2024-11-19T04:59:55,307 Disabling truststore because Python version isn't 3.10+ 2024-11-19T04:59:55,854 Created temporary directory: /tmp/pip-build-tracker-gu_hbf5g 2024-11-19T04:59:55,855 Initialized build tracking at /tmp/pip-build-tracker-gu_hbf5g 2024-11-19T04:59:55,855 Created build tracker: /tmp/pip-build-tracker-gu_hbf5g 2024-11-19T04:59:55,855 Entered build tracker: /tmp/pip-build-tracker-gu_hbf5g 2024-11-19T04:59:55,856 Created temporary directory: /tmp/pip-wheel-uaznnxs3 2024-11-19T04:59:55,861 Created temporary directory: /tmp/pip-ephem-wheel-cache-gy1aou6j 2024-11-19T04:59:55,908 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-11-19T04:59:55,911 2 location(s) to search for versions of kssdutils: 2024-11-19T04:59:55,911 * https://pypi.org/simple/kssdutils/ 2024-11-19T04:59:55,911 * https://www.piwheels.org/simple/kssdutils/ 2024-11-19T04:59:55,911 Fetching project page and analyzing links: https://pypi.org/simple/kssdutils/ 2024-11-19T04:59:55,911 Getting page https://pypi.org/simple/kssdutils/ 2024-11-19T04:59:55,913 Found index url https://pypi.org/simple/ 2024-11-19T04:59:55,933 Fetched page https://pypi.org/simple/kssdutils/ as application/vnd.pypi.simple.v1+json 2024-11-19T04:59:55,934 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 2024-11-19T04:59:55,934 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 2024-11-19T04:59:55,935 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdutils/ 2024-11-19T04:59:55,935 Getting page https://www.piwheels.org/simple/kssdutils/ 2024-11-19T04:59:55,936 Found index url https://www.piwheels.org/simple/ 2024-11-19T04:59:55,974 Fetched page https://www.piwheels.org/simple/kssdutils/ as text/html 2024-11-19T04:59:55,977 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp311-cp311-linux_armv6l.whl#sha256=88788d94e7e118cfdf4e2cb04c558d2032ffa4f9352b663efd1a76f098c9f31d (from https://www.piwheels.org/simple/kssdutils/) 2024-11-19T04:59:55,977 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp311-cp311-linux_armv7l.whl#sha256=88788d94e7e118cfdf4e2cb04c558d2032ffa4f9352b663efd1a76f098c9f31d (from https://www.piwheels.org/simple/kssdutils/) 2024-11-19T04:59:55,977 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/) 2024-11-19T04:59:55,977 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/) 2024-11-19T04:59:55,977 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp39-cp39-linux_armv6l.whl#sha256=0d9c0566cba326dbedbea1c1ea643cc81efe1b0b47b292f956e933d1a9fedb35 (from https://www.piwheels.org/simple/kssdutils/) 2024-11-19T04:59:55,978 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.0-cp39-cp39-linux_armv7l.whl#sha256=0d9c0566cba326dbedbea1c1ea643cc81efe1b0b47b292f956e933d1a9fedb35 (from https://www.piwheels.org/simple/kssdutils/) 2024-11-19T04:59:55,978 Skipping link: not a file: https://www.piwheels.org/simple/kssdutils/ 2024-11-19T04:59:55,978 Skipping link: not a file: https://pypi.org/simple/kssdutils/ 2024-11-19T04:59:55,994 Given no hashes to check 1 links for project 'kssdutils': discarding no candidates 2024-11-19T04:59:55,996 Collecting kssdutils==1.0.1 2024-11-19T04:59:55,998 Created temporary directory: /tmp/pip-unpack-jl4vfaj1 2024-11-19T04:59:56,173 Downloading kssdutils-1.0.1.tar.gz (44 kB) 2024-11-19T04:59:56,257 Added kssdutils==1.0.1 from https://files.pythonhosted.org/packages/6f/f6/cc67acf92ea770b5f6a8bd97d375432881861935beafe9ebd4031a73482c/kssdutils-1.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-gu_hbf5g' 2024-11-19T04:59:56,260 Running setup.py (path:/tmp/pip-wheel-uaznnxs3/kssdutils_91ed59455a014f84b0e6437cb38b882a/setup.py) egg_info for package kssdutils 2024-11-19T04:59:56,261 Created temporary directory: /tmp/pip-pip-egg-info-0eh4_xrg 2024-11-19T04:59:56,261 Preparing metadata (setup.py): started 2024-11-19T04:59:56,262 Running command python setup.py egg_info 2024-11-19T04:59:57,403 running egg_info 2024-11-19T04:59:57,433 creating /tmp/pip-pip-egg-info-0eh4_xrg/kssdutils.egg-info 2024-11-19T04:59:57,435 writing /tmp/pip-pip-egg-info-0eh4_xrg/kssdutils.egg-info/PKG-INFO 2024-11-19T04:59:57,438 writing dependency_links to /tmp/pip-pip-egg-info-0eh4_xrg/kssdutils.egg-info/dependency_links.txt 2024-11-19T04:59:57,441 writing top-level names to /tmp/pip-pip-egg-info-0eh4_xrg/kssdutils.egg-info/top_level.txt 2024-11-19T04:59:57,442 writing manifest file '/tmp/pip-pip-egg-info-0eh4_xrg/kssdutils.egg-info/SOURCES.txt' 2024-11-19T04:59:57,555 reading manifest file '/tmp/pip-pip-egg-info-0eh4_xrg/kssdutils.egg-info/SOURCES.txt' 2024-11-19T04:59:57,557 reading manifest template 'MANIFEST.in' 2024-11-19T04:59:57,563 warning: no files found matching '*.h' under directory 'njheaders' 2024-11-19T04:59:57,564 warning: no files found matching '*.h' under directory 'dnjheaders' 2024-11-19T04:59:57,567 writing manifest file '/tmp/pip-pip-egg-info-0eh4_xrg/kssdutils.egg-info/SOURCES.txt' 2024-11-19T04:59:57,656 Preparing metadata (setup.py): finished with status 'done' 2024-11-19T04:59:57,660 Source in /tmp/pip-wheel-uaznnxs3/kssdutils_91ed59455a014f84b0e6437cb38b882a has version 1.0.1, which satisfies requirement kssdutils==1.0.1 from https://files.pythonhosted.org/packages/6f/f6/cc67acf92ea770b5f6a8bd97d375432881861935beafe9ebd4031a73482c/kssdutils-1.0.1.tar.gz 2024-11-19T04:59:57,661 Removed kssdutils==1.0.1 from https://files.pythonhosted.org/packages/6f/f6/cc67acf92ea770b5f6a8bd97d375432881861935beafe9ebd4031a73482c/kssdutils-1.