2024-11-19T03:56:14,516 Disabling truststore because Python version isn't 3.10+ 2024-11-19T03:56:14,990 Created temporary directory: /tmp/pip-build-tracker-p9_43zhw 2024-11-19T03:56:14,991 Initialized build tracking at /tmp/pip-build-tracker-p9_43zhw 2024-11-19T03:56:14,991 Created build tracker: /tmp/pip-build-tracker-p9_43zhw 2024-11-19T03:56:14,991 Entered build tracker: /tmp/pip-build-tracker-p9_43zhw 2024-11-19T03:56:14,992 Created temporary directory: /tmp/pip-wheel-f_qyakan 2024-11-19T03:56:14,997 Created temporary directory: /tmp/pip-ephem-wheel-cache-ltfkc_p6 2024-11-19T03:56:15,039 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-11-19T03:56:15,042 2 location(s) to search for versions of kssdutils: 2024-11-19T03:56:15,042 * https://pypi.org/simple/kssdutils/ 2024-11-19T03:56:15,042 * https://www.piwheels.org/simple/kssdutils/ 2024-11-19T03:56:15,043 Fetching project page and analyzing links: https://pypi.org/simple/kssdutils/ 2024-11-19T03:56:15,043 Getting page https://pypi.org/simple/kssdutils/ 2024-11-19T03:56:15,045 Found index url https://pypi.org/simple/ 2024-11-19T03:56:15,139 Fetched page https://pypi.org/simple/kssdutils/ as application/vnd.pypi.simple.v1+json 2024-11-19T03:56:15,141 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 2024-11-19T03:56:15,141 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 2024-11-19T03:56:15,141 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdutils/ 2024-11-19T03:56:15,142 Getting page https://www.piwheels.org/simple/kssdutils/ 2024-11-19T03:56:15,143 Found index url https://www.piwheels.org/simple/ 2024-11-19T03:56:15,181 Fetched page https://www.piwheels.org/simple/kssdutils/ as text/html 2024-11-19T03:56:15,182 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp311-cp311-linux_armv6l.whl#sha256=e93f43f34a8ab412f6a0c97bc930a5c9c72997258d109e3f069a56b6270ff331 (from https://www.piwheels.org/simple/kssdutils/) 2024-11-19T03:56:15,183 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp311-cp311-linux_armv7l.whl#sha256=e93f43f34a8ab412f6a0c97bc930a5c9c72997258d109e3f069a56b6270ff331 (from https://www.piwheels.org/simple/kssdutils/) 2024-11-19T03:56:15,183 Skipping link: not a file: https://www.piwheels.org/simple/kssdutils/ 2024-11-19T03:56:15,183 Skipping link: not a file: https://pypi.org/simple/kssdutils/ 2024-11-19T03:56:15,198 Given no hashes to check 1 links for project 'kssdutils': discarding no candidates 2024-11-19T03:56:15,199 Collecting kssdutils==1.0.0 2024-11-19T03:56:15,201 Created temporary directory: /tmp/pip-unpack-2_5fncvz 2024-11-19T03:56:15,216 Downloading kssdutils-1.0.0.tar.gz (44 kB) 2024-11-19T03:56:15,304 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-p9_43zhw' 2024-11-19T03:56:15,306 Running setup.py (path:/tmp/pip-wheel-f_qyakan/kssdutils_c859812343f54cd48643842b5385c308/setup.py) egg_info for package kssdutils 2024-11-19T03:56:15,306 Created temporary directory: /tmp/pip-pip-egg-info-ujouh4st 2024-11-19T03:56:15,307 Preparing metadata (setup.py): started 2024-11-19T03:56:15,307 Running command python setup.py egg_info 2024-11-19T03:56:16,443 running egg_info 2024-11-19T03:56:16,473 creating /tmp/pip-pip-egg-info-ujouh4st/kssdutils.egg-info 2024-11-19T03:56:16,474 writing /tmp/pip-pip-egg-info-ujouh4st/kssdutils.egg-info/PKG-INFO 2024-11-19T03:56:16,478 writing dependency_links to /tmp/pip-pip-egg-info-ujouh4st/kssdutils.egg-info/dependency_links.txt 2024-11-19T03:56:16,480 writing top-level names to /tmp/pip-pip-egg-info-ujouh4st/kssdutils.egg-info/top_level.txt 2024-11-19T03:56:16,482 writing manifest file '/tmp/pip-pip-egg-info-ujouh4st/kssdutils.egg-info/SOURCES.txt' 2024-11-19T03:56:16,591 reading manifest file '/tmp/pip-pip-egg-info-ujouh4st/kssdutils.egg-info/SOURCES.txt' 2024-11-19T03:56:16,592 reading manifest template 'MANIFEST.in' 2024-11-19T03:56:16,598 warning: no files found matching '*.h' under directory 'njheaders' 2024-11-19T03:56:16,599 warning: no files found matching '*.h' under directory 'dnjheaders' 2024-11-19T03:56:16,603 writing manifest file '/tmp/pip-pip-egg-info-ujouh4st/kssdutils.egg-info/SOURCES.txt' 2024-11-19T03:56:16,692 Preparing metadata (setup.py): finished with status 'done' 2024-11-19T03:56:16,696 Source in /tmp/pip-wheel-f_qyakan/kssdutils_c859812343f54cd48643842b5385c308 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 2024-11-19T03:56:16,697 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-p9_43zhw' 2024-11-19T03:56:16,702 Created temporary directory: /tmp/pip-unpack-0dfks0dm 2024-11-19T03:56:16,703 Created temporary directory: /tmp/pip-unpack-fuorgs6h 2024-11-19T03:56:16,703 Building wheels for collected packages: kssdutils 2024-11-19T03:56:16,707 Created temporary directory: /tmp/pip-wheel-a5jnpnw2 2024-11-19T03:56:16,707 Building wheel for kssdutils (setup.py): started 2024-11-19T03:56:16,708 Destination directory: /tmp/pip-wheel-a5jnpnw2 2024-11-19T03:56:16,709 Running command python setup.py bdist_wheel 2024-11-19T03:56:17,709 running bdist_wheel 2024-11-19T03:56:17,842 running build 2024-11-19T03:56:17,843 running build_py 2024-11-19T03:56:17,872 creating build/lib.linux-armv7l-cpython-39 2024-11-19T03:56:17,873 copying kssdutils.py -> build/lib.linux-armv7l-cpython-39 2024-11-19T03:56:17,875 running egg_info 2024-11-19T03:56:17,901 writing kssdutils.egg-info/PKG-INFO 2024-11-19T03:56:17,904 writing dependency_links to kssdutils.egg-info/dependency_links.txt 2024-11-19T03:56:17,906 writing top-level names to kssdutils.egg-info/top_level.txt 2024-11-19T03:56:17,934 reading manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-11-19T03:56:17,937 