2024-11-19T02:53:25,990 Created temporary directory: /tmp/pip-build-tracker-tijezf_x 2024-11-19T02:53:25,991 Initialized build tracking at /tmp/pip-build-tracker-tijezf_x 2024-11-19T02:53:25,991 Created build tracker: /tmp/pip-build-tracker-tijezf_x 2024-11-19T02:53:25,992 Entered build tracker: /tmp/pip-build-tracker-tijezf_x 2024-11-19T02:53:25,993 Created temporary directory: /tmp/pip-wheel-ng26dtg1 2024-11-19T02:53:25,997 Created temporary directory: /tmp/pip-ephem-wheel-cache-g98wmn6o 2024-11-19T02:53:26,041 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-11-19T02:53:26,043 2 location(s) to search for versions of kssdutils: 2024-11-19T02:53:26,043 * https://pypi.org/simple/kssdutils/ 2024-11-19T02:53:26,043 * https://www.piwheels.org/simple/kssdutils/ 2024-11-19T02:53:26,044 Fetching project page and analyzing links: https://pypi.org/simple/kssdutils/ 2024-11-19T02:53:26,045 Getting page https://pypi.org/simple/kssdutils/ 2024-11-19T02:53:26,046 Found index url https://pypi.org/simple/ 2024-11-19T02:53:26,263 Fetched page https://pypi.org/simple/kssdutils/ as application/vnd.pypi.simple.v1+json 2024-11-19T02:53:26,264 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 2024-11-19T02:53:26,265 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 2024-11-19T02:53:26,266 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdutils/ 2024-11-19T02:53:26,267 Getting page https://www.piwheels.org/simple/kssdutils/ 2024-11-19T02:53:26,268 Found index url https://www.piwheels.org/simple/ 2024-11-19T02:53:26,441 Fetched page https://www.piwheels.org/simple/kssdutils/ as text/html 2024-11-19T02:53:26,442 Skipping link: not a file: https://www.piwheels.org/simple/kssdutils/ 2024-11-19T02:53:26,443 Skipping link: not a file: https://pypi.org/simple/kssdutils/ 2024-11-19T02:53:26,461 Given no hashes to check 1 links for project 'kssdutils': discarding no candidates 2024-11-19T02:53:26,463 Collecting kssdutils==1.0.0 2024-11-19T02:53:26,465 Created temporary directory: /tmp/pip-unpack-go7jdgsr 2024-11-19T02:53:26,678 Downloading kssdutils-1.0.0.tar.gz (44 kB) 2024-11-19T02:53:26,777 Added kssdutils==1.0.0 from https://files.pythonhosted.org/packages/61/ef/1bdb91b53dbe31ea0be28ab2c2292994b6228b357a8d54b69ac642f81f01/kssdutils-1.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-tijezf_x' 2024-11-19T02:53:26,779 Running setup.py (path:/tmp/pip-wheel-ng26dtg1/kssdutils_8c5ba9d2fabe47a0bee9149fa081ed44/setup.py) egg_info for package kssdutils 2024-11-19T02:53:26,780 Created temporary directory: /tmp/pip-pip-egg-info-2tn3vt_t 2024-11-19T02:53:26,786 Preparing metadata (setup.py): started 2024-11-19T02:53:26,788 Running command python setup.py egg_info 2024-11-19T02:53:28,076 running egg_info 2024-11-19T02:53:28,106 creating /tmp/pip-pip-egg-info-2tn3vt_t/kssdutils.egg-info 2024-11-19T02:53:28,107 writing /tmp/pip-pip-egg-info-2tn3vt_t/kssdutils.egg-info/PKG-INFO 2024-11-19T02:53:28,111 writing dependency_links to /tmp/pip-pip-egg-info-2tn3vt_t/kssdutils.egg-info/dependency_links.txt 2024-11-19T02:53:28,114 writing top-level names to /tmp/pip-pip-egg-info-2tn3vt_t/kssdutils.egg-info/top_level.txt 2024-11-19T02:53:28,115 writing manifest file '/tmp/pip-pip-egg-info-2tn3vt_t/kssdutils.egg-info/SOURCES.txt' 2024-11-19T02:53:28,228 reading manifest file '/tmp/pip-pip-egg-info-2tn3vt_t/kssdutils.egg-info/SOURCES.txt' 2024-11-19T02:53:28,230 reading manifest template 'MANIFEST.in' 2024-11-19T02:53:28,236 warning: no files found matching '*.h' under directory 'njheaders' 2024-11-19T02:53:28,236 warning: no files found matching '*.h' under directory 'dnjheaders' 2024-11-19T02:53:28,239 writing manifest file '/tmp/pip-pip-egg-info-2tn3vt_t/kssdutils.egg-info/SOURCES.txt' 2024-11-19T02:53:28,347 Preparing metadata (setup.py): finished with status 'done' 2024-11-19T02:53:28,351 Source in /tmp/pip-wheel-ng26dtg1/kssdutils_8c5ba9d2fabe47a0bee9149fa081ed44 has version 1.0.0, which satisfies requirement kssdutils==1.0.0 from https://files.pythonhosted.org/packages/61/ef/1bdb91b53dbe31ea0be28ab2c2292994b6228b357a8d54b69ac642f81f01/kssdutils-1.0.0.tar.gz 2024-11-19T02:53:28,352 Removed kssdutils==1.0.0 from https://files.pythonhosted.org/packages/61/ef/1bdb91b53dbe31ea0be28ab2c2292994b6228b357a8d54b69ac642f81f01/kssdutils-1.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-tijezf_x' 2024-11-19T02:53:28,355 Created temporary directory: /tmp/pip-unpack-cvd38lrf 2024-11-19T02:53:28,356 Created temporary directory: /tmp/pip-unpack-0rnfnq0q 2024-11-19T02:53:28,357 Building wheels for collected packages: kssdutils 2024-11-19T02:53:28,361 Created temporary directory: /tmp/pip-wheel-8hk1p7dh 2024-11-19T02:53:28,361 Building wheel for kssdutils (setup.py): started 2024-11-19T02:53:28,362 Destination directory: /tmp/pip-wheel-8hk1p7dh 2024-11-19T02:53:28,363 Running command python setup.py bdist_wheel 2024-11-19T02:53:29,580 running bdist_wheel 2024-11-19T02:53:29,711 running build 2024-11-19T02:53:29,712 running build_py 2024-11-19T02:53:29,741 creating build/lib.linux-armv7l-cpython-311 2024-11-19T02:53:29,742 copying kssdutils.py -> build/lib.linux-armv7l-cpython-311 2024-11-19T02:53:29,744 running egg_info 2024-11-19T02:53:29,772 writing kssdutils.egg-info/PKG-INFO 2024-11-19T02:53:29,775 writing dependency_links to kssdutils.egg-info/dependency_links.txt 2024-11-19T02:53:29,777 writing top-level names to kssdutils.egg-info/top_level.txt 2024-11-19T02:53:29,806 reading manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-11-19T02:53:29,809 reading manifest template 'MANIFEST.in' 2024-11-19T02:53:29,814 warning: no files found matching '*.h' under directory 'njheaders' 2024-11-19T02:53:29,815 warning: no files found matching '*.h' under directory 'dnjheaders' 2024-11-19T02:53:29,818 writing manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-11-19T02:53:29,820 running build_ext 2024-11-19T02:53:30,371 building 'kssd' extension 2024-11-19T02:53:30,372 creating build/temp.linux-armv7l-cpython-311 2024-11-19T02:53:30,374 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 2024-11-19T02:53:30,568 