2024-03-15T11:29:06,716 Created temporary directory: /tmp/pip-build-tracker-oez6wpl5 2024-03-15T11:29:06,717 Initialized build tracking at /tmp/pip-build-tracker-oez6wpl5 2024-03-15T11:29:06,718 Created build tracker: /tmp/pip-build-tracker-oez6wpl5 2024-03-15T11:29:06,718 Entered build tracker: /tmp/pip-build-tracker-oez6wpl5 2024-03-15T11:29:06,719 Created temporary directory: /tmp/pip-wheel-2ge3d6kn 2024-03-15T11:29:06,722 Created temporary directory: /tmp/pip-ephem-wheel-cache-ilpbjryr 2024-03-15T11:29:06,748 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-03-15T11:29:06,751 2 location(s) to search for versions of kssdtree: 2024-03-15T11:29:06,751 * https://pypi.org/simple/kssdtree/ 2024-03-15T11:29:06,751 * https://www.piwheels.org/simple/kssdtree/ 2024-03-15T11:29:06,752 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-03-15T11:29:06,752 Getting page https://pypi.org/simple/kssdtree/ 2024-03-15T11:29:06,754 Found index url https://pypi.org/simple/ 2024-03-15T11:29:06,965 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-03-15T11:29:06,966 Found link https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.1 2024-03-15T11:29:06,967 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-03-15T11:29:06,968 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-03-15T11:29:06,969 Found index url https://www.piwheels.org/simple/ 2024-03-15T11:29:07,123 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-03-15T11:29:07,124 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-03-15T11:29:07,124 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-03-15T11:29:07,143 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-03-15T11:29:07,161 Collecting kssdtree==1.1.1 2024-03-15T11:29:07,163 Created temporary directory: /tmp/pip-unpack-2ldcx960 2024-03-15T11:29:07,371 Downloading kssdtree-1.1.1.tar.gz (114 kB) 2024-03-15T11:29:07,598 Added kssdtree==1.1.1 from https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-oez6wpl5' 2024-03-15T11:29:07,600 Running setup.py (path:/tmp/pip-wheel-2ge3d6kn/kssdtree_545d6f2cd97343cbb958642c26095999/setup.py) egg_info for package kssdtree 2024-03-15T11:29:07,601 Created temporary directory: /tmp/pip-pip-egg-info-2h5u55j0 2024-03-15T11:29:07,602 Preparing metadata (setup.py): started 2024-03-15T11:29:07,603 Running command python setup.py egg_info 2024-03-15T11:29:08,713 running egg_info 2024-03-15T11:29:08,715 creating /tmp/pip-pip-egg-info-2h5u55j0/kssdtree.egg-info 2024-03-15T11:29:08,739 writing /tmp/pip-pip-egg-info-2h5u55j0/kssdtree.egg-info/PKG-INFO 2024-03-15T11:29:08,742 writing dependency_links to /tmp/pip-pip-egg-info-2h5u55j0/kssdtree.egg-info/dependency_links.txt 2024-03-15T11:29:08,744 writing requirements to /tmp/pip-pip-egg-info-2h5u55j0/kssdtree.egg-info/requires.txt 2024-03-15T11:29:08,745 writing top-level names to /tmp/pip-pip-egg-info-2h5u55j0/kssdtree.egg-info/top_level.txt 2024-03-15T11:29:08,747 writing manifest file '/tmp/pip-pip-egg-info-2h5u55j0/kssdtree.egg-info/SOURCES.txt' 2024-03-15T11:29:08,847 reading manifest file '/tmp/pip-pip-egg-info-2h5u55j0/kssdtree.egg-info/SOURCES.txt' 2024-03-15T11:29:08,849 reading manifest template 'MANIFEST.in' 2024-03-15T11:29:08,865 writing manifest file '/tmp/pip-pip-egg-info-2h5u55j0/kssdtree.egg-info/SOURCES.txt' 2024-03-15T11:29:08,973 Preparing metadata (setup.py): finished with status 'done' 2024-03-15T11:29:08,977 Source in /tmp/pip-wheel-2ge3d6kn/kssdtree_545d6f2cd97343cbb958642c26095999 has version 1.1.1, which satisfies requirement kssdtree==1.1.1 from https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz 2024-03-15T11:29:08,978 Removed kssdtree==1.1.1 from https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-oez6wpl5' 2024-03-15T11:29:08,982 Created temporary directory: /tmp/pip-unpack-6_q5pkrx 2024-03-15T11:29:08,983 Created temporary directory: /tmp/pip-unpack-q5z8mwsc 2024-03-15T11:29:08,989 Building wheels for collected packages: kssdtree 2024-03-15T11:29:08,993 Created temporary directory: /tmp/pip-wheel-qqf8yib1 2024-03-15T11:29:08,994 Building wheel for kssdtree (setup.py): started 2024-03-15T11:29:08,995 Destination directory: /tmp/pip-wheel-qqf8yib1 2024-03-15T11:29:08,995 Running command python setup.py bdist_wheel 2024-03-15T11:29:10,043 running bdist_wheel 2024-03-15T11:29:10,139 running build 2024-03-15T11:29:10,140 running build_py 2024-03-15T11:29:10,167 creating build 2024-03-15T11:29:10,168 creating build/lib.linux-armv7l-cpython-311 2024-03-15T11:29:10,169 copying kssdtree.py -> build/lib.linux-armv7l-cpython-311 2024-03-15T11:29:10,172 copying toolutils.py -> build/lib.linux-armv7l-cpython-311 2024-03-15T11:29:10,174 running egg_info 2024-03-15T11:29:10,230 writing kssdtree.egg-info/PKG-INFO 2024-03-15T11:29:10,233 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-03-15T11:29:10,234 writing requirements to kssdtree.egg-info/requires.txt 2024-03-15T11:29:10,236 writing top-level names to kssdtree.egg-info/top_level.txt 2024-03-15T11:29:10,262 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-03-15T11:29:10,266 reading manifest template 'MANIFEST.in' 2024-03-15T11:29:10,282 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-03-15T11:29:10,284 running build_ext 2024-03-15T11:29:10,777 building 'kssd' extension 2024-03-15T11:29:10,778 creating build/temp.linux-armv7l-cpython-311 2024-03-15T11:29:10,779 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c co2mco.c -o build/temp.linux-armv7l-cpython-311/co2mco.o -fopenmp 2024-03-15T11:29:10,952 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-03-15T11:29:10,953 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T11:29:10,954 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-03-15T11:29:10,954 | ^ 2024-03-15T11:29:10,957 co2mco.c: In function ‘co2unitllmco’: 2024-03-15T11:29:10,957 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T11:29:10,958 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-03-15T11:29:10,959 | ^ 2024-03-15T11:29:11,660 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_composite.c -o build/temp.linux-armv7l-cpython-311/command_composite.o -fopenmp 2024-03-15T11:29:12,040 command_composite.c: In function ‘get_species_abundance’: 2024-03-15T11:29:12,041 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-03-15T11:29:12,041 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-03-15T11:29:12,042 | ^~ 2024-03-15T11:29:12,043 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-03-15T11:29:12,043 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-03-15T11:29:12,044 | ^~ 2024-03-15T11:29:12,045 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:12,046 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-03-15T11:29:12,047 | ^ 2024-03-15T11:29:12,048 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:12,048 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-03-15T11:29:12,049 | ^~~~~~~~~~ 2024-03-15T11:29:12,049 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-03-15T11:29:12,050 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-03-15T11:29:12,050 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,051 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:12,052 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-03-15T11:29:12,052 | ^ 2024-03-15T11:29:12,053 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:12,053 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-03-15T11:29:12,054 | ^~~~~~~~~~ 2024-03-15T11:29:12,054 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-03-15T11:29:12,055 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-03-15T11:29:12,056 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,056 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:12,057 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-03-15T11:29:12,057 | ^ 2024-03-15T11:29:12,058 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:12,059 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-03-15T11:29:12,059 | ^~~~~~~~~~ 2024-03-15T11:29:12,060 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-03-15T11:29:12,061 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-03-15T11:29:12,061 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,062 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:12,062 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-03-15T11:29:12,063 | ^ 2024-03-15T11:29:12,064 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:12,064 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-03-15T11:29:12,065 | ^~~~~~~~~~ 2024-03-15T11:29:12,066 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-03-15T11:29:12,067 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-03-15T11:29:12,067 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,068 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:12,069 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-03-15T11:29:12,070 | ^ 2024-03-15T11:29:12,070 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:12,071 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-03-15T11:29:12,071 | ^~~~~~~~~~~~ 2024-03-15T11:29:12,072 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2024-03-15T11:29:12,072 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-03-15T11:29:12,073 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,300 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist.c -o build/temp.linux-armv7l-cpython-311/command_dist.o -fopenmp 2024-03-15T11:29:12,527 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-03-15T11:29:12,529 command_dist.c:678:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T11:29:12,529 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T11:29:12,530 | ~~^ 2024-03-15T11:29:12,530 | | 2024-03-15T11:29:12,531 | long unsigned int 2024-03-15T11:29:12,532 | %u 2024-03-15T11:29:12,532 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T11:29:12,533 | ~~~~~~~ 2024-03-15T11:29:12,533 | | 2024-03-15T11:29:12,534 | size_t {aka unsigned int} 2024-03-15T11:29:12,535 command_dist.c:678:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T11:29:12,535 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T11:29:12,536 | ~~^ 2024-03-15T11:29:12,537 | | 2024-03-15T11:29:12,538 | long unsigned int 2024-03-15T11:29:12,538 | %u 2024-03-15T11:29:12,539 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T11:29:12,539 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-03-15T11:29:12,540 | ~~~~~~~~~ 2024-03-15T11:29:12,541 | | 2024-03-15T11:29:12,541 | size_t {aka unsigned int} 2024-03-15T11:29:12,542 command_dist.c:678:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-03-15T11:29:12,543 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T11:29:12,543 | ~~^ 2024-03-15T11:29:12,544 | | 2024-03-15T11:29:12,545 | long unsigned int 2024-03-15T11:29:12,545 | %u 2024-03-15T11:29:12,546 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T11:29:12,546 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-03-15T11:29:12,547 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,547 | | 2024-03-15T11:29:12,547 | unsigned int 2024-03-15T11:29:12,548 command_dist.c:716:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-15T11:29:12,549 716 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-03-15T11:29:12,549 | ^ 2024-03-15T11:29:12,555 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-03-15T11:29:12,557 command_dist.c:864:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T11:29:12,557 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-03-15T11:29:12,558 | ~~^ ~~~~~~~ 2024-03-15T11:29:12,558 | | | 2024-03-15T11:29:12,559 | long unsigned int size_t {aka unsigned int} 2024-03-15T11:29:12,560 | %u 2024-03-15T11:29:12,560 command_dist.c:864:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T11:29:12,561 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-03-15T11:29:12,562 | ~~^ 2024-03-15T11:29:12,562 | | 2024-03-15T11:29:12,563 | long unsigned int 2024-03-15T11:29:12,564 | %u 2024-03-15T11:29:12,564 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-03-15T11:29:12,565 | ~~~~~~~~~ 2024-03-15T11:29:12,565 | | 2024-03-15T11:29:12,566 | size_t {aka unsigned int} 2024-03-15T11:29:12,567 command_dist.c:864:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-03-15T11:29:12,567 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-03-15T11:29:12,568 | ~~^ 2024-03-15T11:29:12,569 | | 2024-03-15T11:29:12,570 | long unsigned int 2024-03-15T11:29:12,570 | %u 2024-03-15T11:29:12,571 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-03-15T11:29:12,571 866 | (size_t) b * unitsz_distf_mapped); 2024-03-15T11:29:12,572 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,572 | | 2024-03-15T11:29:12,573 | unsigned int 2024-03-15T11:29:12,573 command_dist.c:811:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-03-15T11:29:12,574 811 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-03-15T11:29:12,574 | ^~~~~~~ 2024-03-15T11:29:12,575 command_dist.c:810:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-03-15T11:29:12,575 810 | struct stat cbd_fcode_stat; 2024-03-15T11:29:12,576 | ^~~~~~~~~~~~~~ 2024-03-15T11:29:12,576 command_dist.c:809:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-03-15T11:29:12,576 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-03-15T11:29:12,577 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,577 command_dist.c:809:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-03-15T11:29:12,578 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-03-15T11:29:12,579 | ^~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,579 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-03-15T11:29:12,580 command_dist.c:1019:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T11:29:12,581 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T11:29:12,581 | ~~^ 2024-03-15T11:29:12,582 | | 2024-03-15T11:29:12,583 | long unsigned int 2024-03-15T11:29:12,583 | %u 2024-03-15T11:29:12,584 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T11:29:12,585 | ~~~~~~~ 2024-03-15T11:29:12,585 | | 2024-03-15T11:29:12,586 | size_t {aka unsigned int} 2024-03-15T11:29:12,587 command_dist.c:1019:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T11:29:12,587 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T11:29:12,588 | ~~^ 2024-03-15T11:29:12,589 | | 2024-03-15T11:29:12,590 | long unsigned int 2024-03-15T11:29:12,590 | %u 2024-03-15T11:29:12,591 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T11:29:12,592 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-03-15T11:29:12,593 | ~~~~~~~~~ 2024-03-15T11:29:12,593 | | 2024-03-15T11:29:12,594 | size_t {aka unsigned int} 2024-03-15T11:29:12,594 command_dist.c:1019:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-03-15T11:29:12,595 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T11:29:12,596 | ~~^ 2024-03-15T11:29:12,596 | | 2024-03-15T11:29:12,597 | long unsigned int 2024-03-15T11:29:12,597 | %u 2024-03-15T11:29:12,598 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T11:29:12,598 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-03-15T11:29:12,599 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,599 | | 2024-03-15T11:29:12,600 | unsigned int 2024-03-15T11:29:12,600 command_dist.c:1035:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-03-15T11:29:12,601 1035 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-03-15T11:29:12,601 | ^ 2024-03-15T11:29:12,602 command_dist.c: In function ‘mco_co_dist_core’: 2024-03-15T11:29:12,603 command_dist.c:1117:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-15T11:29:12,603 1117 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-03-15T11:29:12,604 | ^ 2024-03-15T11:29:12,605 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-03-15T11:29:12,606 command_dist.c:1240:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T11:29:12,607 1240 | for (int rid = 0; rid < ref_num; rid++) 2024-03-15T11:29:12,607 | ^ 2024-03-15T11:29:12,608 command_dist.c:1246:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T11:29:12,609 1246 | for (int rid = 0; rid < ref_num; rid++) { 2024-03-15T11:29:12,609 | ^ 2024-03-15T11:29:12,610 command_dist.c: In function ‘dist_print_nobin’: 2024-03-15T11:29:12,611 command_dist.c:1336:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T11:29:12,611 1336 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-03-15T11:29:12,612 | ^ 2024-03-15T11:29:12,612 command_dist.c:1357:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T11:29:12,613 1357 | for (int rid = 0; rid < ref_num; rid++) { 2024-03-15T11:29:12,614 | ^ 2024-03-15T11:29:12,615 command_dist.c:1383:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T11:29:12,615 1383 | for (int rid = 0; rid < ref_num; rid++) 2024-03-15T11:29:12,616 | ^ 2024-03-15T11:29:12,976 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-03-15T11:29:12,976 command_dist.c:404:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2024-03-15T11:29:12,977 404 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-03-15T11:29:12,977 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:12,978 command_dist.c:376:40: note: ‘com_abund_fp’ was declared here 2024-03-15T11:29:12,979 376 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-03-15T11:29:12,979 | ^~~~~~~~~~~~ 2024-03-15T11:29:13,811 command_dist.c: In function ‘get_dim_shuffle’: 2024-03-15T11:29:13,812 command_dist.c:268:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-03-15T11:29:13,812 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-03-15T11:29:13,813 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:13,813 command_dist.c:268:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-03-15T11:29:13,814 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-03-15T11:29:13,814 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:14,709 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-03-15T11:29:14,710 command_dist.c:597:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:14,710 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T11:29:14,711 | ^~ ~~~~~~~~~ 2024-03-15T11:29:14,712 command_dist.c:597:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-03-15T11:29:14,712 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T11:29:14,713 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:14,713 command_dist.c:626:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T11:29:14,714 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T11:29:14,715 | ^~~~~~~~~~~~~~~ 2024-03-15T11:29:14,715 command_dist.c:626:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-03-15T11:29:14,716 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T11:29:14,717 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:14,717 command_dist.c:682:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T11:29:14,718 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-03-15T11:29:14,718 | ^~~~~~~~~~~ 2024-03-15T11:29:14,719 command_dist.c:682:38: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:14,720 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-03-15T11:29:14,720 | ^~~~~~~~~~~~~~~~~ 2024-03-15T11:29:14,721 command_dist.c:682:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-03-15T11:29:14,722 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-03-15T11:29:14,722 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:14,723 command_dist.c:683:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T11:29:14,724 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-03-15T11:29:14,725 | ^~~~~ 2024-03-15T11:29:14,725 command_dist.c:683:32: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:14,726 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-03-15T11:29:14,726 | ^~~~~~~~~~~ 2024-03-15T11:29:14,727 command_dist.c:683:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-03-15T11:29:14,727 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-03-15T11:29:14,728 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:14,960 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-03-15T11:29:14,961 command_dist.c:764:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:14,962 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T11:29:14,962 | ^~ ~~~~~~~~~ 2024-03-15T11:29:14,963 command_dist.c:764:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-03-15T11:29:14,963 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T11:29:14,964 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:14,964 command_dist.c:791:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T11:29:14,965 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T11:29:14,965 | ^~~~~~~~~~~~~~~ 2024-03-15T11:29:14,966 command_dist.c:791:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-03-15T11:29:14,966 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T11:29:14,967 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:14,968 command_dist.c:824:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T11:29:14,969 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-03-15T11:29:14,969 | ^~~~~~~~~~~~~ 2024-03-15T11:29:14,970 command_dist.c:824:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-03-15T11:29:14,970 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-03-15T11:29:14,971 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:14,972 command_dist.c:850:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:14,972 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-03-15T11:29:14,973 | ^ 2024-03-15T11:29:14,974 command_dist.c:850:33: note: directive argument in the range [0, 536870912] 2024-03-15T11:29:14,974 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-03-15T11:29:14,975 | ^~~~~~~~~~ 2024-03-15T11:29:14,976 command_dist.c:850:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-03-15T11:29:14,976 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-03-15T11:29:14,977 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:14,978 command_dist.c:852:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:14,978 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-03-15T11:29:14,979 | ^ 2024-03-15T11:29:14,980 command_dist.c:852:28: note: directive argument in the range [0, 536870912] 2024-03-15T11:29:14,981 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-03-15T11:29:14,981 | ^~~~~~~~~~ 2024-03-15T11:29:14,982 command_dist.c:852:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-03-15T11:29:14,982 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-03-15T11:29:14,983 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:15,239 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-03-15T11:29:15,240 command_dist.c:928:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:15,241 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T11:29:15,241 | ^~ ~~~~~~~~~ 2024-03-15T11:29:15,242 command_dist.c:928:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-03-15T11:29:15,242 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T11:29:15,242 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:15,243 command_dist.c:957:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T11:29:15,243 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T11:29:15,244 | ^~~~~~~~~~~~~~~ 2024-03-15T11:29:15,245 command_dist.c:957:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-03-15T11:29:15,245 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T11:29:15,246 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:15,247 command_dist.c:991:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T11:29:15,247 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-03-15T11:29:15,248 | ^~~~~~~~~~~~~ 2024-03-15T11:29:15,249 command_dist.c:991:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-03-15T11:29:15,249 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-03-15T11:29:15,250 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:15,251 