:03:26,411 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-17T10:03:26,411 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-12-17T10:03:26,411 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,411 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,411 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-17T10:03:26,412 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:26,412 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-17T10:03:26,412 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-17T10:03:26,412 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,413 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,413 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-17T10:03:26,414 | ^~ ~~~~~~~~~~ 2024-12-17T10:03:26,414 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-17T10:03:26,414 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-17T10:03:26,414 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,414 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-17T10:03:26,414 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:26,414 | ^ 2024-12-17T10:03:26,414 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-17T10:03:26,415 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:26,415 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,616 command_set.c: In function ‘grouping_genomes’: 2024-12-17T10:03:26,616 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,616 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-12-17T10:03:26,616 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:26,617 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-17T10:03:26,617 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-12-17T10:03:26,617 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,617 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,617 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-12-17T10:03:26,617 | ^~ ~~~~~~~~~~ 2024-12-17T10:03:26,618 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-17T10:03:26,618 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-12-17T10:03:26,618 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,619 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,620 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-17T10:03:26,620 | ^~ ~~~~~~~~~~~ 2024-12-17T10:03:26,620 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-17T10:03:26,620 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-17T10:03:26,620 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,621 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-17T10:03:26,621 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-17T10:03:26,621 | ^~ ~~~~~~~~~~ 2024-12-17T10:03:26,621 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-17T10:03:26,621 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-17T10:03:26,622 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,622 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-17T10:03:26,622 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:26,622 | ^ 2024-12-17T10:03:26,622 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-17T10:03:26,623 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-17T10:03:26,623 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:26,892 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-39/command_shuffle.o -fopenmp 2024-12-17T10:03:27,171 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c global_basic.c -o build/temp.linux-armv7l-cpython-39/global_basic.o -fopenmp 2024-12-17T10:03:27,319 global_basic.c: In function ‘organize_infile_list’: 2024-12-17T10:03:27,319 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-12-17T10:03:27,319 195 | while (isspace(*buf)) buf++; 2024-12-17T10:03:27,319 | ^~~~~~~ 2024-12-17T10:03:27,319 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=] 2024-12-17T10:03:27,320 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-12-17T10:03:27,320 | ~~^ 2024-12-17T10:03:27,320 | | 2024-12-17T10:03:27,320 | long unsigned int 2024-12-17T10:03:27,320 | %u 2024-12-17T10:03:27,320 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-12-17T10:03:27,321 | ~~~~~~~~~~~ 2024-12-17T10:03:27,321 | | 2024-12-17T10:03:27,321 | size_t {aka unsigned int} 2024-12-17T10:03:27,321 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=] 2024-12-17T10:03:27,321 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-12-17T10:03:27,321 | ~~^ 2024-12-17T10:03:27,321 | | 2024-12-17T10:03:27,322 | long unsigned int 2024-12-17T10:03:27,322 | %u 2024-12-17T10:03:27,322 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-12-17T10:03:27,322 | ~~~~~~~~~~~ 2024-12-17T10:03:27,322 | | 2024-12-17T10:03:27,322 | size_t {aka unsigned int} 2024-12-17T10:03:27,998 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-39/iseq2comem.o -fopenmp 2024-12-17T10:03:28,150 iseq2comem.c: In function ‘reads2mco’: 2024-12-17T10:03:28,151 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,151 156 | if (base > TL) { 2024-12-17T10:03:28,151 | ^ 2024-12-17T10:03:28,151 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,152 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-17T10:03:28,152 | ^~ 2024-12-17T10:03:28,152 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,152 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-17T10:03:28,152 | ^ 2024-12-17T10:03:28,154 iseq2comem.c: In function ‘fasta2co’: 2024-12-17T10:03:28,155 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,155 239 | if (base > TL) { 2024-12-17T10:03:28,155 | ^ 2024-12-17T10:03:28,156 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,156 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-17T10:03:28,156 | ^~ 2024-12-17T10:03:28,156 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,156 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-17T10:03:28,157 | ^ 2024-12-17T10:03:28,157 iseq2comem.c: In function ‘fastq2co’: 2024-12-17T10:03:28,158 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-12-17T10:03:28,158 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-12-17T10:03:28,158 | ^~ 2024-12-17T10:03:28,160 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,160 318 | if (base > TL) { 