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-11-19T02:53:30,569 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T02:53:30,570 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-11-19T02:53:30,571 | ^ 2024-11-19T02:53:30,573 co2mco.c: In function ‘co2unitllmco’: 2024-11-19T02:53:30,573 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T02:53:30,574 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-11-19T02:53:30,575 | ^ 2024-11-19T02:53:31,326 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 2024-11-19T02:53:31,702 command_composite.c: In function ‘get_species_abundance’: 2024-11-19T02:53:31,703 command_composite.c:32:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-19T02:53:31,704 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-11-19T02:53:31,704 | ^~ 2024-11-19T02:53:31,705 command_composite.c:34:72: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-19T02:53:31,706 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-11-19T02:53:31,706 | ^~ 2024-11-19T02:53:31,707 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:31,707 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T02:53:31,708 | ^ 2024-11-19T02:53:31,708 command_composite.c:64:31: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:31,709 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T02:53:31,709 | ^~~~~~~~~~ 2024-11-19T02:53:31,710 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-11-19T02:53:31,710 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T02:53:31,711 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:31,711 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:31,712 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T02:53:31,712 | ^ 2024-11-19T02:53:31,713 command_composite.c:70:31: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:31,713 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T02:53:31,714 | ^~~~~~~~~~ 2024-11-19T02:53:31,715 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-11-19T02:53:31,716 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T02:53:31,716 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:31,717 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:31,718 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T02:53:31,718 | ^ 2024-11-19T02:53:31,719 command_composite.c:76:31: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:31,720 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T02:53:31,721 | ^~~~~~~~~~ 2024-11-19T02:53:31,721 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-11-19T02:53:31,722 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T02:53:31,723 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:31,723 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:31,724 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T02:53:31,725 | ^ 2024-11-19T02:53:31,725 command_composite.c:82:31: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:31,726 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T02:53:31,727 | ^~~~~~~~~~ 2024-11-19T02:53:31,727 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 269) into a destination of size 256 2024-11-19T02:53:31,728 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T02:53:31,729 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:31,729 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:31,730 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T02:53:31,730 | ^ 2024-11-19T02:53:31,731 command_composite.c:88:31: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:31,731 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T02:53:31,732 | ^~~~~~~~~~~~ 2024-11-19T02:53:31,732 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 271) into a destination of size 256 2024-11-19T02:53:31,732 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T02:53:31,733 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:31,974 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 2024-11-19T02:53:32,220 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-19T02:53:32,222 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=] 2024-11-19T02:53:32,222 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T02:53:32,223 | ~~^ 2024-11-19T02:53:32,224 | | 2024-11-19T02:53:32,224 | long unsigned int 2024-11-19T02:53:32,225 | %u 2024-11-19T02:53:32,225 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T02:53:32,226 | ~~~~~~~ 2024-11-19T02:53:32,227 | | 2024-11-19T02:53:32,227 | size_t {aka unsigned int} 2024-11-19T02:53:32,228 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=] 2024-11-19T02:53:32,229 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T02:53:32,230 | ~~^ 2024-11-19T02:53:32,230 | | 2024-11-19T02:53:32,231 | long unsigned int 2024-11-19T02:53:32,231 | %u 2024-11-19T02:53:32,232 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T02:53:32,233 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T02:53:32,233 | ~~~~~~~~~ 2024-11-19T02:53:32,234 | | 2024-11-19T02:53:32,235 | size_t {aka unsigned int} 2024-11-19T02:53:32,236 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T02:53:32,236 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T02:53:32,237 | ~~^ 2024-11-19T02:53:32,238 | | 2024-11-19T02:53:32,238 | long unsigned int 2024-11-19T02:53:32,239 | %u 2024-11-19T02:53:32,239 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T02:53:32,240 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T02:53:32,240 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:32,241 | | 2024-11-19T02:53:32,241 | unsigned int 2024-11-19T02:53:32,242 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T02:53:32,242 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-11-19T02:53:32,242 | ^ 2024-11-19T02:53:32,243 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-19T02:53:32,243 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=] 2024-11-19T02:53:32,244 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T02:53:32,245 | ~~^ ~~~~~~~ 2024-11-19T02:53:32,245 | | | 2024-11-19T02:53:32,246 | long unsigned int size_t {aka unsigned int} 2024-11-19T02:53:32,247 | %u 2024-11-19T02:53:32,247 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=] 