2024-12-12T05:38:56,159 Disabling truststore because Python version isn't 3.10+ 2024-12-12T05:38:56,773 Created temporary directory: /tmp/pip-build-tracker-73tma2iu 2024-12-12T05:38:56,774 Initialized build tracking at /tmp/pip-build-tracker-73tma2iu 2024-12-12T05:38:56,774 Created build tracker: /tmp/pip-build-tracker-73tma2iu 2024-12-12T05:38:56,774 Entered build tracker: /tmp/pip-build-tracker-73tma2iu 2024-12-12T05:38:56,775 Created temporary directory: /tmp/pip-wheel-mrj84cob 2024-12-12T05:38:56,781 Created temporary directory: /tmp/pip-ephem-wheel-cache-9uvxrwpi 2024-12-12T05:38:56,834 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-12-12T05:38:56,837 2 location(s) to search for versions of kssdutils: 2024-12-12T05:38:56,837 * https://pypi.org/simple/kssdutils/ 2024-12-12T05:38:56,837 * https://www.piwheels.org/simple/kssdutils/ 2024-12-12T05:38:56,838 Fetching project page and analyzing links: https://pypi.org/simple/kssdutils/ 2024-12-12T05:38:56,838 Getting page https://pypi.org/simple/kssdutils/ 2024-12-12T05:38:56,840 Found index url https://pypi.org/simple/ 2024-12-12T05:38:56,939 Fetched page https://pypi.org/simple/kssdutils/ as application/vnd.pypi.simple.v1+json 2024-12-12T05:38:56,941 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 2024-12-12T05:38:56,941 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 2024-12-12T05:38:56,941 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 2024-12-12T05:38:56,942 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 2024-12-12T05:38:56,942 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 2024-12-12T05:38:56,942 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdutils/ 2024-12-12T05:38:56,943 Getting page https://www.piwheels.org/simple/kssdutils/ 2024-12-12T05:38:56,944 Found index url https://www.piwheels.org/simple/ 2024-12-12T05:38:56,984 Fetched page https://www.piwheels.org/simple/kssdutils/ as text/html 2024-12-12T05:38:56,989 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/) 2024-12-12T05:38:56,989 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/) 2024-12-12T05:38:56,989 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/) 2024-12-12T05:38:56,989 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/) 2024-12-12T05:38:56,990 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/) 2024-12-12T05:38:56,990 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/) 2024-12-12T05:38:56,990 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/) 2024-12-12T05:38:56,990 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/) 2024-12-12T05:38:56,990 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/) 2024-12-12T05:38:56,991 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/) 2024-12-12T05:38:56,991 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/) 2024-12-12T05:38:56,991 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/) 2024-12-12T05:38:56,991 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/) 2024-12-12T05:38:56,991 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/) 2024-12-12T05:38:56,992 Skipping link: not a file: https://www.piwheels.org/simple/kssdutils/ 2024-12-12T05:38:56,992 Skipping link: not a file: https://pypi.org/simple/kssdutils/ 2024-12-12T05:38:57,009 Given no hashes to check 1 links for project 'kssdutils': discarding no candidates 2024-12-12T05:38:57,011 Collecting kssdutils==1.0.5 2024-12-12T05:38:57,013 Created temporary directory: /tmp/pip-unpack-8l5oi0fa 2024-12-12T05:38:57,030 Downloading kssdutils-1.0.5.tar.gz (44 kB) 2024-12-12T05:38:57,111 Added kssdutils==1.0.5 from https://files.pythonhosted.org/packages/42/01/15ec102f7ac6b4fc3158ba60de64598a005cefffc773fa69eecbd3c9b016/kssdutils-1.0.5.tar.gz to build tracker '/tmp/pip-build-tracker-73tma2iu' 2024-12-12T05:38:57,122 Running setup.py (path:/tmp/pip-wheel-mrj84cob/kssdutils_56bfd2e7a247425abaf9258da821bd4d/setup.py) egg_info for package kssdutils 2024-12-12T05:38:57,123 Created temporary directory: /tmp/pip-pip-egg-info-_xx4jla_ 2024-12-12T05:38:57,123 Preparing metadata (setup.py): started 2024-12-12T05:38:57,124 Running command python setup.py egg_info 2024-12-12T05:38:58,299 running egg_info 2024-12-12T05:38:58,331 creating /tmp/pip-pip-egg-info-_xx4jla_/kssdutils.egg-info 2024-12-12T05:38:58,332 writing /tmp/pip-pip-egg-info-_xx4jla_/kssdutils.egg-info/PKG-INFO 2024-12-12T05:38:58,336 writing dependency_links to /tmp/pip-pip-egg-info-_xx4jla_/kssdutils.egg-info/dependency_links.txt 2024-12-12T05:38:58,338 writing top-level names to /tmp/pip-pip-egg-info-_xx4jla_/kssdutils.egg-info/top_level.txt 2024-12-12T05:38:58,340 writing manifest file '/tmp/pip-pip-egg-info-_xx4jla_/kssdutils.egg-info/SOURCES.txt' 2024-12-12T05:38:58,460 reading manifest file '/tmp/pip-pip-egg-info-_xx4jla_/kssdutils.egg-info/SOURCES.txt' 2024-12-12T05:38:58,462 reading manifest template 'MANIFEST.in' 2024-12-12T05:38:58,471 writing manifest file '/tmp/pip-pip-egg-info-_xx4jla_/kssdutils.egg-info/SOURCES.txt' 2024-12-12T05:38:58,560 Preparing metadata (setup.py): finished with status 'done' 2024-12-12T05:38:58,564 Source in /tmp/pip-wheel-mrj84cob/kssdutils_56bfd2e7a247425abaf9258da821bd4d has version 1.0.5, which satisfies requirement kssdutils==1.0.5 from https://files.pythonhosted.org/packages/42/01/15ec102f7ac6b4fc3158ba60de64598a005cefffc773fa69eecbd3c9b016/kssdutils-1.0.5.tar.gz 2024-12-12T05:38:58,565 Removed kssdutils==1.0.5 from https://files.pythonhosted.org/packages/42/01/15ec102f7ac6b4fc3158ba60de64598a005cefffc773fa69eecbd3c9b016/kssdutils-1.0.5.tar.gz from build tracker '/tmp/pip-build-tracker-73tma2iu' 2024-12-12T05:38:58,569 Created temporary directory: /tmp/pip-unpack-_ddjb7uf 2024-12-12T05:38:58,570 