reading manifest template 'MANIFEST.in' 2024-11-19T03:56:17,943 warning: no files found matching '*.h' under directory 'njheaders' 2024-11-19T03:56:17,943 warning: no files found matching '*.h' under directory 'dnjheaders' 2024-11-19T03:56:17,947 writing manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-11-19T03:56:17,949 running build_ext 2024-11-19T03:56:18,518 building 'kssd' extension 2024-11-19T03:56:18,519 creating build/temp.linux-armv7l-cpython-39 2024-11-19T03:56:18,521 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c co2mco.c -o build/temp.linux-armv7l-cpython-39/co2mco.o -fopenmp 2024-11-19T03:56:18,729 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-11-19T03:56:18,729 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T03:56:18,729 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-11-19T03:56:18,729 | ^ 2024-11-19T03:56:18,732 co2mco.c: In function ‘co2unitllmco’: 2024-11-19T03:56:18,732 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T03:56:18,732 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-11-19T03:56:18,732 | ^ 2024-11-19T03:56:19,349 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_composite.c -o build/temp.linux-armv7l-cpython-39/command_composite.o -fopenmp 2024-11-19T03:56:19,655 command_composite.c: In function ‘get_species_abundance’: 2024-11-19T03:56:19,656 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-19T03:56:19,656 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-11-19T03:56:19,656 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:19,656 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-19T03:56:19,656 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-11-19T03:56:19,656 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:19,657 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:19,658 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T03:56:19,658 | ^ 2024-11-19T03:56:19,658 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T03:56:19,658 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T03:56:19,658 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:19,659 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:19,659 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T03:56:19,659 | ^ 2024-11-19T03:56:19,659 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T03:56:19,659 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T03:56:19,660 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:19,660 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:19,660 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T03:56:19,660 | ^ 2024-11-19T03:56:19,660 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T03:56:19,661 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T03:56:19,661 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:19,661 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:19,661 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T03:56:19,661 | ^ 2024-11-19T03:56:19,662 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T03:56:19,662 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T03:56:19,662 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:19,662 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:19,662 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T03:56:19,662 | ^ 2024-11-19T03:56:19,663 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-11-19T03:56:19,663 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T03:56:19,663 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:19,900 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist.c -o build/temp.linux-armv7l-cpython-39/command_dist.o -fopenmp 2024-11-19T03:56:20,104 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-19T03:56:20,105 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=] 2024-11-19T03:56:20,105 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T03:56:20,105 | ~~^ 2024-11-19T03:56:20,106 | | 2024-11-19T03:56:20,106 | long unsigned int 2024-11-19T03:56:20,106 | %u 2024-11-19T03:56:20,106 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T03:56:20,106 | ~~~~~~~ 2024-11-19T03:56:20,106 | | 2024-11-19T03:56:20,106 | size_t {aka unsigned int} 2024-11-19T03:56:20,108 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=] 2024-11-19T03:56:20,108 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T03:56:20,108 | ~~^ 2024-11-19T03:56:20,108 | | 2024-11-19T03:56:20,108 | long unsigned int 2024-11-19T03:56:20,108 | %u 2024-11-19T03:56:20,108 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T03:56:20,108 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T03:56:20,109 | ~~~~~~~~~ 2024-11-19T03:56:20,109 | | 2024-11-19T03:56:20,109 | size_t {aka unsigned int} 2024-11-19T03:56:20,110 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T03:56:20,110 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T03:56:20,110 | ~~^ 2024-11-19T03:56:20,111 | | 2024-11-19T03:56:20,111 | long unsigned int 2024-11-19T03:56:20,111 | %u 2024-11-19T03:56:20,111 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T03:56:20,111 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T03:56:20,111 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:20,111 | | 2024-11-19T03:56:20,111 | unsigned int 2024-11-19T03:56:20,114 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T03:56:20,114 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-11-19T03:56:20,114 | ^ 2024-11-19T03:56:20,121 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-19T03:56:20,122 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=] 2024-11-19T03:56:20,122 