2024-11-19T02:53:32,248 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T02:53:32,249 | ~~^ 2024-11-19T02:53:32,250 | | 2024-11-19T02:53:32,250 | long unsigned int 2024-11-19T02:53:32,251 | %u 2024-11-19T02:53:32,251 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-19T02:53:32,252 | ~~~~~~~~~ 2024-11-19T02:53:32,252 | | 2024-11-19T02:53:32,253 | size_t {aka unsigned int} 2024-11-19T02:53:32,253 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T02:53:32,254 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T02:53:32,255 | ~~^ 2024-11-19T02:53:32,255 | | 2024-11-19T02:53:32,256 | long unsigned int 2024-11-19T02:53:32,256 | %u 2024-11-19T02:53:32,257 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-19T02:53:32,257 865 | (size_t) b * unitsz_distf_mapped); 2024-11-19T02:53:32,258 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:32,258 | | 2024-11-19T02:53:32,259 | unsigned int 2024-11-19T02:53:32,259 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-11-19T02:53:32,260 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-11-19T02:53:32,260 | ^~~~~~~ 2024-11-19T02:53:32,261 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-11-19T02:53:32,261 809 | struct stat cbd_fcode_stat; 2024-11-19T02:53:32,262 | ^~~~~~~~~~~~~~ 2024-11-19T02:53:32,263 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-11-19T02:53:32,263 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-19T02:53:32,264 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:32,265 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-11-19T02:53:32,266 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-19T02:53:32,266 | ^~~~~~~~~~~~~~~~~ 2024-11-19T02:53:32,267 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-19T02:53:32,267 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=] 2024-11-19T02:53:32,268 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T02:53:32,269 | ~~^ 2024-11-19T02:53:32,269 | | 2024-11-19T02:53:32,270 | long unsigned int 2024-11-19T02:53:32,270 | %u 2024-11-19T02:53:32,271 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T02:53:32,271 | ~~~~~~~ 2024-11-19T02:53:32,272 | | 2024-11-19T02:53:32,272 | size_t {aka unsigned int} 2024-11-19T02:53:32,273 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=] 2024-11-19T02:53:32,273 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T02:53:32,274 | ~~^ 2024-11-19T02:53:32,275 | | 2024-11-19T02:53:32,275 | long unsigned int 2024-11-19T02:53:32,276 | %u 2024-11-19T02:53:32,277 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T02:53:32,277 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T02:53:32,278 | ~~~~~~~~~ 2024-11-19T02:53:32,278 | | 2024-11-19T02:53:32,279 | size_t {aka unsigned int} 2024-11-19T02:53:32,279 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T02:53:32,280 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T02:53:32,280 | ~~^ 2024-11-19T02:53:32,281 | | 2024-11-19T02:53:32,281 | long unsigned int 2024-11-19T02:53:32,282 | %u 2024-11-19T02:53:32,282 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T02:53:32,283 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T02:53:32,283 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:32,284 | | 2024-11-19T02:53:32,285 | unsigned int 2024-11-19T02:53:32,285 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-11-19T02:53:32,286 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-11-19T02:53:32,287 | ^ 2024-11-19T02:53:32,288 command_dist.c: In function ‘mco_co_dist_core’: 2024-11-19T02:53:32,288 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T02:53:32,289 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-11-19T02:53:32,290 | ^ 2024-11-19T02:53:32,294 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-11-19T02:53:32,295 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T02:53:32,296 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T02:53:32,296 | ^ 2024-11-19T02:53:32,298 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T02:53:32,298 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-19T02:53:32,299 | ^ 2024-11-19T02:53:32,305 command_dist.c: In function ‘dist_print_nobin’: 2024-11-19T02:53:32,306 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T02:53:32,307 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-11-19T02:53:32,308 | ^ 2024-11-19T02:53:32,310 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T02:53:32,310 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-19T02:53:32,312 | ^ 2024-11-19T02:53:32,313 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T02:53:32,313 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T02:53:32,314 | ^ 2024-11-19T02:53:32,675 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-11-19T02:53:32,676 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized [-Wmaybe-uninitialized] 2024-11-19T02:53:32,676 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-11-19T02:53:32,677 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:32,677 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-11-19T02:53:32,678 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-11-19T02:53:32,678 | ^~~~~~~~~~~~ 2024-11-19T02:53:33,514 command_dist.c: In function ‘get_dim_shuffle’: 2024-11-19T02:53:33,514 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-11-19T02:53:33,515 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-19T02:53:33,515 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:33,516 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-11-19T02:53:33,516 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-19T02:53:33,517 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,415 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-19T02:53:34,416 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:34,416 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T02:53:34,417 | ^~ ~~~~~~~~~ 2024-11-19T02:53:34,418 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T02:53:34,418 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T02:53:34,419 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,420 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T02:53:34,420 