Created temporary directory: /tmp/pip-unpack-g5ok03nu 2024-12-12T05:38:58,570 Building wheels for collected packages: kssdutils 2024-12-12T05:38:58,575 Created temporary directory: /tmp/pip-wheel-h9gu43hi 2024-12-12T05:38:58,575 Building wheel for kssdutils (setup.py): started 2024-12-12T05:38:58,576 Destination directory: /tmp/pip-wheel-h9gu43hi 2024-12-12T05:38:58,576 Running command python setup.py bdist_wheel 2024-12-12T05:39:01,103 running bdist_wheel 2024-12-12T05:39:01,304 running build 2024-12-12T05:39:01,305 running build_py 2024-12-12T05:39:01,343 creating build/lib.linux-armv7l-cpython-39 2024-12-12T05:39:01,345 copying kssdutils.py -> build/lib.linux-armv7l-cpython-39 2024-12-12T05:39:01,348 running egg_info 2024-12-12T05:39:01,380 writing kssdutils.egg-info/PKG-INFO 2024-12-12T05:39:01,384 writing dependency_links to kssdutils.egg-info/dependency_links.txt 2024-12-12T05:39:01,387 writing top-level names to kssdutils.egg-info/top_level.txt 2024-12-12T05:39:01,429 reading manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-12-12T05:39:01,433 reading manifest template 'MANIFEST.in' 2024-12-12T05:39:01,450 writing manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-12-12T05:39:01,452 running build_ext 2024-12-12T05:39:01,973 building 'kssdtool' extension 2024-12-12T05:39:01,974 creating build/temp.linux-armv7l-cpython-39 2024-12-12T05:39:01,976 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 2024-12-12T05:39:02,209 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-12-12T05:39:02,209 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-12-12T05:39:02,210 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-12-12T05:39:02,210 | ^ 2024-12-12T05:39:02,212 co2mco.c: In function ‘co2unitllmco’: 2024-12-12T05:39:02,212 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-12-12T05:39:02,212 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-12-12T05:39:02,213 | ^ 2024-12-12T05:39:02,847 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 2024-12-12T05:39:03,174 command_composite.c: In function ‘get_species_abundance’: 2024-12-12T05:39:03,175 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-12-12T05:39:03,175 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-12-12T05:39:03,175 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,176 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-12-12T05:39:03,176 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-12-12T05:39:03,176 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,177 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:03,177 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-12-12T05:39:03,177 | ^ 2024-12-12T05:39:03,178 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-12-12T05:39:03,178 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-12-12T05:39:03,178 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,178 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:03,178 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-12-12T05:39:03,178 | ^ 2024-12-12T05:39:03,179 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-12-12T05:39:03,179 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-12-12T05:39:03,179 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,179 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:03,179 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-12-12T05:39:03,180 | ^ 2024-12-12T05:39:03,180 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-12-12T05:39:03,180 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-12-12T05:39:03,180 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,180 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:03,181 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-12-12T05:39:03,181 | ^ 2024-12-12T05:39:03,181 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-12-12T05:39:03,181 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-12-12T05:39:03,181 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,182 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:03,182 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-12-12T05:39:03,182 | ^ 2024-12-12T05:39:03,182 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-12-12T05:39:03,182 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-12-12T05:39:03,182 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,426 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 2024-12-12T05:39:03,670 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-12-12T05:39:03,671 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=] 2024-12-12T05:39:03,671 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-12T05:39:03,671 | ~~^ 2024-12-12T05:39:03,671 | | 2024-12-12T05:39:03,671 | long unsigned int 2024-12-12T05:39:03,671 | %u 2024-12-12T05:39:03,672 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-12T05:39:03,672 | ~~~~~~~ 2024-12-12T05:39:03,672 | | 2024-12-12T05:39:03,672 | size_t {aka unsigned int} 2024-12-12T05:39:03,672 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=] 2024-12-12T05:39:03,672 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-12T05:39:03,672 | ~~^ 2024-12-12T05:39:03,672 | | 2024-12-12T05:39:03,673 | long unsigned int 2024-12-12T05:39:03,673 | %u 2024-12-12T05:39:03,673 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-12T05:39:03,673 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-12-12T05:39:03,673 | ~~~~~~~~~ 2024-12-12T05:39:03,673 | | 2024-12-12T05:39:03,673 | size_t {aka unsigned int} 2024-12-12T05:39:03,674 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-12-12T05:39:03,674 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-12T05:39:03,674 | ~~^ 2024-12-12T05:39:03,674 | | 2024-12-12T05:39:03,674 | long unsigned int 2024-12-12T05:39:03,674 | %u 2024-12-12T05:39:03,674 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-12T05:39:03,675 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-12-12T05:39:03,675 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,675 | | 2024-12-12T05:39:03,675 | unsigned int 2024-12-12T05:39:03,676 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-12-12T05:39:03,676 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-12-12T05:39:03,676 | ^ 2024-12-12T05:39:03,682 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-12-12T05:39:03,683 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=] 2024-12-12T05:39:03,683 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-12-12T05:39:03,683 | ~~^ ~~~~~~~ 2024-12-12T05:39:03,683 | | | 2024-12-12T05:39:03,684 | long unsigned int size_t {aka unsigned int} 2024-12-12T05:39:03,684 | %u 2024-12-12T05:39:03,684 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=] 2024-12-12T05:39:03,685 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-12-12T05:39:03,685 | ~~^ 2024-12-12T05:39:03,685 | | 2024-12-12T05:39:03,685 | long unsigned int 2024-12-12T05:39:03,685 | %u 2024-12-12T05:39:03,685 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-12-12T05:39:03,685 | ~~~~~~~~~ 2024-12-12T05:39:03,685 | | 2024-12-12T05:39:03,686 | size_t {aka unsigned int} 2024-12-12T05:39:03,686 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-12-12T05:39:03,686 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-12-12T05:39:03,686 | ~~^ 2024-12-12T05:39:03,686 | | 2024-12-12T05:39:03,687 | long unsigned int 2024-12-12T05:39:03,687 | %u 2024-12-12T05:39:03,687 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-12-12T05:39:03,687 865 | (size_t) b * unitsz_distf_mapped); 2024-12-12T05:39:03,687 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,687 | | 2024-12-12T05:39:03,687 | unsigned int 2024-12-12T05:39:03,688 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-12-12T05:39:03,688 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-12-12T05:39:03,688 | ^~~~~~~ 2024-12-12T05:39:03,689 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-12-12T05:39:03,689 809 | struct stat cbd_fcode_stat; 2024-12-12T05:39:03,689 | ^~~~~~~~~~~~~~ 2024-12-12T05:39:03,689 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-12-12T05:39:03,689 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-12-12T05:39:03,689 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,690 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-12-12T05:39:03,690 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-12-12T05:39:03,690 | ^~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,695 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-12-12T05:39:03,697 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=] 2024-12-12T05:39:03,697 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-12T05:39:03,697 | ~~^ 2024-12-12T05:39:03,697 | | 2024-12-12T05:39:03,697 | long unsigned int 2024-12-12T05:39:03,697 | %u 2024-12-12T05:39:03,697 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-12T05:39:03,698 | ~~~~~~~ 2024-12-12T05:39:03,698 | | 2024-12-12T05:39:03,698 | size_t {aka unsigned int} 2024-12-12T05:39:03,698 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=] 2024-12-12T05:39:03,699 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-12T05:39:03,699 | ~~^ 2024-12-12T05:39:03,699 | | 2024-12-12T05:39:03,699 | long unsigned int 2024-12-12T05:39:03,699 | %u 2024-12-12T05:39:03,699 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-12T05:39:03,699 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-12-12T05:39:03,699 | ~~~~~~~~~ 2024-12-12T05:39:03,699 | | 2024-12-12T05:39:03,700 | size_t {aka unsigned int} 2024-12-12T05:39:03,700 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-12-12T05:39:03,700 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-12-12T05:39:03,700 | ~~^ 2024-12-12T05:39:03,701 | | 2024-12-12T05:39:03,701 | long unsigned int 2024-12-12T05:39:03,701 | %u 2024-12-12T05:39:03,701 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-12-12T05:39:03,701 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-12-12T05:39:03,701 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,701 | | 2024-12-12T05:39:03,701 | unsigned int 2024-12-12T05:39:03,702 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-12-12T05:39:03,702 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-12-12T05:39:03,702 | ^ 2024-12-12T05:39:03,705 command_dist.c: In function ‘mco_co_dist_core’: 2024-12-12T05:39:03,706 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-12-12T05:39:03,706 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-12-12T05:39:03,706 | ^ 2024-12-12T05:39:03,712 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-12-12T05:39:03,712 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-12T05:39:03,712 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-12-12T05:39:03,713 | ^ 2024-12-12T05:39:03,714 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-12T05:39:03,714 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-12-12T05:39:03,714 | ^ 2024-12-12T05:39:03,719 command_dist.c: In function ‘dist_print_nobin’: 2024-12-12T05:39:03,720 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-12T05:39:03,720 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-12-12T05:39:03,720 | ^ 2024-12-12T05:39:03,722 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-12T05:39:03,722 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-12-12T05:39:03,722 | ^ 2024-12-12T05:39:03,723 command_dist.c:1380:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-12T05:39:03,724 1380 | for (int rid = 0; rid < ref_num; rid++) 