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T03:56:20,123 | ~~^ ~~~~~~~ 2024-11-19T03:56:20,123 | | | 2024-11-19T03:56:20,123 | long unsigned int size_t {aka unsigned int} 2024-11-19T03:56:20,123 | %u 2024-11-19T03:56:20,125 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=] 2024-11-19T03:56:20,125 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T03:56:20,125 | ~~^ 2024-11-19T03:56:20,125 | | 2024-11-19T03:56:20,125 | long unsigned int 2024-11-19T03:56:20,125 | %u 2024-11-19T03:56:20,125 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-19T03:56:20,125 | ~~~~~~~~~ 2024-11-19T03:56:20,126 | | 2024-11-19T03:56:20,126 | size_t {aka unsigned int} 2024-11-19T03:56:20,127 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T03:56:20,127 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T03:56:20,128 | ~~^ 2024-11-19T03:56:20,128 | | 2024-11-19T03:56:20,128 | long unsigned int 2024-11-19T03:56:20,128 | %u 2024-11-19T03:56:20,128 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-19T03:56:20,128 865 | (size_t) b * unitsz_distf_mapped); 2024-11-19T03:56:20,128 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:20,128 | | 2024-11-19T03:56:20,128 | unsigned int 2024-11-19T03:56:20,131 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-11-19T03:56:20,131 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-11-19T03:56:20,131 | ^~~~~~~ 2024-11-19T03:56:20,132 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-11-19T03:56:20,132 809 | struct stat cbd_fcode_stat; 2024-11-19T03:56:20,132 | ^~~~~~~~~~~~~~ 2024-11-19T03:56:20,133 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-11-19T03:56:20,133 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-19T03:56:20,133 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:20,134 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-11-19T03:56:20,134 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-19T03:56:20,134 | ^~~~~~~~~~~~~~~~~ 2024-11-19T03:56:20,140 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-19T03:56:20,142 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=] 2024-11-19T03:56:20,142 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T03:56:20,142 | ~~^ 2024-11-19T03:56:20,142 | | 2024-11-19T03:56:20,142 | long unsigned int 2024-11-19T03:56:20,142 | %u 2024-11-19T03:56:20,142 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T03:56:20,142 | ~~~~~~~ 2024-11-19T03:56:20,143 | | 2024-11-19T03:56:20,143 | size_t {aka unsigned int} 2024-11-19T03:56:20,145 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=] 2024-11-19T03:56:20,145 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T03:56:20,145 | ~~^ 2024-11-19T03:56:20,145 | | 2024-11-19T03:56:20,145 | long unsigned int 2024-11-19T03:56:20,145 | %u 2024-11-19T03:56:20,145 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T03:56:20,145 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T03:56:20,146 | ~~~~~~~~~ 2024-11-19T03:56:20,146 | | 2024-11-19T03:56:20,146 | size_t {aka unsigned int} 2024-11-19T03:56:20,148 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T03:56:20,148 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T03:56:20,148 | ~~^ 2024-11-19T03:56:20,148 | | 2024-11-19T03:56:20,148 | long unsigned int 2024-11-19T03:56:20,148 | %u 2024-11-19T03:56:20,148 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T03:56:20,149 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T03:56:20,149 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:20,149 | | 2024-11-19T03:56:20,149 | unsigned int 2024-11-19T03:56:20,151 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-11-19T03:56:20,151 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-11-19T03:56:20,151 | ^ 2024-11-19T03:56:20,154 command_dist.c: In function ‘mco_co_dist_core’: 2024-11-19T03:56:20,155 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T03:56:20,156 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-11-19T03:56:20,156 | ^ 2024-11-19T03:56:20,162 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-11-19T03:56:20,163 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T03:56:20,163 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T03:56:20,163 | ^ 2024-11-19T03:56:20,165 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T03:56:20,165 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-19T03:56:20,165 | ^ 2024-11-19T03:56:20,171 command_dist.c: In function ‘dist_print_nobin’: 2024-11-19T03:56:20,172 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T03:56:20,172 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-11-19T03:56:20,172 | ^ 2024-11-19T03:56:20,174 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T03:56:20,174 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-19T03:56:20,174 | ^ 2024-11-19T03:56:20,176 command_dist.c:1380:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T03:56:20,176 1380 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T03:56:20,177 | ^ 2024-11-19T03:56:20,178 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T03:56:20,178 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T03:56:20,178 | ^ 2024-11-19T03:56:20,429 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-11-19T03:56:20,430 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-11-19T03:56:20,430 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-11-19T03:56:20,430 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:20,430 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-11-19T03:56:20,431 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-11-19T03:56:20,431 | ^~~~~~~~~~~~ 2024-11-19T03:56:21,153 command_dist.c: In function ‘get_dim_shuffle’: 2024-11-19T03:56:21,153 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-11-19T03:56:21,153 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-19T03:56:21,154 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:21,154 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-11-19T03:56:21,154 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-19T03:56:21,154 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:21,936 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-19T03:56:21,937 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:21,937 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T03:56:21,938 | ^~ ~~~~~~~~~ 2024-11-19T03:56:21,938 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T03:56:21,938 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T03:56:21,938 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:21,939 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T03:56:21,940 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T03:56:21,940 | ^~~~~~~~~~~~~~~ 2024-11-19T03:56:21,940 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T03:56:21,940 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T03:56:21,941 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:21,942 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T03:56:21,942 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T03:56:21,942 | ^~~~~~~~~~~ 2024-11-19T03:56:21,943 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-19T03:56:21,943 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T03:56:21,943 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:21,944 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T03:56:21,944 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T03:56:21,944 | ^~~~~ 2024-11-19T03:56:21,945 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T03:56:21,945 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T03:56:21,945 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,151 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-19T03:56:22,152 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:22,152 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T03:56:22,152 | ^~ ~~~~~~~~~ 2024-11-19T03:56:22,153 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T03:56:22,153 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T03:56:22,153 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,154 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T03:56:22,154 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T03:56:22,154 | ^~~~~~~~~~~~~~~ 2024-11-19T03:56:22,155 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T03:56:22,155 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T03:56:22,155 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,156 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T03:56:22,156 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T03:56:22,156 | ^~~~~~~~~~~~~ 2024-11-19T03:56:22,157 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T03:56:22,157 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T03:56:22,157 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,159 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:22,159 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T03:56:22,159 | ^ 2024-11-19T03:56:22,160 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-11-19T03:56:22,160 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T03:56:22,160 | ^~~~~~~~~~ 2024-11-19T03:56:22,161 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-19T03:56:22,161 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T03:56:22,161 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,162 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:22,162 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T03:56:22,162 | ^ 2024-11-19T03:56:22,163 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-11-19T03:56:22,163 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T03:56:22,163 | ^~~~~~~~~~ 2024-11-19T03:56:22,164 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-19T03:56:22,164 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T03:56:22,164 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,401 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-19T03:56:22,402 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:22,402 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T03:56:22,402 | ^~ ~~~~~~~~~ 2024-11-19T03:56:22,403 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T03:56:22,403 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T03:56:22,403 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,404 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T03:56:22,405 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T03:56:22,405 | ^~~~~~~~~~~~~~~ 2024-11-19T03:56:22,406 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T03:56:22,406 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T03:56:22,406 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,407 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T03:56:22,407 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T03:56:22,407 | ^~~~~~~~~~~~~ 2024-11-19T03:56:22,408 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T03:56:22,408 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T03:56:22,408 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,410 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T03:56:22,410 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T03:56:22,410 | ^~~~~~~~~~~ 2024-11-19T03:56:22,411 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-19T03:56:22,411 