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-gu_hbf5g' 2024-11-19T04:59:57,665 Created temporary directory: /tmp/pip-unpack-2_gg8bk8 2024-11-19T04:59:57,666 Created temporary directory: /tmp/pip-unpack-05751y8b 2024-11-19T04:59:57,667 Building wheels for collected packages: kssdutils 2024-11-19T04:59:57,670 Created temporary directory: /tmp/pip-wheel-nqzafsvy 2024-11-19T04:59:57,671 Building wheel for kssdutils (setup.py): started 2024-11-19T04:59:57,672 Destination directory: /tmp/pip-wheel-nqzafsvy 2024-11-19T04:59:57,672 Running command python setup.py bdist_wheel 2024-11-19T04:59:58,711 running bdist_wheel 2024-11-19T04:59:58,856 running build 2024-11-19T04:59:58,856 running build_py 2024-11-19T04:59:58,886 creating build/lib.linux-armv7l-cpython-39 2024-11-19T04:59:58,887 copying kssdutils.py -> build/lib.linux-armv7l-cpython-39 2024-11-19T04:59:58,890 running egg_info 2024-11-19T04:59:58,918 writing kssdutils.egg-info/PKG-INFO 2024-11-19T04:59:58,921 writing dependency_links to kssdutils.egg-info/dependency_links.txt 2024-11-19T04:59:58,923 writing top-level names to kssdutils.egg-info/top_level.txt 2024-11-19T04:59:58,953 reading manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-11-19T04:59:58,957 reading manifest template 'MANIFEST.in' 2024-11-19T04:59:58,962 warning: no files found matching '*.h' under directory 'njheaders' 2024-11-19T04:59:58,963 warning: no files found matching '*.h' under directory 'dnjheaders' 2024-11-19T04:59:58,967 writing manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-11-19T04:59:58,968 running build_ext 2024-11-19T04:59:59,589 building 'kssd' extension 2024-11-19T04:59:59,590 creating build/temp.linux-armv7l-cpython-39 2024-11-19T04:59:59,592 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 2024-11-19T04:59:59,758 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-11-19T04:59:59,758 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T04:59:59,758 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-11-19T04:59:59,759 | ^ 2024-11-19T04:59:59,761 co2mco.c: In function ‘co2unitllmco’: 2024-11-19T04:59:59,761 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T04:59:59,761 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-11-19T04:59:59,761 | ^ 2024-11-19T05:00:00,377 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 command_composite.c -o build/temp.linux-armv7l-cpython-39/command_composite.o -fopenmp 2024-11-19T05:00:00,685 command_composite.c: In function ‘get_species_abundance’: 2024-11-19T05:00:00,686 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-19T05:00:00,686 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-11-19T05:00:00,686 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:00,686 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-19T05:00:00,686 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-11-19T05:00:00,687 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:00,687 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:00,687 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T05:00:00,687 | ^ 2024-11-19T05:00:00,687 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:00,687 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-19T05:00:00,687 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:00,688 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:00,688 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T05:00:00,688 | ^ 2024-11-19T05:00:00,688 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:00,688 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-19T05:00:00,688 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:00,688 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:00,688 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:00,689 | ^ 2024-11-19T05:00:00,689 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:00,689 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:00,689 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:00,689 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:00,689 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T05:00:00,689 | ^ 2024-11-19T05:00:00,690 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-19T05:00:00,690 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-19T05:00:00,690 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:00,690 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:00,690 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:00,690 | ^ 2024-11-19T05:00:00,690 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-11-19T05:00:00,690 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-19T05:00:00,691 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:00,925 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 2024-11-19T05:00:01,135 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-19T05:00:01,136 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=] 2024-11-19T05:00:01,136 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:01,136 | ~~^ 2024-11-19T05:00:01,136 | | 2024-11-19T05:00:01,136 | long unsigned int 2024-11-19T05:00:01,136 | %u 2024-11-19T05:00:01,136 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:01,137 | ~~~~~~~ 2024-11-19T05:00:01,137 | | 2024-11-19T05:00:01,137 | size_t {aka unsigned int} 2024-11-19T05:00:01,137 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=] 2024-11-19T05:00:01,137 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:01,137 | ~~^ 