command_dist.c:1023:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T11:29:15,251 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-03-15T11:29:15,252 | ^~~~~~~~~~~ 2024-03-15T11:29:15,252 command_dist.c:1023:38: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:15,253 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-03-15T11:29:15,253 | ^~~~~~~~~~~~~~~~~ 2024-03-15T11:29:15,254 command_dist.c:1023:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-03-15T11:29:15,254 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-03-15T11:29:15,255 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:15,256 command_dist.c:1024:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T11:29:15,257 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-03-15T11:29:15,258 | ^~~~~ 2024-03-15T11:29:15,259 command_dist.c:1024:32: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:15,259 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-03-15T11:29:15,260 | ^~~~~~~~~~~ 2024-03-15T11:29:15,260 command_dist.c:1024:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-03-15T11:29:15,261 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-03-15T11:29:15,261 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:15,527 command_dist.c: In function ‘combine_queries’: 2024-03-15T11:29:15,529 command_dist.c:1493:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T11:29:15,529 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-03-15T11:29:15,529 | ^ 2024-03-15T11:29:15,530 command_dist.c:1493:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T11:29:15,531 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-03-15T11:29:15,531 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:15,532 command_dist.c:1500:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T11:29:15,532 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-03-15T11:29:15,533 | ^ 2024-03-15T11:29:15,534 command_dist.c:1500:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T11:29:15,534 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-03-15T11:29:15,535 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:15,537 command_dist.c:1604:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:15,537 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-03-15T11:29:15,538 | ^~ ~~~~~~~~ 2024-03-15T11:29:15,539 command_dist.c:1604:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-03-15T11:29:15,539 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-03-15T11:29:15,540 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,017 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o -fopenmp 2024-03-15T11:29:16,190 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_set.c -o build/temp.linux-armv7l-cpython-311/command_set.o -fopenmp 2024-03-15T11:29:16,362 command_set.c: In function ‘sketch_operate’: 2024-03-15T11:29:16,363 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-15T11:29:16,364 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-03-15T11:29:16,365 | ^ 2024-03-15T11:29:16,376 command_set.c: In function ‘combin_subset_pans’: 2024-03-15T11:29:16,377 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-03-15T11:29:16,378 458 | free(co_dstat_fpath); 2024-03-15T11:29:16,379 | ^~~~~~~~~~~~~~ 2024-03-15T11:29:16,380 In file included from kssdheaders/global_basic.h:159, 2024-03-15T11:29:16,380 from command_set.c:15: 2024-03-15T11:29:16,381 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-03-15T11:29:16,381 568 | extern void free (void *__ptr) __THROW; 2024-03-15T11:29:16,382 | ~~~~~~^~~~~ 2024-03-15T11:29:16,385 command_set.c: In function ‘grouping_genomes’: 2024-03-15T11:29:16,386 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-03-15T11:29:16,386 563 | free(co_dstat_fpath); 2024-03-15T11:29:16,387 | ^~~~~~~~~~~~~~ 2024-03-15T11:29:16,388 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-03-15T11:29:16,388 568 | extern void free (void *__ptr) __THROW; 2024-03-15T11:29:16,389 | ~~~~~~^~~~~ 2024-03-15T11:29:16,554 command_set.c: In function ‘sketch_union’: 2024-03-15T11:29:16,555 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T11:29:16,556 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:16,556 | ^ 2024-03-15T11:29:16,557 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T11:29:16,557 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:16,558 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,559 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:16,559 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-03-15T11:29:16,560 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:16,561 command_set.c:83:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:16,562 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-03-15T11:29:16,562 | ^~~~~~~~~~ 2024-03-15T11:29:16,563 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T11:29:16,564 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-03-15T11:29:16,564 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,565 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:16,565 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-03-15T11:29:16,566 | ^~ ~~~~~~~~~~ 2024-03-15T11:29:16,567 command_set.c:93:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:16,567 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-03-15T11:29:16,568 | ^~~~~~~~~~ 2024-03-15T11:29:16,569 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-03-15T11:29:16,569 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-03-15T11:29:16,570 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,686 command_set.c: In function ‘sketch_operate’: 2024-03-15T11:29:16,687 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:16,688 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-03-15T11:29:16,688 | ^~ ~~~~~~~~~~ 2024-03-15T11:29:16,689 command_set.c:154:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:16,689 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-03-15T11:29:16,690 | ^~~~~~~~~~ 2024-03-15T11:29:16,690 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-03-15T11:29:16,691 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-03-15T11:29:16,691 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,692 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:16,692 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-03-15T11:29:16,693 | ^~ ~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,693 command_set.c:156:29: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:16,694 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-03-15T11:29:16,694 | ^~~~~~~~~~ 2024-03-15T11:29:16,695 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-03-15T11:29:16,695 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-03-15T11:29:16,696 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,696 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:16,697 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-03-15T11:29:16,698 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:16,698 command_set.c:166:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:16,699 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-03-15T11:29:16,700 | ^~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,700 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T11:29:16,701 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-03-15T11:29:16,702 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,702 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:16,703 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-03-15T11:29:16,703 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:16,704 command_set.c:170:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:16,705 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-03-15T11:29:16,705 | ^~~~~~~~~~ 2024-03-15T11:29:16,706 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T11:29:16,707 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-03-15T11:29:16,707 