2024-12-12T05:39:03,724 | ^ 2024-12-12T05:39:03,724 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-12-12T05:39:03,725 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-12-12T05:39:03,725 | ^ 2024-12-12T05:39:03,976 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-12-12T05:39:03,976 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-12-12T05:39:03,976 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-12-12T05:39:03,977 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:03,977 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-12-12T05:39:03,977 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-12-12T05:39:03,977 | ^~~~~~~~~~~~ 2024-12-12T05:39:04,699 command_dist.c: In function ‘get_dim_shuffle’: 2024-12-12T05:39:04,699 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-12-12T05:39:04,700 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-12-12T05:39:04,700 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:04,700 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-12-12T05:39:04,700 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-12-12T05:39:04,700 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,482 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-12-12T05:39:05,483 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:05,483 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-12T05:39:05,483 | ^~ ~~~~~~~~~ 2024-12-12T05:39:05,483 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-12-12T05:39:05,483 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-12T05:39:05,483 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,484 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-12T05:39:05,484 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-12T05:39:05,484 | ^~~~~~~~~~~~~~~ 2024-12-12T05:39:05,484 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-12-12T05:39:05,484 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-12T05:39:05,485 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,485 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-12T05:39:05,486 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-12-12T05:39:05,486 | ^~~~~~~~~~~ 2024-12-12T05:39:05,486 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-12-12T05:39:05,486 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-12-12T05:39:05,486 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,486 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-12T05:39:05,487 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-12-12T05:39:05,487 | ^~~~~ 2024-12-12T05:39:05,487 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-12-12T05:39:05,487 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-12-12T05:39:05,487 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,692 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-12-12T05:39:05,693 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:05,693 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-12T05:39:05,693 | ^~ ~~~~~~~~~ 2024-12-12T05:39:05,693 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-12-12T05:39:05,693 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-12T05:39:05,694 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,694 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-12T05:39:05,694 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-12T05:39:05,694 | ^~~~~~~~~~~~~~~ 2024-12-12T05:39:05,695 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-12-12T05:39:05,695 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-12T05:39:05,695 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,695 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-12T05:39:05,695 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-12-12T05:39:05,695 | ^~~~~~~~~~~~~ 2024-12-12T05:39:05,696 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-12-12T05:39:05,696 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-12-12T05:39:05,696 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,697 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:05,697 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-12-12T05:39:05,697 | ^ 2024-12-12T05:39:05,697 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-12-12T05:39:05,698 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-12-12T05:39:05,698 | ^~~~~~~~~~ 2024-12-12T05:39:05,698 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-12-12T05:39:05,698 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-12-12T05:39:05,698 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,699 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:05,699 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-12-12T05:39:05,699 | ^ 2024-12-12T05:39:05,699 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-12-12T05:39:05,699 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-12-12T05:39:05,700 | ^~~~~~~~~~ 2024-12-12T05:39:05,700 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-12-12T05:39:05,700 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-12-12T05:39:05,700 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,936 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-12-12T05:39:05,937 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:05,937 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-12T05:39:05,937 | ^~ ~~~~~~~~~ 2024-12-12T05:39:05,937 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-12-12T05:39:05,937 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-12-12T05:39:05,938 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,938 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-12T05:39:05,938 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-12T05:39:05,939 | ^~~~~~~~~~~~~~~ 2024-12-12T05:39:05,939 