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T03:56:22,411 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,412 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T03:56:22,413 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T03:56:22,413 | ^~~~~ 2024-11-19T03:56:22,413 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T03:56:22,414 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T03:56:22,414 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,662 command_dist.c: In function ‘combine_queries’: 2024-11-19T03:56:22,663 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T03:56:22,663 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-19T03:56:22,663 | ^ 2024-11-19T03:56:22,665 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T03:56:22,665 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-19T03:56:22,665 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,666 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T03:56:22,666 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-19T03:56:22,667 | ^ 2024-11-19T03:56:22,668 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T03:56:22,668 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-19T03:56:22,668 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:22,670 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:22,671 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-19T03:56:22,671 | ^~ ~~~~~~~~ 2024-11-19T03:56:22,672 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T03:56:22,672 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-19T03:56:22,672 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,147 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o -fopenmp 2024-11-19T03:56:23,320 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_set.c -o build/temp.linux-armv7l-cpython-39/command_set.o -fopenmp 2024-11-19T03:56:23,472 command_set.c: In function ‘sketch_operate’: 2024-11-19T03:56:23,473 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T03:56:23,473 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-11-19T03:56:23,473 | ^ 2024-11-19T03:56:23,483 command_set.c: In function ‘combin_subset_pans’: 2024-11-19T03:56:23,484 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-19T03:56:23,484 457 | free(co_dstat_fpath); 2024-11-19T03:56:23,484 | ^~~~~~~~~~~~~~ 2024-11-19T03:56:23,485 In file included from kssdheaders/global_basic.h:159, 2024-11-19T03:56:23,485 from command_set.c:15: 2024-11-19T03:56:23,485 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-19T03:56:23,485 565 | extern void free (void *__ptr) __THROW; 2024-11-19T03:56:23,485 | ~~~~~~^~~~~ 2024-11-19T03:56:23,490 command_set.c: In function ‘grouping_genomes’: 2024-11-19T03:56:23,491 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-19T03:56:23,491 562 | free(co_dstat_fpath); 2024-11-19T03:56:23,491 | ^~~~~~~~~~~~~~ 2024-11-19T03:56:23,491 In file included from kssdheaders/global_basic.h:159, 2024-11-19T03:56:23,492 from command_set.c:15: 2024-11-19T03:56:23,492 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-19T03:56:23,492 565 | extern void free (void *__ptr) __THROW; 2024-11-19T03:56:23,492 | ~~~~~~^~~~~ 2024-11-19T03:56:23,608 command_set.c: In function ‘sketch_union’: 2024-11-19T03:56:23,608 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T03:56:23,608 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:23,609 | ^ 2024-11-19T03:56:23,609 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T03:56:23,609 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:23,609 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,610 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:23,610 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T03:56:23,610 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:23,610 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T03:56:23,610 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T03:56:23,610 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,611 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:23,611 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T03:56:23,611 | ^~ ~~~~~~~~~~ 2024-11-19T03:56:23,612 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T03:56:23,612 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T03:56:23,612 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,725 command_set.c: In function ‘sketch_operate’: 2024-11-19T03:56:23,725 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:23,726 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T03:56:23,726 | ^~ ~~~~~~~~~~ 2024-11-19T03:56:23,726 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T03:56:23,726 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T03:56:23,726 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,727 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:23,727 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T03:56:23,727 | ^~ ~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,727 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-19T03:56:23,727 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T03:56:23,727 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,728 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:23,728 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T03:56:23,728 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:23,729 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T03:56:23,729 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T03:56:23,729 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,729 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:23,730 