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,708 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:16,708 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-03-15T11:29:16,709 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:16,710 command_set.c:175:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:16,711 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-03-15T11:29:16,711 | ^~~~~~~~~~ 2024-03-15T11:29:16,712 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T11:29:16,712 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-03-15T11:29:16,713 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,713 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:16,713 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-03-15T11:29:16,714 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:16,714 command_set.c:188:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:16,715 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-03-15T11:29:16,715 | ^~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,716 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T11:29:16,716 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-03-15T11:29:16,717 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,717 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T11:29:16,718 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:16,719 | ^ 2024-03-15T11:29:16,719 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T11:29:16,720 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:16,721 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,865 command_set.c: In function ‘uniq_sketch_union’: 2024-03-15T11:29:16,865 command_set.c:220:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T11:29:16,866 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-03-15T11:29:16,867 | ^ 2024-03-15T11:29:16,867 command_set.c:220:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2024-03-15T11:29:16,868 220 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-03-15T11:29:16,869 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,870 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T11:29:16,870 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:16,871 | ^ 2024-03-15T11:29:16,872 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T11:29:16,872 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:16,873 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,874 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:16,874 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-03-15T11:29:16,875 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:16,876 command_set.c:248:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:16,877 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-03-15T11:29:16,877 | ^~~~~~~~~~ 2024-03-15T11:29:16,878 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T11:29:16,879 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-03-15T11:29:16,879 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,880 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:16,880 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-03-15T11:29:16,881 | ^~ ~~~~~~~~~~~~~~~ 2024-03-15T11:29:16,882 command_set.c:260:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:16,882 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-03-15T11:29:16,883 | ^~~~~~~~~~ 2024-03-15T11:29:16,883 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-03-15T11:29:16,884 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-03-15T11:29:16,884 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,015 command_set.c: In function ‘combin_pans’: 2024-03-15T11:29:17,015 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:17,016 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T11:29:17,016 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:17,017 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-03-15T11:29:17,017 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T11:29:17,018 | ^~~~~~~~~~ 2024-03-15T11:29:17,019 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-03-15T11:29:17,019 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T11:29:17,020 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,021 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:17,022 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T11:29:17,022 | ^~ ~~~~~~~~~~ 2024-03-15T11:29:17,023 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-03-15T11:29:17,024 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T11:29:17,025 | ^~~~~~~~~~ 2024-03-15T11:29:17,025 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-03-15T11:29:17,026 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T11:29:17,026 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,027 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T11:29:17,028 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:17,028 | ^ 2024-03-15T11:29:17,029 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T11:29:17,029 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:17,030 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,236 command_set.c: In function ‘combin_subset_pans’: 2024-03-15T11:29:17,236 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:17,237 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-03-15T11:29:17,238 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:17,238 command_set.c:470:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:17,239 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-03-15T11:29:17,239 | ^~~~~~~~~~ 2024-03-15T11:29:17,239 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T11:29:17,240 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-03-15T11:29:17,240 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,241 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:17,241 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-03-15T11:29:17,242 | ^~ ~~~~~~~~~~ 2024-03-15T11:29:17,242 command_set.c:476:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:17,242 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-03-15T11:29:17,243 | ^~~~~~~~~~ 2024-03-15T11:29:17,243 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T11:29:17,244 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-03-15T11:29:17,244 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,245 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:17,245 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T11:29:17,246 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:17,246 command_set.c:482:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:17,247 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T11:29:17,248 | ^~~~~~~~~~ 2024-03-15T11:29:17,248 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T11:29:17,249 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T11:29:17,250 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,250 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:17,251 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T11:29:17,252 | ^~ ~~~~~~~~~~ 2024-03-15T11:29:17,252 command_set.c:513:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:17,253 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T11:29:17,254 | ^~~~~~~~~~ 2024-03-15T11:29:17,254 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T11:29:17,255 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T11:29:17,256 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,256 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T11:29:17,257 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:17,258 | ^ 2024-03-15T11:29:17,259 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T11:29:17,259 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:17,259 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,485 command_set.c: In function ‘grouping_genomes’: 2024-03-15T11:29:17,486 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:17,487 