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T02:53:34,421 | ^~~~~~~~~~~~~~~ 2024-11-19T02:53:34,421 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T02:53:34,422 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T02:53:34,422 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,423 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T02:53:34,423 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T02:53:34,424 | ^~~~~~~~~~~ 2024-11-19T02:53:34,425 command_dist.c:681:38: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:34,425 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T02:53:34,426 | ^~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,427 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-19T02:53:34,428 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T02:53:34,429 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,429 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T02:53:34,430 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T02:53:34,430 | ^~~~~ 2024-11-19T02:53:34,431 command_dist.c:682:32: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:34,431 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T02:53:34,432 | ^~~~~~~~~~~ 2024-11-19T02:53:34,432 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T02:53:34,433 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T02:53:34,434 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,667 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-19T02:53:34,669 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:34,669 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T02:53:34,670 | ^~ ~~~~~~~~~ 2024-11-19T02:53:34,670 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T02:53:34,671 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T02:53:34,671 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,672 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T02:53:34,672 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T02:53:34,673 | ^~~~~~~~~~~~~~~ 2024-11-19T02:53:34,673 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T02:53:34,674 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T02:53:34,675 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,675 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T02:53:34,676 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T02:53:34,677 | ^~~~~~~~~~~~~ 2024-11-19T02:53:34,677 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T02:53:34,678 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T02:53:34,678 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,679 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:34,679 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T02:53:34,680 | ^ 2024-11-19T02:53:34,681 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-11-19T02:53:34,681 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T02:53:34,682 | ^~~~~~~~~~ 2024-11-19T02:53:34,683 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-19T02:53:34,684 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T02:53:34,684 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,685 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:34,686 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T02:53:34,686 | ^ 2024-11-19T02:53:34,687 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-11-19T02:53:34,687 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T02:53:34,688 | ^~~~~~~~~~ 2024-11-19T02:53:34,688 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-19T02:53:34,689 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T02:53:34,689 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,950 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-19T02:53:34,951 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:34,952 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T02:53:34,952 | ^~ ~~~~~~~~~ 2024-11-19T02:53:34,952 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T02:53:34,953 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T02:53:34,953 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,954 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T02:53:34,955 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T02:53:34,955 | ^~~~~~~~~~~~~~~ 2024-11-19T02:53:34,956 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T02:53:34,957 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T02:53:34,957 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,958 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T02:53:34,959 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T02:53:34,959 | ^~~~~~~~~~~~~ 2024-11-19T02:53:34,960 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T02:53:34,961 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T02:53:34,961 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,962 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T02:53:34,962 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T02:53:34,963 | ^~~~~~~~~~~ 2024-11-19T02:53:34,964 command_dist.c:1022:38: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:34,964 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T02:53:34,965 | ^~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,965 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-19T02:53:34,966 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T02:53:34,967 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:34,967 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T02:53:34,968 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T02:53:34,968 | ^~~~~ 2024-11-19T02:53:34,969 command_dist.c:1023:32: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:34,969 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T02:53:34,970 | ^~~~~~~~~~~ 2024-11-19T02:53:34,970 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T02:53:34,971 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T02:53:34,971 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:35,243 command_dist.c: In function ‘combine_queries’: 2024-11-19T02:53:35,244 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T02:53:35,245 