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-12-12T05:39:05,939 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-12-12T05:39:05,939 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,940 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-12T05:39:05,940 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-12-12T05:39:05,940 | ^~~~~~~~~~~~~ 2024-12-12T05:39:05,940 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-12-12T05:39:05,941 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-12-12T05:39:05,941 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,942 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-12T05:39:05,942 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-12-12T05:39:05,942 | ^~~~~~~~~~~ 2024-12-12T05:39:05,943 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-12-12T05:39:05,943 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-12-12T05:39:05,943 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:05,943 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-12-12T05:39:05,943 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-12-12T05:39:05,944 | ^~~~~ 2024-12-12T05:39:05,944 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-12-12T05:39:05,944 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-12-12T05:39:05,944 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:06,190 command_dist.c: In function ‘combine_queries’: 2024-12-12T05:39:06,191 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-12T05:39:06,191 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-12-12T05:39:06,192 | ^ 2024-12-12T05:39:06,192 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-12T05:39:06,192 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-12-12T05:39:06,193 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:06,193 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-12T05:39:06,194 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-12-12T05:39:06,194 | ^ 2024-12-12T05:39:06,194 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-12T05:39:06,195 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-12-12T05:39:06,195 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:06,197 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:06,197 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-12-12T05:39:06,197 | ^~ ~~~~~~~~ 2024-12-12T05:39:06,198 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-12-12T05:39:06,198 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-12-12T05:39:06,198 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:06,669 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 2024-12-12T05:39:06,837 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 2024-12-12T05:39:06,984 command_set.c: In function ‘sketch_operate’: 2024-12-12T05:39:06,985 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-12-12T05:39:06,985 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-12-12T05:39:06,985 | ^ 2024-12-12T05:39:06,994 command_set.c: In function ‘combin_subset_pans’: 2024-12-12T05:39:06,994 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-12-12T05:39:06,995 457 | free(co_dstat_fpath); 2024-12-12T05:39:06,995 | ^~~~~~~~~~~~~~ 2024-12-12T05:39:06,995 In file included from kssdheaders/global_basic.h:159, 2024-12-12T05:39:06,995 from command_set.c:15: 2024-12-12T05:39:06,995 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-12-12T05:39:06,995 565 | extern void free (void *__ptr) __THROW; 2024-12-12T05:39:06,996 | ~~~~~~^~~~~ 2024-12-12T05:39:06,999 command_set.c: In function ‘grouping_genomes’: 2024-12-12T05:39:07,000 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-12-12T05:39:07,000 562 | free(co_dstat_fpath); 2024-12-12T05:39:07,000 | ^~~~~~~~~~~~~~ 2024-12-12T05:39:07,000 In file included from kssdheaders/global_basic.h:159, 2024-12-12T05:39:07,000 from command_set.c:15: 2024-12-12T05:39:07,000 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-12-12T05:39:07,001 565 | extern void free (void *__ptr) __THROW; 2024-12-12T05:39:07,001 | ~~~~~~^~~~~ 2024-12-12T05:39:07,116 command_set.c: In function ‘sketch_union’: 2024-12-12T05:39:07,116 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-12T05:39:07,116 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,116 | ^ 2024-12-12T05:39:07,117 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-12T05:39:07,117 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,117 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,117 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,117 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-12-12T05:39:07,117 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,117 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-12T05:39:07,118 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-12-12T05:39:07,118 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,118 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,118 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-12-12T05:39:07,118 | ^~ ~~~~~~~~~~ 2024-12-12T05:39:07,118 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-12-12T05:39:07,118 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-12-12T05:39:07,119 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,229 command_set.c: In function ‘sketch_operate’: 2024-12-12T05:39:07,229 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,230 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-12-12T05:39:07,230 | ^~ ~~~~~~~~~~ 2024-12-12T05:39:07,230 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-12-12T05:39:07,230 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-12-12T05:39:07,230 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,230 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,230 