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-03-15T11:29:17,487 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:17,488 command_set.c:575:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:17,488 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-03-15T11:29:17,488 | ^~~~~~~~~~ 2024-03-15T11:29:17,489 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T11:29:17,489 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-03-15T11:29:17,490 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,490 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:17,491 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-03-15T11:29:17,491 | ^~ ~~~~~~~~~~ 2024-03-15T11:29:17,491 command_set.c:581:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:17,492 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-03-15T11:29:17,493 | ^~~~~~~~~~ 2024-03-15T11:29:17,494 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T11:29:17,494 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-03-15T11:29:17,495 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,495 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:17,496 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T11:29:17,497 | ^~ ~~~~~~~~~~~ 2024-03-15T11:29:17,497 command_set.c:613:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:17,498 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T11:29:17,499 | ^~~~~~~~~~ 2024-03-15T11:29:17,499 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T11:29:17,500 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T11:29:17,501 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,501 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T11:29:17,502 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T11:29:17,503 | ^~ ~~~~~~~~~~ 2024-03-15T11:29:17,503 command_set.c:635:25: note: directive argument in the range [-2147483644, 2147483646] 2024-03-15T11:29:17,504 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T11:29:17,505 | ^~~~~~~~~~ 2024-03-15T11:29:17,506 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T11:29:17,506 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T11:29:17,507 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,508 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T11:29:17,508 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:17,508 | ^ 2024-03-15T11:29:17,509 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T11:29:17,509 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T11:29:17,510 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:17,780 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-311/command_shuffle.o -fopenmp 2024-03-15T11:29:18,094 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c global_basic.c -o build/temp.linux-armv7l-cpython-311/global_basic.o -fopenmp 2024-03-15T11:29:18,260 global_basic.c: In function ‘organize_infile_list’: 2024-03-15T11:29:18,260 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-03-15T11:29:18,261 195 | while (isspace(*buf)) buf++; 2024-03-15T11:29:18,261 | ^~~~~~~ 2024-03-15T11:29:18,262 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2024-03-15T11:29:18,263 34 | #include 2024-03-15T11:29:18,263 +++ |+#include 2024-03-15T11:29:18,264 35 | 2024-03-15T11:29:18,264 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=] 2024-03-15T11:29:18,265 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-03-15T11:29:18,266 | ~~^ 2024-03-15T11:29:18,267 | | 2024-03-15T11:29:18,268 | long unsigned int 2024-03-15T11:29:18,268 | %u 2024-03-15T11:29:18,269 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-03-15T11:29:18,270 | ~~~~~~~~~~~ 2024-03-15T11:29:18,270 | | 2024-03-15T11:29:18,271 | size_t {aka unsigned int} 2024-03-15T11:29:18,272 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=] 2024-03-15T11:29:18,272 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-03-15T11:29:18,273 | ~~^ 2024-03-15T11:29:18,274 | | 2024-03-15T11:29:18,274 | long unsigned int 2024-03-15T11:29:18,275 | %u 2024-03-15T11:29:18,276 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-03-15T11:29:18,277 | ~~~~~~~~~~~ 2024-03-15T11:29:18,277 | | 2024-03-15T11:29:18,278 | size_t {aka unsigned int} 2024-03-15T11:29:19,029 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-311/iseq2comem.o -fopenmp 2024-03-15T11:29:19,205 iseq2comem.c: In function ‘reads2mco’: 2024-03-15T11:29:19,206 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,207 156 | if (base > TL) { 2024-03-15T11:29:19,207 | ^ 2024-03-15T11:29:19,208 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,208 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T11:29:19,209 | ^~ 2024-03-15T11:29:19,210 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,210 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T11:29:19,211 | ^ 2024-03-15T11:29:19,211 iseq2comem.c: In function ‘fasta2co’: 2024-03-15T11:29:19,212 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,213 239 | if (base > TL) { 2024-03-15T11:29:19,213 | ^ 2024-03-15T11:29:19,214 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,214 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T11:29:19,215 | ^~ 2024-03-15T11:29:19,216 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,216 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T11:29:19,217 | ^ 2024-03-15T11:29:19,218 iseq2comem.c: In function ‘fastq2co’: 2024-03-15T11:29:19,219 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-03-15T11:29:19,219 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-03-15T11:29:19,220 | ^~ 2024-03-15T11:29:19,220 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,221 318 | if (base > TL) { 2024-03-15T11:29:19,222 | ^ 2024-03-15T11:29:19,222 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,223 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T11:29:19,224 | ^~ 2024-03-15T11:29:19,225 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,226 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T11:29:19,226 | ^ 2024-03-15T11:29:19,227 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,228 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-03-15T11:29:19,228 | ^ 2024-03-15T11:29:19,229 iseq2comem.c: In function ‘fastq2koc’: 2024-03-15T11:29:19,229 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,230 402 | if (base > TL) { 2024-03-15T11:29:19,230 | ^ 2024-03-15T11:29:19,231 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,232 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T11:29:19,232 | ^~ 2024-03-15T11:29:19,233 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,233 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T11:29:19,234 | ^ 2024-03-15T11:29:19,234 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-03-15T11:29:19,235 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,236 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T11:29:19,237 | ^~ 2024-03-15T11:29:19,238 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:19,239 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T11:29:19,239 | ^ 2024-03-15T11:29:20,583 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2024-03-15T11:29:20,637 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c mytime.c -o build/temp.linux-armv7l-cpython-311/mytime.o -fopenmp 2024-03-15T11:29:20,758 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.11 -c pykssd.c -o build/temp.linux-armv7l-cpython-311/pykssd.o -fopenmp 2024-03-15T11:29:21,145 pykssd.c: In function ‘py_dist_dispatch’: 2024-03-15T11:29:21,146 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-03-15T11:29:21,147 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-03-15T11:29:21,147 | ^~~~~~ 2024-03-15T11:29:21,149 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-03-15T11:29:21,149 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-03-15T11:29:21,150 | ^~~~~~ 2024-03-15T11:29:21,152 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-03-15T11:29:21,152 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-03-15T11:29:21,153 | ^~~~~~ 2024-03-15T11:29:21,715 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/co2mco.o build/temp.linux-armv7l-cpython-311/command_composite.o build/temp.linux-armv7l-cpython-311/command_dist.o build/temp.linux-armv7l-cpython-311/command_dist_wrapper.o build/temp.linux-armv7l-cpython-311/command_set.o build/temp.linux-armv7l-cpython-311/command_shuffle.o build/temp.linux-armv7l-cpython-311/global_basic.o build/temp.linux-armv7l-cpython-311/iseq2comem.