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-19T02:53:35,245 | ^ 2024-11-19T02:53:35,246 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T02:53:35,247 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-19T02:53:35,247 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:35,248 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T02:53:35,248 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-19T02:53:35,249 | ^ 2024-11-19T02:53:35,250 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T02:53:35,250 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-19T02:53:35,251 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:35,252 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:35,253 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-19T02:53:35,254 | ^~ ~~~~~~~~ 2024-11-19T02:53:35,254 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T02:53:35,255 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-19T02:53:35,256 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:35,737 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 2024-11-19T02:53:35,911 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 2024-11-19T02:53:36,080 command_set.c: In function ‘sketch_operate’: 2024-11-19T02:53:36,081 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T02:53:36,082 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-11-19T02:53:36,083 | ^ 2024-11-19T02:53:36,094 command_set.c: In function ‘combin_subset_pans’: 2024-11-19T02:53:36,095 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-19T02:53:36,095 457 | free(co_dstat_fpath); 2024-11-19T02:53:36,096 | ^~~~~~~~~~~~~~ 2024-11-19T02:53:36,096 In file included from kssdheaders/global_basic.h:159, 2024-11-19T02:53:36,097 from command_set.c:15: 2024-11-19T02:53:36,098 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-19T02:53:36,098 568 | extern void free (void *__ptr) __THROW; 2024-11-19T02:53:36,099 | ~~~~~~^~~~~ 2024-11-19T02:53:36,101 command_set.c: In function ‘grouping_genomes’: 2024-11-19T02:53:36,102 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-19T02:53:36,102 562 | free(co_dstat_fpath); 2024-11-19T02:53:36,103 | ^~~~~~~~~~~~~~ 2024-11-19T02:53:36,104 /usr/include/stdlib.h:568:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-19T02:53:36,104 568 | extern void free (void *__ptr) __THROW; 2024-11-19T02:53:36,105 | ~~~~~~^~~~~ 2024-11-19T02:53:36,270 command_set.c: In function ‘sketch_union’: 2024-11-19T02:53:36,271 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T02:53:36,271 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:36,272 | ^ 2024-11-19T02:53:36,273 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T02:53:36,274 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:36,274 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,275 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,275 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T02:53:36,276 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:36,276 command_set.c:82:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,277 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T02:53:36,277 | ^~~~~~~~~~ 2024-11-19T02:53:36,278 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T02:53:36,279 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T02:53:36,279 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,280 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,281 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T02:53:36,282 | ^~ ~~~~~~~~~~ 2024-11-19T02:53:36,282 command_set.c:92:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,283 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T02:53:36,283 | ^~~~~~~~~~ 2024-11-19T02:53:36,284 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T02:53:36,284 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T02:53:36,285 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,401 command_set.c: In function ‘sketch_operate’: 2024-11-19T02:53:36,402 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,403 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T02:53:36,403 | ^~ ~~~~~~~~~~ 2024-11-19T02:53:36,404 command_set.c:153:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,404 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T02:53:36,405 | ^~~~~~~~~~ 2024-11-19T02:53:36,405 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T02:53:36,406 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T02:53:36,406 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,407 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,407 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T02:53:36,408 | ^~ ~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,409 command_set.c:155:29: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,409 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T02:53:36,410 | ^~~~~~~~~~ 2024-11-19T02:53:36,410 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-19T02:53:36,411 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T02:53:36,411 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,412 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,413 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T02:53:36,413 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:36,414 command_set.c:165:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,415 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T02:53:36,415 | ^~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,416 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T02:53:36,417 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T02:53:36,417 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,418 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,419 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T02:53:36,419 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:36,420 command_set.c:169:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,420 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T02:53:36,421 | ^~~~~~~~~~ 2024-11-19T02:53:36,422 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T02:53:36,422 