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-12-12T05:39:07,231 | ^~ ~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,231 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-12-12T05:39:07,231 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-12-12T05:39:07,231 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,231 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,231 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-12-12T05:39:07,231 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,231 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-12T05:39:07,232 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-12-12T05:39:07,232 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,232 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,232 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-12-12T05:39:07,232 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,232 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-12T05:39:07,232 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-12-12T05:39:07,233 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,233 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,233 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-12-12T05:39:07,233 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,233 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-12T05:39:07,233 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-12-12T05:39:07,233 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,234 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,234 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-12-12T05:39:07,234 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,234 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-12T05:39:07,234 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-12-12T05:39:07,234 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,234 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-12T05:39:07,234 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,235 | ^ 2024-12-12T05:39:07,235 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-12T05:39:07,235 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,235 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,383 command_set.c: In function ‘uniq_sketch_union’: 2024-12-12T05:39:07,383 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-12T05:39:07,383 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,384 | ^ 2024-12-12T05:39:07,384 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-12T05:39:07,384 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,384 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,384 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,384 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-12-12T05:39:07,384 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,385 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-12T05:39:07,385 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-12-12T05:39:07,385 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,385 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,385 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-12-12T05:39:07,385 | ^~ ~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,385 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-12-12T05:39:07,386 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-12-12T05:39:07,386 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,512 command_set.c: In function ‘combin_pans’: 2024-12-12T05:39:07,513 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,513 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-12T05:39:07,513 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,513 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2024-12-12T05:39:07,513 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-12T05:39:07,513 | ^~~~~~~~~~ 2024-12-12T05:39:07,514 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-12-12T05:39:07,514 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-12T05:39:07,514 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,514 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,514 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-12T05:39:07,514 | ^~ ~~~~~~~~~~ 2024-12-12T05:39:07,514 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2024-12-12T05:39:07,514 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-12T05:39:07,515 | ^~~~~~~~~~ 2024-12-12T05:39:07,515 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-12-12T05:39:07,515 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-12T05:39:07,515 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,515 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-12T05:39:07,515 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,515 | ^ 2024-12-12T05:39:07,516 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-12T05:39:07,516 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,516 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,704 command_set.c: In function ‘combin_subset_pans’: 2024-12-12T05:39:07,704 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,704 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-12-12T05:39:07,704 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,704 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-12T05:39:07,705 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-12-12T05:39:07,705 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,705 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,705 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-12-12T05:39:07,705 | ^~ ~~~~~~~~~~ 2024-12-12T05:39:07,705 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-12T05:39:07,705 