2024-11-19T05:00:01,137 | | 2024-11-19T05:00:01,137 | long unsigned int 2024-11-19T05:00:01,137 | %u 2024-11-19T05:00:01,138 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:01,138 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:01,138 | ~~~~~~~~~ 2024-11-19T05:00:01,138 | | 2024-11-19T05:00:01,138 | size_t {aka unsigned int} 2024-11-19T05:00:01,138 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T05:00:01,138 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:01,139 | ~~^ 2024-11-19T05:00:01,139 | | 2024-11-19T05:00:01,139 | long unsigned int 2024-11-19T05:00:01,139 | %u 2024-11-19T05:00:01,139 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:01,139 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:01,139 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:01,139 | | 2024-11-19T05:00:01,140 | unsigned int 2024-11-19T05:00:01,140 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T05:00:01,141 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-11-19T05:00:01,141 | ^ 2024-11-19T05:00:01,147 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-19T05:00:01,148 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=] 2024-11-19T05:00:01,148 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T05:00:01,148 | ~~^ ~~~~~~~ 2024-11-19T05:00:01,148 | | | 2024-11-19T05:00:01,148 | long unsigned int size_t {aka unsigned int} 2024-11-19T05:00:01,148 | %u 2024-11-19T05:00:01,149 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=] 2024-11-19T05:00:01,149 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T05:00:01,149 | ~~^ 2024-11-19T05:00:01,150 | | 2024-11-19T05:00:01,150 | long unsigned int 2024-11-19T05:00:01,150 | %u 2024-11-19T05:00:01,150 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-19T05:00:01,150 | ~~~~~~~~~ 2024-11-19T05:00:01,150 | | 2024-11-19T05:00:01,150 | size_t {aka unsigned int} 2024-11-19T05:00:01,151 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T05:00:01,151 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-19T05:00:01,151 | ~~^ 2024-11-19T05:00:01,151 | | 2024-11-19T05:00:01,151 | long unsigned int 2024-11-19T05:00:01,151 | %u 2024-11-19T05:00:01,151 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-19T05:00:01,152 865 | (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:01,152 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:01,152 | | 2024-11-19T05:00:01,152 | unsigned int 2024-11-19T05:00:01,153 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-11-19T05:00:01,153 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-11-19T05:00:01,153 | ^~~~~~~ 2024-11-19T05:00:01,153 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-11-19T05:00:01,154 809 | struct stat cbd_fcode_stat; 2024-11-19T05:00:01,154 | ^~~~~~~~~~~~~~ 2024-11-19T05:00:01,154 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-11-19T05:00:01,154 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-19T05:00:01,154 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:01,154 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-11-19T05:00:01,155 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-19T05:00:01,155 | ^~~~~~~~~~~~~~~~~ 2024-11-19T05:00:01,160 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-19T05:00:01,161 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=] 2024-11-19T05:00:01,162 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:01,162 | ~~^ 2024-11-19T05:00:01,162 | | 2024-11-19T05:00:01,162 | long unsigned int 2024-11-19T05:00:01,162 | %u 2024-11-19T05:00:01,162 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:01,162 | ~~~~~~~ 2024-11-19T05:00:01,162 | | 2024-11-19T05:00:01,162 | size_t {aka unsigned int} 2024-11-19T05:00:01,163 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=] 2024-11-19T05:00:01,163 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:01,163 | ~~^ 2024-11-19T05:00:01,164 | | 2024-11-19T05:00:01,164 | long unsigned int 2024-11-19T05:00:01,164 | %u 2024-11-19T05:00:01,164 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:01,164 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:01,164 | ~~~~~~~~~ 2024-11-19T05:00:01,164 | | 2024-11-19T05:00:01,164 | size_t {aka unsigned int} 2024-11-19T05:00:01,165 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-19T05:00:01,165 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-19T05:00:01,165 | ~~^ 2024-11-19T05:00:01,165 | | 2024-11-19T05:00:01,165 | long unsigned int 2024-11-19T05:00:01,166 | %u 2024-11-19T05:00:01,166 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-19T05:00:01,166 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-19T05:00:01,166 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:01,166 | | 2024-11-19T05:00:01,166 | unsigned int 2024-11-19T05:00:01,167 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:01,167 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-11-19T05:00:01,167 | ^ 2024-11-19T05:00:01,170 command_dist.c: In function ‘mco_co_dist_core’: 2024-11-19T05:00:01,170 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T05:00:01,170 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-11-19T05:00:01,171 | ^ 2024-11-19T05:00:01,176 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-11-19T05:00:01,177 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:01,177 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T05:00:01,177 | ^ 2024-11-19T05:00:01,179 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:01,179 