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T02:53:36,423 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,424 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,425 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T02:53:36,425 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:36,426 command_set.c:174:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,426 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T02:53:36,427 | ^~~~~~~~~~ 2024-11-19T02:53:36,427 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T02:53:36,428 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T02:53:36,428 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,429 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,429 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T02:53:36,430 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:36,430 command_set.c:187:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,431 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T02:53:36,431 | ^~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,432 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T02:53:36,433 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T02:53:36,433 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,434 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T02:53:36,435 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:36,436 | ^ 2024-11-19T02:53:36,437 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T02:53:36,437 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:36,438 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,576 command_set.c: In function ‘uniq_sketch_union’: 2024-11-19T02:53:36,577 command_set.c:219:39: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T02:53:36,578 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-11-19T02:53:36,578 | ^ 2024-11-19T02:53:36,579 command_set.c:219:17: note: ‘sprintf’ output between 11 and 21 bytes into a destination of size 20 2024-11-19T02:53:36,579 219 | sprintf(unionco,"%s.%d",uniq_pan_prefix,i); 2024-11-19T02:53:36,580 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,581 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T02:53:36,582 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:36,582 | ^ 2024-11-19T02:53:36,583 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T02:53:36,584 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:36,585 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,586 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,586 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T02:53:36,587 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:36,588 command_set.c:247:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,589 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T02:53:36,589 | ^~~~~~~~~~ 2024-11-19T02:53:36,590 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T02:53:36,590 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T02:53:36,591 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,591 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,592 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T02:53:36,592 | ^~ ~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,593 command_set.c:259:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,593 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T02:53:36,594 | ^~~~~~~~~~ 2024-11-19T02:53:36,594 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-19T02:53:36,595 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T02:53:36,595 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,722 command_set.c: In function ‘combin_pans’: 2024-11-19T02:53:36,722 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,723 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T02:53:36,723 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:36,724 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2024-11-19T02:53:36,724 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T02:53:36,725 | ^~~~~~~~~~ 2024-11-19T02:53:36,726 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-11-19T02:53:36,726 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T02:53:36,727 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,728 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,729 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T02:53:36,729 | ^~ ~~~~~~~~~~ 2024-11-19T02:53:36,730 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2024-11-19T02:53:36,731 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T02:53:36,731 | ^~~~~~~~~~ 2024-11-19T02:53:36,732 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-11-19T02:53:36,732 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T02:53:36,733 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,734 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T02:53:36,734 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:36,735 | ^ 2024-11-19T02:53:36,736 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T02:53:36,737 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:36,738 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,940 command_set.c: In function ‘combin_subset_pans’: 2024-11-19T02:53:36,941 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,941 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T02:53:36,941 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:36,942 command_set.c:469:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,942 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T02:53:36,943 | ^~~~~~~~~~ 2024-11-19T02:53:36,943 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T02:53:36,944 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T02:53:36,944 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,945 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,945 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T02:53:36,946 | ^~ ~~~~~~~~~~ 2024-11-19T02:53:36,946 command_set.c:475:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,947 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T02:53:36,947 | ^~~~~~~~~~ 2024-11-19T02:53:36,948 