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/mytime.o build/temp.linux-armv7l-cpython-311/pykssd.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -fopenmp 2024-03-15T11:29:21,860 building 'nj' extension 2024-03-15T11:29:21,860 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c align.c -o build/temp.linux-armv7l-cpython-311/align.o 2024-03-15T11:29:22,352 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c buildtree.c -o build/temp.linux-armv7l-cpython-311/buildtree.o 2024-03-15T11:29:22,502 buildtree.c: In function ‘UPGMA_buildtree’: 2024-03-15T11:29:22,502 buildtree.c:716:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T11:29:22,503 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-03-15T11:29:22,504 | ^~ 2024-03-15T11:29:22,505 buildtree.c:716:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T11:29:22,506 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-03-15T11:29:22,506 | ^~ 2024-03-15T11:29:23,161 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c cluster.c -o build/temp.linux-armv7l-cpython-311/cluster.o 2024-03-15T11:29:23,530 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c distancemat.c -o build/temp.linux-armv7l-cpython-311/distancemat.o 2024-03-15T11:29:23,666 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-03-15T11:29:23,667 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T11:29:23,668 226 | for( i=0; i < dest->size; i++) { 2024-03-15T11:29:23,668 | ^ 2024-03-15T11:29:23,669 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-03-15T11:29:23,670 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T11:29:23,670 260 | for( i=0; i < mat->size; i++) { 2024-03-15T11:29:23,671 | ^ 2024-03-15T11:29:23,672 distancemat.c: In function ‘print_DistanceMatrix’: 2024-03-15T11:29:23,673 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T11:29:23,673 349 | for(row=0; row < mat->size; row++) { 2024-03-15T11:29:23,674 | ^ 2024-03-15T11:29:23,675 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-03-15T11:29:23,676 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-03-15T11:29:23,677 410 | while(c = fgetc(handle)) { 2024-03-15T11:29:23,677 | ^ 2024-03-15T11:29:24,093 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c pynj.c -o build/temp.linux-armv7l-cpython-311/pynj.o 2024-03-15T11:29:24,717 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c sequence.c -o build/temp.linux-armv7l-cpython-311/sequence.o 2024-03-15T11:29:24,947 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c tree.c -o build/temp.linux-armv7l-cpython-311/tree.o 2024-03-15T11:29:25,771 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.11 -c util.c -o build/temp.linux-armv7l-cpython-311/util.o 2024-03-15T11:29:25,949 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/align.o build/temp.linux-armv7l-cpython-311/buildtree.o build/temp.linux-armv7l-cpython-311/cluster.o build/temp.linux-armv7l-cpython-311/distancemat.o build/temp.linux-armv7l-cpython-311/pynj.o build/temp.linux-armv7l-cpython-311/sequence.o build/temp.linux-armv7l-cpython-311/tree.o build/temp.linux-armv7l-cpython-311/util.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so 2024-03-15T11:29:26,057 building 'dnj' extension 2024-03-15T11:29:26,058 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c bytescale.c -o build/temp.linux-armv7l-cpython-311/bytescale.o -fopenmp 2024-03-15T11:29:26,113 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c dnj.c -o build/temp.linux-armv7l-cpython-311/dnj.o -fopenmp 2024-03-15T11:29:26,250 dnj.c: In function ‘minQpair’: 2024-03-15T11:29:26,251 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,252 70 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,253 | ^~~ 2024-03-15T11:29:26,253 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,254 126 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,255 | ^~~ 2024-03-15T11:29:26,255 dnj.c: In function ‘maxQpair’: 2024-03-15T11:29:26,256 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,256 157 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,257 | ^~~ 2024-03-15T11:29:26,258 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,258 213 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,259 | ^~~ 2024-03-15T11:29:26,260 dnj.c: In function ‘UPGMApair’: 2024-03-15T11:29:26,260 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,261 237 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,262 | ^~~ 2024-03-15T11:29:26,262 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,263 284 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,264 | ^~~ 2024-03-15T11:29:26,265 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,265 291 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,266 | ^~~ 2024-03-15T11:29:26,266 dnj.c: In function ‘minQrow’: 2024-03-15T11:29:26,267 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,267 374 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,268 | ^~~ 2024-03-15T11:29:26,268 dnj.c: In function ‘maxQrow’: 2024-03-15T11:29:26,269 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,269 435 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,270 | ^~~ 2024-03-15T11:29:26,270 dnj.c: In function ‘UPGMArow’: 2024-03-15T11:29:26,271 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,271 488 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,272 | ^~~ 2024-03-15T11:29:26,272 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,273 494 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,273 | ^~~ 2024-03-15T11:29:26,274 dnj.c: In function ‘minQ_thread’: 2024-03-15T11:29:26,274 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:26,275 553 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:26,275 | ^~~ 2024-03-15T11:29:27,620 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c filebuff.c -o build/temp.linux-armv7l-cpython-311/filebuff.o -fopenmp 2024-03-15T11:29:27,740 filebuff.c: In function ‘BuffgzFileBuff’: 2024-03-15T11:29:27,741 filebuff.c:99:54: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:27,741 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-03-15T11:29:27,742 | ^~ 2024-03-15T11:29:28,065 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c hclust.c -o build/temp.linux-armv7l-cpython-311/hclust.o -fopenmp 2024-03-15T11:29:28,208 hclust.c: In function ‘minQ’: 2024-03-15T11:29:28,209 hclust.c:364:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T11:29:28,210 364 | while(++i < Q->n) { 2024-03-15T11:29:28,210 | ^ 2024-03-15T11:29:28,211 hclust.c:377:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:28,212 377 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:28,212 | ^~~ 2024-03-15T11:29:28,213 hclust.c: In function ‘maxQ’: 2024-03-15T11:29:28,214 hclust.c:394:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T11:29:28,214 394 | while(++i < Q->n) { 2024-03-15T11:29:28,215 | ^ 2024-03-15T11:29:28,216 hclust.c:407:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:28,216 407 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:28,217 | ^~~ 2024-03-15T11:29:30,594 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c matrix.c -o build/temp.linux-armv7l-cpython-311/matrix.o -fopenmp 2024-03-15T11:29:30,726 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-03-15T11:29:30,727 matrix.c:538:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T11:29:30,728 538 | if(pos != n) { 2024-03-15T11:29:30,728 | ^~ 2024-03-15T11:29:31,604 