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-19T05:00:01,179 | ^ 2024-11-19T05:00:01,184 command_dist.c: In function ‘dist_print_nobin’: 2024-11-19T05:00:01,185 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:01,185 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-11-19T05:00:01,185 | ^ 2024-11-19T05:00:01,187 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:01,187 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-19T05:00:01,187 | ^ 2024-11-19T05:00:01,188 command_dist.c:1380:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:01,188 1380 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T05:00:01,188 | ^ 2024-11-19T05:00:01,189 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-19T05:00:01,189 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-11-19T05:00:01,189 | ^ 2024-11-19T05:00:01,440 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-11-19T05:00:01,440 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-11-19T05:00:01,440 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-11-19T05:00:01,440 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:01,440 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-11-19T05:00:01,441 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-11-19T05:00:01,441 | ^~~~~~~~~~~~ 2024-11-19T05:00:02,162 command_dist.c: In function ‘get_dim_shuffle’: 2024-11-19T05:00:02,162 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-11-19T05:00:02,162 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-19T05:00:02,162 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:02,163 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-11-19T05:00:02,163 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-19T05:00:02,163 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:02,944 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-19T05:00:02,945 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:02,945 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:02,945 | ^~ ~~~~~~~~~ 2024-11-19T05:00:02,945 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T05:00:02,945 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:02,946 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:02,946 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:02,946 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:02,946 | ^~~~~~~~~~~~~~~ 2024-11-19T05:00:02,946 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T05:00:02,947 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:02,947 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:02,948 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:02,948 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:02,948 | ^~~~~~~~~~~ 2024-11-19T05:00:02,948 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-19T05:00:02,948 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:02,948 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:02,949 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:02,949 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:02,949 | ^~~~~ 2024-11-19T05:00:02,949 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:02,949 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:02,949 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,156 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-19T05:00:03,156 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:03,156 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:03,157 | ^~ ~~~~~~~~~ 2024-11-19T05:00:03,157 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T05:00:03,157 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:03,157 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,158 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:03,158 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:03,158 | ^~~~~~~~~~~~~~~ 2024-11-19T05:00:03,158 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T05:00:03,158 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:03,158 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,159 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:03,159 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:03,159 | ^~~~~~~~~~~~~ 2024-11-19T05:00:03,159 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T05:00:03,159 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:03,160 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,160 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:03,161 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T05:00:03,161 | ^ 2024-11-19T05:00:03,161 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-11-19T05:00:03,161 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T05:00:03,161 | ^~~~~~~~~~ 2024-11-19T05:00:03,162 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-19T05:00:03,162 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-19T05:00:03,162 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,162 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:03,162 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T05:00:03,163 | ^ 2024-11-19T05:00:03,163 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-11-19T05:00:03,163 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T05:00:03,163 | ^~~~~~~~~~ 2024-11-19T05:00:03,163 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-19T05:00:03,164 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-19T05:00:03,164 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,400 