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T02:53:36,948 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T02:53:36,949 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,950 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,950 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T02:53:36,951 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:36,952 command_set.c:481:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,953 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T02:53:36,954 | ^~~~~~~~~~ 2024-11-19T02:53:36,955 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T02:53:36,955 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T02:53:36,956 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,956 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:36,957 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T02:53:36,958 | ^~ ~~~~~~~~~~ 2024-11-19T02:53:36,958 command_set.c:512:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:36,959 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T02:53:36,959 | ^~~~~~~~~~ 2024-11-19T02:53:36,960 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T02:53:36,961 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T02:53:36,962 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:36,963 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T02:53:36,963 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:36,963 | ^ 2024-11-19T02:53:36,964 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T02:53:36,964 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:36,965 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:37,187 command_set.c: In function ‘grouping_genomes’: 2024-11-19T02:53:37,188 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:37,189 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T02:53:37,189 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:37,190 command_set.c:574:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:37,190 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T02:53:37,191 | ^~~~~~~~~~ 2024-11-19T02:53:37,191 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T02:53:37,192 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T02:53:37,192 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:37,192 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:37,193 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T02:53:37,194 | ^~ ~~~~~~~~~~ 2024-11-19T02:53:37,194 command_set.c:580:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:37,195 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T02:53:37,196 | ^~~~~~~~~~ 2024-11-19T02:53:37,196 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T02:53:37,197 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T02:53:37,198 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:37,198 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:37,199 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T02:53:37,199 | ^~ ~~~~~~~~~~~ 2024-11-19T02:53:37,200 command_set.c:612:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:37,200 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T02:53:37,201 | ^~~~~~~~~~ 2024-11-19T02:53:37,202 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T02:53:37,202 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T02:53:37,203 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:37,204 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T02:53:37,205 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T02:53:37,205 | ^~ ~~~~~~~~~~ 2024-11-19T02:53:37,206 command_set.c:634:25: note: directive argument in the range [-2147483644, 2147483646] 2024-11-19T02:53:37,207 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T02:53:37,207 | ^~~~~~~~~~ 2024-11-19T02:53:37,208 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T02:53:37,208 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T02:53:37,209 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:37,209 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T02:53:37,210 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:37,210 | ^ 2024-11-19T02:53:37,211 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T02:53:37,211 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T02:53:37,212 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T02:53:37,490 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 2024-11-19T02:53:37,805 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 2024-11-19T02:53:37,973 global_basic.c: In function ‘organize_infile_list’: 2024-11-19T02:53:37,974 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-11-19T02:53:37,975 195 | while (isspace(*buf)) buf++; 2024-11-19T02:53:37,975 | ^~~~~~~ 2024-11-19T02:53:37,976 global_basic.c:35:1: note: include ‘’ or provide a declaration of ‘isspace’ 2024-11-19T02:53:37,976 34 | #include 2024-11-19T02:53:37,977 +++ |+#include 2024-11-19T02:53:37,978 35 | 2024-11-19T02:53:37,978 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=] 2024-11-19T02:53:37,979 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-19T02:53:37,980 | ~~^ 2024-11-19T02:53:37,980 | | 2024-11-19T02:53:37,981 | long unsigned int 2024-11-19T02:53:37,982 | %u 2024-11-19T02:53:37,982 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-19T02:53:37,983 | ~~~~~~~~~~~ 2024-11-19T02:53:37,984 | | 2024-11-19T02:53:37,984 | size_t {aka unsigned int} 2024-11-19T02:53:37,985 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=] 2024-11-19T02:53:37,986 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-19T02:53:37,986 | ~~^ 2024-11-19T02:53:37,988 | | 2024-11-19T02:53:37,989 | long unsigned int 2024-11-19T02:53:37,989 | %u 2024-11-19T02:53:37,990 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-19T02:53:37,990 | ~~~~~~~~~~~ 2024-11-19T02:53:37,991 | | 2024-11-19T02:53:37,991 | size_t {aka unsigned int} 2024-11-19T02:53:38,747 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 2024-11-19T02:53:38,923 iseq2comem.c: In function ‘reads2mco’: 2024-11-19T02:53:38,924 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,924 156 | if (base > TL) { 2024-11-19T02:53:38,925 | ^ 2024-11-19T02:53:38,925 