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-12-12T05:39:07,705 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,706 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,706 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-12T05:39:07,706 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,706 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-12T05:39:07,706 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-12T05:39:07,706 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,708 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,708 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-12T05:39:07,708 | ^~ ~~~~~~~~~~ 2024-12-12T05:39:07,708 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-12T05:39:07,708 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-12T05:39:07,708 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,709 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-12T05:39:07,709 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,709 | ^ 2024-12-12T05:39:07,709 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-12T05:39:07,709 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,709 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,910 command_set.c: In function ‘grouping_genomes’: 2024-12-12T05:39:07,910 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,910 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-12-12T05:39:07,911 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,911 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-12T05:39:07,911 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-12-12T05:39:07,911 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,911 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,912 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-12-12T05:39:07,912 | ^~ ~~~~~~~~~~ 2024-12-12T05:39:07,912 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-12T05:39:07,912 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-12-12T05:39:07,912 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,914 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,914 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-12T05:39:07,914 | ^~ ~~~~~~~~~~~ 2024-12-12T05:39:07,914 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-12-12T05:39:07,914 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-12-12T05:39:07,914 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,915 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-12-12T05:39:07,915 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-12T05:39:07,915 | ^~ ~~~~~~~~~~ 2024-12-12T05:39:07,915 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-12-12T05:39:07,916 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-12-12T05:39:07,916 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:07,916 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-12-12T05:39:07,916 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,916 | ^ 2024-12-12T05:39:07,917 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-12-12T05:39:07,917 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-12-12T05:39:07,917 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:08,224 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 2024-12-12T05:39:08,506 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 2024-12-12T05:39:08,652 global_basic.c: In function ‘organize_infile_list’: 2024-12-12T05:39:08,652 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-12-12T05:39:08,652 195 | while (isspace(*buf)) buf++; 2024-12-12T05:39:08,653 | ^~~~~~~ 2024-12-12T05:39:08,653 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=] 2024-12-12T05:39:08,653 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-12-12T05:39:08,653 | ~~^ 2024-12-12T05:39:08,653 | | 2024-12-12T05:39:08,653 | long unsigned int 2024-12-12T05:39:08,654 | %u 2024-12-12T05:39:08,654 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-12-12T05:39:08,654 | ~~~~~~~~~~~ 2024-12-12T05:39:08,654 | | 2024-12-12T05:39:08,654 | size_t {aka unsigned int} 2024-12-12T05:39:08,654 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=] 2024-12-12T05:39:08,654 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-12-12T05:39:08,655 | ~~^ 2024-12-12T05:39:08,655 | | 2024-12-12T05:39:08,655 | long unsigned int 2024-12-12T05:39:08,655 | %u 2024-12-12T05:39:08,655 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-12-12T05:39:08,655 | ~~~~~~~~~~~ 2024-12-12T05:39:08,655 | | 2024-12-12T05:39:08,656 | size_t {aka unsigned int} 2024-12-12T05:39:09,871 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 2024-12-12T05:39:10,027 iseq2comem.c: In function ‘reads2mco’: 2024-12-12T05:39:10,027 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,027 156 | if (base > TL) { 2024-12-12T05:39:10,028 | ^ 2024-12-12T05:39:10,028 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,028 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-12T05:39:10,028 | ^~ 2024-12-12T05:39:10,029 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,029 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-12T05:39:10,029 | ^ 2024-12-12T05:39:10,031 iseq2comem.c: In function ‘fasta2co’: 2024-12-12T05:39:10,032 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,032 239 | if (base > TL) { 2024-12-12T05:39:10,032 | ^ 2024-12-12T05:39:10,032 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,032 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-12T05:39:10,033 | ^~ 2024-12-12T05:39:10,033 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,033 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-12T05:39:10,033 | ^ 2024-12-12T05:39:10,034 iseq2comem.c: In function ‘fastq2co’: 2024-12-12T05:39:10,035 