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c mman.c -o build/temp.linux-armv7l-cpython-311/mman.o -fopenmp 2024-03-15T11:29:31,658 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nj.c -o build/temp.linux-armv7l-cpython-311/nj.o -fopenmp 2024-03-15T11:29:31,787 nj.c: In function ‘initQ’: 2024-03-15T11:29:31,788 nj.c:243:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:31,789 243 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:31,789 | ^~~ 2024-03-15T11:29:31,790 nj.c: In function ‘initQ_MN’: 2024-03-15T11:29:31,791 nj.c:358:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:31,791 358 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:31,792 | ^~~ 2024-03-15T11:29:31,795 nj.c: In function ‘minD’: 2024-03-15T11:29:31,796 nj.c:559:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:31,797 559 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:31,797 | ^~~ 2024-03-15T11:29:31,798 nj.c: In function ‘maxD’: 2024-03-15T11:29:31,799 nj.c:642:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:31,800 642 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:31,800 | ^~~ 2024-03-15T11:29:31,803 nj.c: In function ‘minPair’: 2024-03-15T11:29:31,804 nj.c:826:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T11:29:31,804 826 | pos <<= sizeof(unsigned) * 8; 2024-03-15T11:29:31,805 | ^~~ 2024-03-15T11:29:35,170 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c nwck.c -o build/temp.linux-armv7l-cpython-311/nwck.o -fopenmp 2024-03-15T11:29:35,725 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pherror.c -o build/temp.linux-armv7l-cpython-311/pherror.o -fopenmp 2024-03-15T11:29:35,820 pherror.c: In function ‘cfread’: 2024-03-15T11:29:35,820 pherror.c:58:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T11:29:35,821 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-03-15T11:29:35,822 | ^~ 2024-03-15T11:29:35,913 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c phy.c -o build/temp.linux-armv7l-cpython-311/phy.o -fopenmp 2024-03-15T11:29:36,975 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c pydnj.c -o build/temp.linux-armv7l-cpython-311/pydnj.o -fopenmp 2024-03-15T11:29:37,344 In file included from pydnj.c:11: 2024-03-15T11:29:37,345 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-03-15T11:29:37,346 20 | #define _XOPEN_SOURCE 600 2024-03-15T11:29:37,346 | 2024-03-15T11:29:37,347 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-03-15T11:29:37,347 from /usr/include/stdlib.h:26, 2024-03-15T11:29:37,348 from /usr/include/python3.11/Python.h:23, 2024-03-15T11:29:37,348 from pydnj.c:1: 2024-03-15T11:29:37,349 /usr/include/features.h:214: note: this is the location of the previous definition 2024-03-15T11:29:37,349 214 | # define _XOPEN_SOURCE 700 2024-03-15T11:29:37,350 | 2024-03-15T11:29:37,369 pydnj.c: In function ‘py_build’: 2024-03-15T11:29:37,370 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-03-15T11:29:37,370 165 | p = omp_get_num_procs(); 2024-03-15T11:29:37,371 | ^~~~~~~~~~~~~~~~~ 2024-03-15T11:29:37,489 pydnj.c:169:5: warning: ‘free’ called on pointer returned from a mismatched allocation function [-Wmismatched-dealloc] 2024-03-15T11:29:37,490 169 | free(file); 2024-03-15T11:29:37,491 | ^~~~~~~~~~ 2024-03-15T11:29:37,491 pydnj.c:125:12: note: returned from ‘fopen’ 2024-03-15T11:29:37,492 125 | file = fopen(inputfilename, "r"); 2024-03-15T11:29:37,492 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T11:29:37,563 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c qseqs.c -o build/temp.linux-armv7l-cpython-311/qseqs.o -fopenmp 2024-03-15T11:29:37,770 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c str.c -o build/temp.linux-armv7l-cpython-311/str.o -fopenmp 2024-03-15T11:29:37,879 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c tmp.c -o build/temp.linux-armv7l-cpython-311/tmp.o -fopenmp 2024-03-15T11:29:38,108 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.11 -c vector.c -o build/temp.linux-armv7l-cpython-311/vector.o -fopenmp 2024-03-15T11:29:38,268 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/bytescale.o build/temp.linux-armv7l-cpython-311/dnj.o build/temp.linux-armv7l-cpython-311/filebuff.o build/temp.linux-armv7l-cpython-311/hclust.o build/temp.linux-armv7l-cpython-311/matrix.o build/temp.linux-armv7l-cpython-311/mman.o build/temp.linux-armv7l-cpython-311/nj.o build/temp.linux-armv7l-cpython-311/nwck.o build/temp.linux-armv7l-cpython-311/pherror.o build/temp.linux-armv7l-cpython-311/phy.o build/temp.linux-armv7l-cpython-311/pydnj.o build/temp.linux-armv7l-cpython-311/qseqs.o build/temp.linux-armv7l-cpython-311/str.o build/temp.linux-armv7l-cpython-311/tmp.o build/temp.linux-armv7l-cpython-311/vector.o -L/usr/lib/arm-linux-gnueabihf -lz -o build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -fopenmp 2024-03-15T11:29:38,430 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-03-15T11:29:38,430 !! 2024-03-15T11:29:38,431 ******************************************************************************** 2024-03-15T11:29:38,432 Please avoid running ``setup.py`` directly. 2024-03-15T11:29:38,433 Instead, use pypa/build, pypa/installer or other 2024-03-15T11:29:38,433 standards-based tools. 2024-03-15T11:29:38,434 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-03-15T11:29:38,435 ******************************************************************************** 2024-03-15T11:29:38,437 !! 2024-03-15T11:29:38,437 self.initialize_options() 2024-03-15T11:29:38,461 installing to build/bdist.linux-armv7l/wheel 2024-03-15T11:29:38,462 running install 2024-03-15T11:29:38,486 running install_lib 2024-03-15T11:29:38,510 creating build/bdist.linux-armv7l 2024-03-15T11:29:38,511 creating build/bdist.linux-armv7l/wheel 2024-03-15T11:29:38,512 copying build/lib.linux-armv7l-cpython-311/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-03-15T11:29:38,515 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-03-15T11:29:38,523 copying build/lib.linux-armv7l-cpython-311/dnj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-03-15T11:29:38,530 copying build/lib.linux-armv7l-cpython-311/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-03-15T11:29:38,532 copying build/lib.linux-armv7l-cpython-311/nj.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-03-15T11:29:38,536 running install_egg_info 2024-03-15T11:29:38,566 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-1.1.1-py3.11.egg-info 2024-03-15T11:29:38,578 running install_scripts 2024-03-15T11:29:38,627 creating build/bdist.linux-armv7l/wheel/kssdtree-1.1.1.dist-info/WHEEL 2024-03-15T11:29:38,630 creating '/tmp/pip-wheel-qqf8yib1/kssdtree-1.1.1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-03-15T11:29:38,697 adding 'dnj.cpython-311-arm-linux-gnueabihf.so' 2024-03-15T11:29:38,808 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2024-03-15T11:29:38,815 adding 'kssdtree.py' 2024-03-15T11:29:38,845 adding 'nj.cpython-311-arm-linux-gnueabihf.so' 2024-03-15T11:29:38,847 adding 'toolutils.py' 2024-03-15T11:29:38,849 adding 'kssdtree-1.1.1.dist-info/METADATA' 2024-03-15T11:29:38,850 adding 'kssdtree-1.1.1.dist-info/WHEEL' 2024-03-15T11:29:38,852 adding 'kssdtree-1.1.1.dist-info/dependency_links.txt' 2024-03-15T11:29:38,853 adding 'kssdtree-1.1.1.dist-info/top_level.txt' 2024-03-15T11:29:38,853 adding 'kssdtree-1.1.1.dist-info/RECORD' 2024-03-15T11:29:38,859 removing build/bdist.linux-armv7l/wheel 2024-03-15T11:29:39,021 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-03-15T11:29:39,028 Created wheel for kssdtree: filename=kssdtree-1.1.1-cp311-cp311-linux_armv7l.whl size=380321 sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb 2024-03-15T11:29:39,029 Stored in directory: /tmp/pip-ephem-wheel-cache-ilpbjryr/wheels/79/fa/cb/1596f481d73817bd32de92cec7e0f070e463436147b41168d2 2024-03-15T11:29:39,038 Successfully built kssdtree 2024-03-15T11:29:39,090 Removed build tracker: '/tmp/pip-build-tracker-oez6wpl5'