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T03:56:23,730 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:23,730 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T03:56:23,730 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T03:56:23,730 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,731 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:23,731 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T03:56:23,731 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:23,731 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T03:56:23,731 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T03:56:23,732 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,732 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:23,733 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T03:56:23,733 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:23,733 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T03:56:23,733 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T03:56:23,733 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,734 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T03:56:23,734 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:23,734 | ^ 2024-11-19T03:56:23,734 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T03:56:23,735 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:23,735 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,885 command_set.c: In function ‘uniq_sketch_union’: 2024-11-19T03:56:23,885 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T03:56:23,885 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:23,886 | ^ 2024-11-19T03:56:23,886 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T03:56:23,886 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:23,886 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,887 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:23,887 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T03:56:23,887 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:23,888 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T03:56:23,888 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T03:56:23,888 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,889 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:23,889 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T03:56:23,889 | ^~ ~~~~~~~~~~~~~~~ 2024-11-19T03:56:23,889 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-19T03:56:23,889 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T03:56:23,890 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,015 command_set.c: In function ‘combin_pans’: 2024-11-19T03:56:24,016 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:24,016 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T03:56:24,016 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:24,017 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2024-11-19T03:56:24,017 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T03:56:24,017 | ^~~~~~~~~~ 2024-11-19T03:56:24,017 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-11-19T03:56:24,017 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T03:56:24,017 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,018 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:24,018 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T03:56:24,018 | ^~ ~~~~~~~~~~ 2024-11-19T03:56:24,019 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2024-11-19T03:56:24,019 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T03:56:24,019 | ^~~~~~~~~~ 2024-11-19T03:56:24,019 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-11-19T03:56:24,019 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T03:56:24,020 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,021 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T03:56:24,021 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:24,021 | ^ 2024-11-19T03:56:24,022 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T03:56:24,022 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:24,022 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,205 command_set.c: In function ‘combin_subset_pans’: 2024-11-19T03:56:24,206 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:24,206 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T03:56:24,206 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:24,207 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T03:56:24,207 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T03:56:24,207 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,208 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:24,208 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T03:56:24,208 | ^~ ~~~~~~~~~~ 2024-11-19T03:56:24,208 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T03:56:24,209 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T03:56:24,209 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,209 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:24,210 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T03:56:24,210 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:24,210 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T03:56:24,210 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T03:56:24,211 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,212 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:24,212 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T03:56:24,213 | ^~ ~~~~~~~~~~ 2024-11-19T03:56:24,213 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T03:56:24,213 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T03:56:24,213 