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-19T05:00:03,401 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:03,401 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:03,401 | ^~ ~~~~~~~~~ 2024-11-19T05:00:03,401 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-19T05:00:03,401 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-19T05:00:03,401 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,402 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:03,402 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:03,402 | ^~~~~~~~~~~~~~~ 2024-11-19T05:00:03,403 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-19T05:00:03,403 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-19T05:00:03,403 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,404 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:03,404 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:03,404 | ^~~~~~~~~~~~~ 2024-11-19T05:00:03,404 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T05:00:03,404 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-19T05:00:03,405 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,406 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:03,406 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:03,406 | ^~~~~~~~~~~ 2024-11-19T05:00:03,406 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-19T05:00:03,407 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-19T05:00:03,407 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,407 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-19T05:00:03,407 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:03,407 | ^~~~~ 2024-11-19T05:00:03,408 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:03,408 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-19T05:00:03,408 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,655 command_dist.c: In function ‘combine_queries’: 2024-11-19T05:00:03,656 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:03,656 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-19T05:00:03,657 | ^ 2024-11-19T05:00:03,657 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:03,657 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-19T05:00:03,657 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,658 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:03,658 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-19T05:00:03,659 | ^ 2024-11-19T05:00:03,659 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:03,659 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-19T05:00:03,660 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:03,661 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:03,662 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-19T05:00:03,662 | ^~ ~~~~~~~~ 2024-11-19T05:00:03,663 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-19T05:00:03,663 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-19T05:00:03,663 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:09,192 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 2024-11-19T05:00:13,179 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 2024-11-19T05:00:14,835 command_set.c: In function ‘sketch_operate’: 2024-11-19T05:00:14,835 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-19T05:00:14,835 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-11-19T05:00:14,836 | ^ 2024-11-19T05:00:14,855 command_set.c: In function ‘combin_subset_pans’: 2024-11-19T05:00:14,856 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-19T05:00:14,856 457 | free(co_dstat_fpath); 2024-11-19T05:00:14,856 | ^~~~~~~~~~~~~~ 2024-11-19T05:00:14,894 In file included from kssdheaders/global_basic.h:159, 2024-11-19T05:00:14,895 from command_set.c:15: 2024-11-19T05:00:14,895 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-19T05:00:14,895 565 | extern void free (void *__ptr) __THROW; 2024-11-19T05:00:14,895 | ~~~~~~^~~~~ 2024-11-19T05:00:14,903 command_set.c: In function ‘grouping_genomes’: 2024-11-19T05:00:14,904 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-19T05:00:14,904 562 | free(co_dstat_fpath); 2024-11-19T05:00:14,904 | ^~~~~~~~~~~~~~ 2024-11-19T05:00:14,905 In file included from kssdheaders/global_basic.h:159, 2024-11-19T05:00:14,905 from command_set.c:15: 2024-11-19T05:00:14,905 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-19T05:00:14,906 565 | extern void free (void *__ptr) __THROW; 2024-11-19T05:00:14,906 | ~~~~~~^~~~~ 2024-11-19T05:00:15,036 command_set.c: In function ‘sketch_union’: 2024-11-19T05:00:15,036 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:15,036 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,036 | ^ 2024-11-19T05:00:15,036 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:15,036 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,037 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,037 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,037 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:15,037 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,037 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:15,037 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:15,037 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,038 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,038 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T05:00:15,038 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:15,038 