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-12-12T05:39:10,035 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-12-12T05:39:10,035 | ^~ 2024-12-12T05:39:10,037 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,037 318 | if (base > TL) { 2024-12-12T05:39:10,037 | ^ 2024-12-12T05:39:10,037 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,038 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-12T05:39:10,038 | ^~ 2024-12-12T05:39:10,038 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,038 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-12T05:39:10,038 | ^ 2024-12-12T05:39:10,040 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,040 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-12-12T05:39:10,040 | ^ 2024-12-12T05:39:10,042 iseq2comem.c: In function ‘fastq2koc’: 2024-12-12T05:39:10,042 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,042 402 | if (base > TL) { 2024-12-12T05:39:10,042 | ^ 2024-12-12T05:39:10,043 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,043 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-12T05:39:10,043 | ^~ 2024-12-12T05:39:10,044 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,044 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-12T05:39:10,044 | ^ 2024-12-12T05:39:10,049 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-12-12T05:39:10,049 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,050 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-12T05:39:10,050 | ^~ 2024-12-12T05:39:10,050 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-12-12T05:39:10,050 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-12-12T05:39:10,050 | ^ 2024-12-12T05:39:11,213 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 2024-12-12T05:39:11,280 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 2024-12-12T05:39:11,627 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 2024-12-12T05:39:11,949 pykssd.c: In function ‘py_dist_dispatch’: 2024-12-12T05:39:11,950 pykssd.c:329:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-12-12T05:39:11,950 329 | int state1 = dist_dispatch(&dist_opt_val1); 2024-12-12T05:39:11,950 | ^~~~~~ 2024-12-12T05:39:11,950 pykssd.c:386:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-12-12T05:39:11,950 386 | int state2 = dist_dispatch(&dist_opt_val2); 2024-12-12T05:39:11,951 | ^~~~~~ 2024-12-12T05:39:11,952 pykssd.c:510:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-12-12T05:39:11,952 510 | int state4 = dist_dispatch(&dist_opt_val4); 2024-12-12T05:39:11,952 | ^~~~~~ 2024-12-12T05:39:12,129 pykssd.c: In function ‘rename_file’: 2024-12-12T05:39:12,129 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-12-12T05:39:12,130 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-12-12T05:39:12,130 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-12-12T05:39:12,130 pykssd.c:41:15: note: length computed here 2024-12-12T05:39:12,130 41 | int len = strlen(p1); 2024-12-12T05:39:12,130 | ^~~~~~~~~~ 2024-12-12T05:39:12,550 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 2024-12-12T05:39:14,009 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-12-12T05:39:14,010 !! 2024-12-12T05:39:14,010 ******************************************************************************** 2024-12-12T05:39:14,011 Please avoid running ``setup.py`` directly. 2024-12-12T05:39:14,011 Instead, use pypa/build, pypa/installer or other 2024-12-12T05:39:14,011 standards-based tools. 2024-12-12T05:39:14,012 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-12-12T05:39:14,012 ******************************************************************************** 2024-12-12T05:39:14,012 !! 2024-12-12T05:39:14,013 self.initialize_options() 2024-12-12T05:39:14,096 installing to build/bdist.linux-armv7l/wheel 2024-12-12T05:39:14,096 running install 2024-12-12T05:39:14,136 running install_lib 2024-12-12T05:39:14,200 creating build/bdist.linux-armv7l/wheel 2024-12-12T05:39:14,206 copying build/lib.linux-armv7l-cpython-39/kssdtool.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-12-12T05:39:14,236 copying build/lib.linux-armv7l-cpython-39/kssdutils.py -> build/bdist.linux-armv7l/wheel/. 2024-12-12T05:39:14,240 running install_egg_info 2024-12-12T05:39:14,296 Copying kssdutils.egg-info to build/bdist.linux-armv7l/wheel/./kssdutils-1.0.5-py3.9.egg-info 2024-12-12T05:39:14,324 running install_scripts 2024-12-12T05:39:14,385 creating build/bdist.linux-armv7l/wheel/kssdutils-1.0.5.dist-info/WHEEL 2024-12-12T05:39:14,389 creating '/tmp/pip-wheel-h9gu43hi/kssdutils-1.0.5-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-12-12T05:39:14,483 adding 'kssdtool.cpython-39-arm-linux-gnueabihf.so' 2024-12-12T05:39:14,488 adding 'kssdutils.py' 2024-12-12T05:39:14,491 adding 'kssdutils-1.0.5.dist-info/METADATA' 2024-12-12T05:39:14,492 adding 'kssdutils-1.0.5.dist-info/WHEEL' 2024-12-12T05:39:14,494 adding 'kssdutils-1.0.5.dist-info/dependency_links.txt' 2024-12-12T05:39:14,495 adding 'kssdutils-1.0.5.dist-info/top_level.txt' 2024-12-12T05:39:14,496 adding 'kssdutils-1.0.5.dist-info/RECORD' 2024-12-12T05:39:15,563 removing build/bdist.linux-armv7l/wheel 2024-12-12T05:39:15,958 Building wheel for kssdutils (setup.py): finished with status 'done' 2024-12-12T05:39:16,227 Created wheel for kssdutils: filename=kssdutils-1.0.5-cp39-cp39-linux_armv7l.whl size=179755 sha256=fb21de5c7d85619ac9cc1fafe3280f0130178032b169f1cf7ceac0cb6326d42e 2024-12-12T05:39:16,228 Stored in directory: /tmp/pip-ephem-wheel-cache-9uvxrwpi/wheels/ea/01/53/5093cc2524d9223614d5b92f91cc4f8127f87e11733459d0ac 2024-12-12T05:39:16,282 Successfully built kssdutils 2024-12-12T05:39:16,295 Removed build tracker: '/tmp/pip-build-tracker-73tma2iu'