2024-12-17T10:03:28,160 | ^ 2024-12-17T10:03:28,161 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,161 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-17T10:03:28,161 | ^~ 2024-12-17T10:03:28,161 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,162 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-17T10:03:28,162 | ^ 2024-12-17T10:03:28,163 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,163 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-12-17T10:03:28,163 | ^ 2024-12-17T10:03:28,165 iseq2comem.c: In function ‘fastq2koc’: 2024-12-17T10:03:28,165 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,166 402 | if (base > TL) { 2024-12-17T10:03:28,166 | ^ 2024-12-17T10:03:28,166 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,166 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-17T10:03:28,166 | ^~ 2024-12-17T10:03:28,167 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,167 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-17T10:03:28,167 | ^ 2024-12-17T10:03:28,173 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-12-17T10:03:28,174 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,174 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-17T10:03:28,174 | ^~ 2024-12-17T10:03:28,174 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-17T10:03:28,175 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-17T10:03:28,175 | ^ 2024-12-17T10:03:29,343 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-12-17T10:03:29,404 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mytime.c -o build/temp.linux-armv7l-cpython-39/mytime.o -fopenmp 2024-12-17T10:03:29,527 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c pykssd.c -o build/temp.linux-armv7l-cpython-39/pykssd.o -fopenmp 2024-12-17T10:03:29,855 pykssd.c: In function ‘py_dist_dispatch’: 2024-12-17T10:03:29,856 pykssd.c:335:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-12-17T10:03:29,856 335 | int state1 = dist_dispatch(&dist_opt_val1); 2024-12-17T10:03:29,856 | ^~~~~~ 2024-12-17T10:03:29,856 pykssd.c:397:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-12-17T10:03:29,857 397 | int state2 = dist_dispatch(&dist_opt_val2); 2024-12-17T10:03:29,857 | ^~~~~~ 2024-12-17T10:03:29,858 pykssd.c:531:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-12-17T10:03:29,858 531 | int state4 = dist_dispatch(&dist_opt_val4); 2024-12-17T10:03:29,858 | ^~~~~~ 2024-12-17T10:03:30,003 pykssd.c: In function ‘rename_file’: 2024-12-17T10:03:30,004 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-12-17T10:03:30,004 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-12-17T10:03:30,004 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-17T10:03:30,004 pykssd.c:41:15: note: length computed here 2024-12-17T10:03:30,004 41 | int len = strlen(p1); 2024-12-17T10:03:30,004 | ^~~~~~~~~~ 2024-12-17T10:03:30,432 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/co2mco.o build/temp.linux-armv7l-cpython-39/command_composite.o build/temp.linux-armv7l-cpython-39/command_dist.o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o build/temp.linux-armv7l-cpython-39/command_set.o build/temp.linux-armv7l-cpython-39/command_shuffle.o build/temp.linux-armv7l-cpython-39/global_basic.o build/temp.linux-armv7l-cpython-39/iseq2comem.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/mytime.o build/temp.linux-armv7l-cpython-39/pykssd.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/kssdtool.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-12-17T10:03:30,621 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-12-17T10:03:30,621 !! 2024-12-17T10:03:30,622 ******************************************************************************** 2024-12-17T10:03:30,622 Please avoid running ``setup.py`` directly. 2024-12-17T10:03:30,622 Instead, use pypa/build, pypa/installer or other 2024-12-17T10:03:30,622 standards-based tools. 2024-12-17T10:03:30,622 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-12-17T10:03:30,622 ******************************************************************************** 2024-12-17T10:03:30,622 !! 2024-12-17T10:03:30,623 self.initialize_options() 2024-12-17T10:03:30,655 installing to build/bdist.linux-armv7l/wheel 2024-12-17T10:03:30,655 running install 2024-12-17T10:03:30,682 running install_lib 2024-12-17T10:03:30,716 creating build/bdist.linux-armv7l/wheel 2024-12-17T10:03:30,718 copying build/lib.linux-armv7l-cpython-39/kssdutils.py -> build/bdist.linux-armv7l/wheel/. 2024-12-17T10:03:30,721 copying build/lib.linux-armv7l-cpython-39/kssdtool.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-12-17T10:03:30,731 running install_egg_info 2024-12-17T10:03:30,779 Copying kssdutils.egg-info to build/bdist.linux-armv7l/wheel/./kssdutils-1.0.6-py3.9.egg-info 2024-12-17T10:03:30,789 running install_scripts 2024-12-17T10:03:30,840 creating build/bdist.linux-armv7l/wheel/kssdutils-1.0.6.dist-info/WHEEL 2024-12-17T10:03:30,843 creating '/tmp/pip-wheel-_tbx7rys/kssdutils-1.0.6-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-12-17T10:03:30,938 adding 'kssdtool.cpython-39-arm-linux-gnueabihf.so' 2024-12-17T10:03:30,943 adding 'kssdutils.py' 2024-12-17T10:03:30,945 adding 'kssdutils-1.0.6.dist-info/METADATA' 2024-12-17T10:03:30,946 adding 'kssdutils-1.0.6.dist-info/WHEEL' 2024-12-17T10:03:30,947 adding 'kssdutils-1.0.6.dist-info/dependency_links.txt' 2024-12-17T10:03:30,947 adding 'kssdutils-1.0.6.dist-info/top_level.txt' 2024-12-17T10:03:30,948 adding 'kssdutils-1.0.6.dist-info/RECORD' 2024-12-17T10:03:30,953 removing build/bdist.linux-armv7l/wheel 2024-12-17T10:03:31,084 Building wheel for kssdutils (setup.py): finished with status 'done' 2024-12-17T10:03:31,089 Created wheel for kssdutils: filename=kssdutils-1.0.6-cp39-cp39-linux_armv7l.whl size=179910 sha256=bfe64af80d2aab63dccf6fb0418e3b806f4ee1b2fcff0eab77094040d2b6dca5 2024-12-17T10:03:31,090 Stored in directory: /tmp/pip-ephem-wheel-cache-vay16w3r/wheels/dc/09/c9/3554b7c5d7ca36ecfa7425d6ad54294033cef64614e02024ba 2024-12-17T10:03:31,099 Successfully built kssdutils 2024-12-17T10:03:31,109 Removed build tracker: '/tmp/pip-build-tracker-guvqi24m'