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:15,038 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-19T05:00:15,038 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,149 command_set.c: In function ‘sketch_operate’: 2024-11-19T05:00:15,150 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,150 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T05:00:15,150 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:15,150 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-19T05:00:15,150 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-19T05:00:15,150 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,150 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,151 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T05:00:15,151 | ^~ ~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,151 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-19T05:00:15,151 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-19T05:00:15,151 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,151 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,151 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:15,151 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,152 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:15,152 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:15,152 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,152 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,152 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:15,152 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,152 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:15,152 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-19T05:00:15,153 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,153 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,153 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:15,153 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,153 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:15,153 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:15,153 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,154 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,154 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:15,154 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,154 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:15,154 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-19T05:00:15,154 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,154 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:15,154 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,155 | ^ 2024-11-19T05:00:15,155 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:15,155 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,155 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,304 command_set.c: In function ‘uniq_sketch_union’: 2024-11-19T05:00:15,304 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:15,304 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,304 | ^ 2024-11-19T05:00:15,304 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:15,305 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,305 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,305 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,305 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:15,305 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,305 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:15,305 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-19T05:00:15,306 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,306 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,306 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T05:00:15,306 | ^~ ~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,306 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-19T05:00:15,306 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-19T05:00:15,306 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,431 command_set.c: In function ‘combin_pans’: 2024-11-19T05:00:15,431 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,431 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:15,431 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,432 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2024-11-19T05:00:15,432 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:15,432 | ^~~~~~~~~~ 2024-11-19T05:00:15,432 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-11-19T05:00:15,432 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:15,432 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,432 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,432 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:15,432 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:15,433 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2024-11-19T05:00:15,433 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:15,433 | ^~~~~~~~~~ 2024-11-19T05:00:15,433 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-11-19T05:00:15,433 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:15,433 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,434 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:15,434 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,434 | ^ 2024-11-19T05:00:15,434 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:15,434 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,434 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,617 command_set.c: In