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,214 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T03:56:24,214 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:24,214 | ^ 2024-11-19T03:56:24,215 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T03:56:24,215 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:24,215 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,418 command_set.c: In function ‘grouping_genomes’: 2024-11-19T03:56:24,419 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:24,419 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T03:56:24,419 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:24,420 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T03:56:24,420 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T03:56:24,420 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,421 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:24,421 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T03:56:24,421 | ^~ ~~~~~~~~~~ 2024-11-19T03:56:24,422 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T03:56:24,422 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T03:56:24,422 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,424 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:24,424 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T03:56:24,424 | ^~ ~~~~~~~~~~~ 2024-11-19T03:56:24,425 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T03:56:24,425 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T03:56:24,425 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,427 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T03:56:24,427 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T03:56:24,427 | ^~ ~~~~~~~~~~ 2024-11-19T03:56:24,427 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T03:56:24,428 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T03:56:24,428 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,429 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T03:56:24,429 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:24,429 | ^ 2024-11-19T03:56:24,430 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T03:56:24,430 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T03:56:24,430 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:24,705 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-39/command_shuffle.o -fopenmp 2024-11-19T03:56:24,997 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c global_basic.c -o build/temp.linux-armv7l-cpython-39/global_basic.o -fopenmp 2024-11-19T03:56:25,169 global_basic.c: In function ‘organize_infile_list’: 2024-11-19T03:56:25,169 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-11-19T03:56:25,169 195 | while (isspace(*buf)) buf++; 2024-11-19T03:56:25,170 | ^~~~~~~ 2024-11-19T03:56:25,170 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=] 2024-11-19T03:56:25,170 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-19T03:56:25,171 | ~~^ 2024-11-19T03:56:25,171 | | 2024-11-19T03:56:25,171 | long unsigned int 2024-11-19T03:56:25,171 | %u 2024-11-19T03:56:25,171 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-19T03:56:25,172 | ~~~~~~~~~~~ 2024-11-19T03:56:25,172 | | 2024-11-19T03:56:25,172 | size_t {aka unsigned int} 2024-11-19T03:56:25,172 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=] 2024-11-19T03:56:25,172 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-19T03:56:25,173 | ~~^ 2024-11-19T03:56:25,173 | | 2024-11-19T03:56:25,173 | long unsigned int 2024-11-19T03:56:25,173 | %u 2024-11-19T03:56:25,173 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-19T03:56:25,174 | ~~~~~~~~~~~ 2024-11-19T03:56:25,174 | | 2024-11-19T03:56:25,174 | size_t {aka unsigned int} 2024-11-19T03:56:25,849 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-39/iseq2comem.o -fopenmp 2024-11-19T03:56:26,004 iseq2comem.c: In function ‘reads2mco’: 2024-11-19T03:56:26,005 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,005 156 | if (base > TL) { 2024-11-19T03:56:26,005 | ^ 2024-11-19T03:56:26,005 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,005 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T03:56:26,005 | ^~ 2024-11-19T03:56:26,006 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,006 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T03:56:26,006 | ^ 2024-11-19T03:56:26,006 iseq2comem.c: In function ‘fasta2co’: 2024-11-19T03:56:26,007 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,007 239 | if (base > TL) { 2024-11-19T03:56:26,007 | ^ 2024-11-19T03:56:26,007 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,007 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T03:56:26,007 | ^~ 2024-11-19T03:56:26,007 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,008 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T03:56:26,008 | ^ 2024-11-19T03:56:26,008 iseq2comem.c: In function ‘fastq2co’: 2024-11-19T03:56:26,008 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-11-19T03:56:26,008 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-11-19T03:56:26,008 | ^~ 2024-11-19T03:56:26,009 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,009 318 | if (base > TL) { 2024-11-19T03:56:26,009 | ^ 2024-11-19T03:56:26,010 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,010 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T03:56:26,010 | ^~ 2024-11-19T03:56:26,010 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,010 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T03:56:26,010 | ^ 2024-11-19T03:56:26,011 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,011 