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,926 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T02:53:38,926 | ^~ 2024-11-19T02:53:38,927 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,928 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T02:53:38,928 | ^ 2024-11-19T02:53:38,930 iseq2comem.c: In function ‘fasta2co’: 2024-11-19T02:53:38,931 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,932 239 | if (base > TL) { 2024-11-19T02:53:38,933 | ^ 2024-11-19T02:53:38,934 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,934 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T02:53:38,935 | ^~ 2024-11-19T02:53:38,936 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,937 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T02:53:38,937 | ^ 2024-11-19T02:53:38,938 iseq2comem.c: In function ‘fastq2co’: 2024-11-19T02:53:38,938 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-11-19T02:53:38,939 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-11-19T02:53:38,940 | ^~ 2024-11-19T02:53:38,940 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,941 318 | if (base > TL) { 2024-11-19T02:53:38,941 | ^ 2024-11-19T02:53:38,942 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,943 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T02:53:38,944 | ^~ 2024-11-19T02:53:38,944 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,945 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T02:53:38,945 | ^ 2024-11-19T02:53:38,946 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,947 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-11-19T02:53:38,947 | ^ 2024-11-19T02:53:38,949 iseq2comem.c: In function ‘fastq2koc’: 2024-11-19T02:53:38,950 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,950 402 | if (base > TL) { 2024-11-19T02:53:38,951 | ^ 2024-11-19T02:53:38,951 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,952 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T02:53:38,952 | ^~ 2024-11-19T02:53:38,953 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,953 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T02:53:38,954 | ^ 2024-11-19T02:53:38,961 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-11-19T02:53:38,962 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,962 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T02:53:38,963 | ^~ 2024-11-19T02:53:38,964 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T02:53:38,964 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T02:53:38,965 | ^ 2024-11-19T02:53:40,347 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 2024-11-19T02:53:40,402 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 2024-11-19T02:53:40,527 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 2024-11-19T02:53:41,149 pykssd.c: In function ‘py_dist_dispatch’: 2024-11-19T02:53:41,150 pykssd.c:329:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-11-19T02:53:41,151 329 | int state1 = dist_dispatch(&dist_opt_val1); 2024-11-19T02:53:41,151 | ^~~~~~ 2024-11-19T02:53:41,152 pykssd.c:386:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-11-19T02:53:41,153 386 | int state2 = dist_dispatch(&dist_opt_val2); 2024-11-19T02:53:41,153 | ^~~~~~ 2024-11-19T02:53:41,154 pykssd.c:510:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-11-19T02:53:41,154 510 | int state4 = dist_dispatch(&dist_opt_val4); 2024-11-19T02:53:41,155 | ^~~~~~ 2024-11-19T02:53:41,791 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 2024-11-19T02:53:41,986 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-11-19T02:53:41,987 !! 2024-11-19T02:53:41,988 ******************************************************************************** 2024-11-19T02:53:41,988 Please avoid running ``setup.py`` directly. 2024-11-19T02:53:41,989 Instead, use pypa/build, pypa/installer or other 2024-11-19T02:53:41,990 standards-based tools. 2024-11-19T02:53:41,991 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-11-19T02:53:41,992 ******************************************************************************** 2024-11-19T02:53:41,993 !! 2024-11-19T02:53:41,993 self.initialize_options() 2024-11-19T02:53:42,019 installing to build/bdist.linux-armv7l/wheel 2024-11-19T02:53:42,020 running install 2024-11-19T02:53:42,044 running install_lib 2024-11-19T02:53:42,076 creating build/bdist.linux-armv7l/wheel 2024-11-19T02:53:42,078 copying build/lib.linux-armv7l-cpython-311/kssd.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-11-19T02:53:42,093 copying build/lib.linux-armv7l-cpython-311/kssdutils.py -> build/bdist.linux-armv7l/wheel/. 2024-11-19T02:53:42,096 running install_egg_info 2024-11-19T02:53:42,135 Copying kssdutils.egg-info to build/bdist.linux-armv7l/wheel/./kssdutils-1.0.0-py3.11.egg-info 2024-11-19T02:53:42,157 running install_scripts 2024-11-19T02:53:42,221 creating build/bdist.linux-armv7l/wheel/kssdutils-1.0.0.dist-info/WHEEL 2024-11-19T02:53:42,226 creating '/tmp/pip-wheel-8hk1p7dh/kssdutils-1.0.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-11-19T02:53:42,311 adding 'kssd.cpython-311-arm-linux-gnueabihf.so' 2024-11-19T02:53:42,315 adding 'kssdutils.py' 2024-11-19T02:53:42,317 adding 'kssdutils-1.0.0.dist-info/METADATA' 2024-11-19T02:53:42,318 adding 'kssdutils-1.0.0.dist-info/WHEEL' 2024-11-19T02:53:42,319 adding 'kssdutils-1.0.0.dist-info/dependency_links.txt' 2024-11-19T02:53:42,320 adding 'kssdutils-1.0.0.dist-info/top_level.txt' 2024-11-19T02:53:42,321 adding 'kssdutils-1.0.0.dist-info/RECORD' 2024-11-19T02:53:42,324 removing build/bdist.linux-armv7l/wheel 2024-11-19T02:53:42,468 Building wheel for kssdutils (setup.py): finished with status 'done' 2024-11-19T02:53:42,473 Created wheel for kssdutils: filename=kssdutils-1.0.0-cp311-cp311-linux_armv7l.whl size=178553 sha256=e93f43f34a8ab412f6a0c97bc930a5c9c72997258d109e3f069a56b6270ff331 2024-11-19T02:53:42,474 Stored in directory: /tmp/pip-ephem-wheel-cache-g98wmn6o/wheels/a7/de/9a/71fc4599ce90112fdf1318354ea71e01bf95966802b3df58ee 2024-11-19T02:53:42,482 Successfully built kssdutils 2024-11-19T02:53:42,492 Removed build tracker: '/tmp/pip-build-tracker-tijezf_x'