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-11-19T03:56:26,011 | ^ 2024-11-19T03:56:26,012 iseq2comem.c: In function ‘fastq2koc’: 2024-11-19T03:56:26,012 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,013 402 | if (base > TL) { 2024-11-19T03:56:26,013 | ^ 2024-11-19T03:56:26,013 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,013 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T03:56:26,013 | ^~ 2024-11-19T03:56:26,013 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,013 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T03:56:26,013 | ^ 2024-11-19T03:56:26,018 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-11-19T03:56:26,019 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,019 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T03:56:26,019 | ^~ 2024-11-19T03:56:26,019 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T03:56:26,019 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T03:56:26,019 | ^ 2024-11-19T03:56:27,189 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-11-19T03:56:27,255 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mytime.c -o build/temp.linux-armv7l-cpython-39/mytime.o -fopenmp 2024-11-19T03:56:27,377 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c pykssd.c -o build/temp.linux-armv7l-cpython-39/pykssd.o -fopenmp 2024-11-19T03:56:27,720 pykssd.c: In function ‘py_dist_dispatch’: 2024-11-19T03:56:27,720 pykssd.c:329:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-11-19T03:56:27,721 329 | int state1 = dist_dispatch(&dist_opt_val1); 2024-11-19T03:56:27,721 | ^~~~~~ 2024-11-19T03:56:27,721 pykssd.c:386:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-11-19T03:56:27,721 386 | int state2 = dist_dispatch(&dist_opt_val2); 2024-11-19T03:56:27,721 | ^~~~~~ 2024-11-19T03:56:27,723 pykssd.c:510:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-11-19T03:56:27,723 510 | int state4 = dist_dispatch(&dist_opt_val4); 2024-11-19T03:56:27,723 | ^~~~~~ 2024-11-19T03:56:27,867 pykssd.c: In function ‘rename_file’: 2024-11-19T03:56:27,867 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-11-19T03:56:27,867 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-11-19T03:56:27,867 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T03:56:27,867 pykssd.c:41:15: note: length computed here 2024-11-19T03:56:27,868 41 | int len = strlen(p1); 2024-11-19T03:56:27,868 | ^~~~~~~~~~ 2024-11-19T03:56:28,289 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/co2mco.o build/temp.linux-armv7l-cpython-39/command_composite.o build/temp.linux-armv7l-cpython-39/command_dist.o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o build/temp.linux-armv7l-cpython-39/command_set.o build/temp.linux-armv7l-cpython-39/command_shuffle.o build/temp.linux-armv7l-cpython-39/global_basic.o build/temp.linux-armv7l-cpython-39/iseq2comem.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/mytime.o build/temp.linux-armv7l-cpython-39/pykssd.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-11-19T03:56:28,486 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-11-19T03:56:28,486 !! 2024-11-19T03:56:28,487 ******************************************************************************** 2024-11-19T03:56:28,487 Please avoid running ``setup.py`` directly. 2024-11-19T03:56:28,487 Instead, use pypa/build, pypa/installer or other 2024-11-19T03:56:28,487 standards-based tools. 2024-11-19T03:56:28,487 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-11-19T03:56:28,487 ******************************************************************************** 2024-11-19T03:56:28,488 !! 2024-11-19T03:56:28,488 self.initialize_options() 2024-11-19T03:56:28,511 installing to build/bdist.linux-armv7l/wheel 2024-11-19T03:56:28,512 running install 2024-11-19T03:56:28,539 running install_lib 2024-11-19T03:56:28,564 creating build/bdist.linux-armv7l/wheel 2024-11-19T03:56:28,566 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-11-19T03:56:28,574 copying build/lib.linux-armv7l-cpython-39/kssdutils.py -> build/bdist.linux-armv7l/wheel/. 2024-11-19T03:56:28,576 running install_egg_info 2024-11-19T03:56:28,619 Copying kssdutils.egg-info to build/bdist.linux-armv7l/wheel/./kssdutils-1.0.0-py3.9.egg-info 2024-11-19T03:56:28,630 running install_scripts 2024-11-19T03:56:28,682 creating build/bdist.linux-armv7l/wheel/kssdutils-1.0.0.dist-info/WHEEL 2024-11-19T03:56:28,685 creating '/tmp/pip-wheel-a5jnpnw2/kssdutils-1.0.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-11-19T03:56:28,787 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2024-11-19T03:56:28,792 adding 'kssdutils.py' 2024-11-19T03:56:28,795 adding 'kssdutils-1.0.0.dist-info/METADATA' 2024-11-19T03:56:28,796 adding 'kssdutils-1.0.0.dist-info/WHEEL' 2024-11-19T03:56:28,797 adding 'kssdutils-1.0.0.dist-info/dependency_links.txt' 2024-11-19T03:56:28,798 adding 'kssdutils-1.0.0.dist-info/top_level.txt' 2024-11-19T03:56:28,799 adding 'kssdutils-1.0.0.dist-info/RECORD' 2024-11-19T03:56:28,803 removing build/bdist.linux-armv7l/wheel 2024-11-19T03:56:28,933 Building wheel for kssdutils (setup.py): finished with status 'done' 2024-11-19T03:56:28,937 Created wheel for kssdutils: filename=kssdutils-1.0.0-cp39-cp39-linux_armv7l.whl size=179737 sha256=0d9c0566cba326dbedbea1c1ea643cc81efe1b0b47b292f956e933d1a9fedb35 2024-11-19T03:56:28,938 Stored in directory: /tmp/pip-ephem-wheel-cache-ltfkc_p6/wheels/bd/5c/c9/db50ca480fe87a916667731a47178c93a87575ce473cd2d9f5 2024-11-19T03:56:28,948 Successfully built kssdutils 2024-11-19T03:56:28,957 Removed build tracker: '/tmp/pip-build-tracker-p9_43zhw'