function ‘combin_subset_pans’: 2024-11-19T05:00:15,617 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,617 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:15,618 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,618 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:15,618 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:15,618 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,618 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,618 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:15,618 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:15,619 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:15,619 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:15,619 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,619 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,619 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:15,619 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,619 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:15,620 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:15,620 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,621 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,621 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:15,621 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:15,621 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:15,622 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:15,622 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,622 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:15,622 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,622 | ^ 2024-11-19T05:00:15,622 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:15,622 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,622 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,824 command_set.c: In function ‘grouping_genomes’: 2024-11-19T05:00:15,824 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,824 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:15,824 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,824 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:15,825 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-19T05:00:15,825 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,825 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,825 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:15,825 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:15,826 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:15,826 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-19T05:00:15,826 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,827 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,828 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:15,828 | ^~ ~~~~~~~~~~~ 2024-11-19T05:00:15,828 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-19T05:00:15,828 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-19T05:00:15,828 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,829 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-19T05:00:15,829 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:15,829 | ^~ ~~~~~~~~~~ 2024-11-19T05:00:15,829 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-19T05:00:15,829 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-19T05:00:15,829 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:15,830 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-19T05:00:15,830 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,830 | ^ 2024-11-19T05:00:15,830 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-19T05:00:15,830 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-19T05:00:15,831 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:17,411 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 2024-11-19T05:00:17,728 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 2024-11-19T05:00:17,910 global_basic.c: In function ‘organize_infile_list’: 2024-11-19T05:00:17,911 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-11-19T05:00:17,911 195 | while (isspace(*buf)) buf++; 2024-11-19T05:00:17,911 | ^~~~~~~ 2024-11-19T05:00:17,911 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=] 2024-11-19T05:00:17,912 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-19T05:00:17,912 | ~~^ 2024-11-19T05:00:17,912 | | 2024-11-19T05:00:17,912 | long unsigned int 2024-11-19T05:00:17,912 | %u 2024-11-19T05:00:17,912 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-19T05:00:17,912 | ~~~~~~~~~~~ 2024-11-19T05:00:17,912 | | 2024-11-19T05:00:17,913 | size_t {aka unsigned int} 2024-11-19T05:00:17,913 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=] 2024-11-19T05:00:17,913 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-19T05:00:17,913 | ~~^ 2024-11-19T05:00:17,913 | | 2024-11-19T05:00:17,913 | long unsigned int 2024-11-19T05:00:17,914 | %u 2024-11-19T05:00:17,914 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-19T05:00:17,914 | ~~~~~~~~~~~ 2024-11-19T05:00:17,914 | | 2024-11-19T05:00:17,914 | size_t {aka unsigned int} 2024-11-19T05:00:18,622 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 2024-11-19T05:00:18,796 iseq2comem.c: In function ‘reads2mco’: 2024-11-19T05:00:18,797 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,797 156 | if (base > TL) { 2024-11-19T05:00:18,797 | ^ 2024-11-19T05:00:18,797 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,797 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:18,797 | ^~ 2024-11-19T05:00:18,798 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,798 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:18,798 | ^ 2024-11-19T05:00:18,799 iseq2comem.c: In function ‘fasta2co’: 2024-11-19T05:00:18,799 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,799 239 | if (base > TL) { 2024-11-19T05:00:18,799 | ^ 2024-11-19T05:00:18,799 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,800 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:18,800 | ^~ 2024-11-19T05:00:18,800 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,800 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:18,800 | ^ 2024-11-19T05:00:18,800 iseq2comem.c: In function ‘fastq2co’: 2024-11-19T05:00:18,801 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-11-19T05:00:18,801 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-11-19T05:00:18,801 | ^~ 2024-11-19T05:00:18,802 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,802 318 | if (base > TL) { 2024-11-19T05:00:18,802 | ^ 2024-11-19T05:00:18,802 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,802 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:18,802 | ^~ 2024-11-19T05:00:18,802 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,803 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:18,803 | ^ 2024-11-19T05:00:18,803 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,803 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-11-19T05:00:18,803 | ^ 2024-11-19T05:00:18,805 iseq2comem.c: In function ‘fastq2koc’: 2024-11-19T05:00:18,805 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,805 402 | if (base > TL) { 2024-11-19T05:00:18,805 | ^ 2024-11-19T05:00:18,805 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,805 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:18,805 | ^~ 2024-11-19T05:00:18,806 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,806 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:18,806 | ^ 2024-11-19T05:00:18,811 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-11-19T05:00:18,811 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,811 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:18,811 | ^~ 2024-11-19T05:00:18,811 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-19T05:00:18,812 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-19T05:00:18,812 | ^ 2024-11-19T05:00:25,260 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 2024-11-19T05:00:25,338 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 2024-11-19T05:00:25,479 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 2024-11-19T05:00:25,866 pykssd.c: In function ‘py_dist_dispatch’: 2024-11-19T05:00:25,866 pykssd.c:329:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-11-19T05:00:25,866 329 | int state1 = dist_dispatch(&dist_opt_val1); 2024-11-19T05:00:25,866 | ^~~~~~ 2024-11-19T05:00:25,867 pykssd.c:386:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-11-19T05:00:25,867 386 | int state2 = dist_dispatch(&dist_opt_val2); 2024-11-19T05:00:25,867 | ^~~~~~ 2024-11-19T05:00:25,868 pykssd.c:510:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-11-19T05:00:25,868 510 | int state4 = dist_dispatch(&dist_opt_val4); 2024-11-19T05:00:25,869 | ^~~~~~ 2024-11-19T05:00:26,012 pykssd.c: In function ‘rename_file’: 2024-11-19T05:00:26,012 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-11-19T05:00:26,012 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-11-19T05:00:26,012 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-19T05:00:26,012 pykssd.c:41:15: note: length computed here 2024-11-19T05:00:26,012 41 | int len = strlen(p1); 2024-11-19T05:00:26,013 | ^~~~~~~~~~ 2024-11-19T05:00:26,435 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 2024-11-19T05:00:26,638 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-11-19T05:00:26,638 !! 2024-11-19T05:00:26,638 ******************************************************************************** 2024-11-19T05:00:26,639 Please avoid running ``setup.py`` directly. 2024-11-19T05:00:26,639 Instead, use pypa/build, pypa/installer or other 2024-11-19T05:00:26,639 standards-based tools. 2024-11-19T05:00:26,639 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-11-19T05:00:26,639 ******************************************************************************** 2024-11-19T05:00:26,639 !! 2024-11-19T05:00:26,640 self.initialize_options() 2024-11-19T05:00:26,674 installing to build/bdist.linux-armv7l/wheel 2024-11-19T05:00:26,674 running install 2024-11-19T05:00:26,700 running install_lib 2024-11-19T05:00:26,730 creating build/bdist.linux-armv7l/wheel 2024-11-19T05:00:26,731 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:00:26,741 copying build/lib.linux-armv7l-cpython-39/kssdutils.py -> build/bdist.linux-armv7l/wheel/. 2024-11-19T05:00:26,744 running install_egg_info 2024-11-19T05:00:26,785 Copying kssdutils.egg-info to build/bdist.linux-armv7l/wheel/./kssdutils-1.0.1-py3.9.egg-info 2024-11-19T05:00:26,800 running install_scripts 2024-11-19T05:00:26,853 creating build/bdist.linux-armv7l/wheel/kssdutils-1.0.1.dist-info/WHEEL 2024-11-19T05:00:26,856 creating '/tmp/pip-wheel-nqzafsvy/kssdutils-1.0.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-11-19T05:00:26,949 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2024-11-19T05:00:26,954 adding 'kssdutils.py' 2024-11-19T05:00:26,956 adding 'kssdutils-1.0.1.dist-info/METADATA' 2024-11-19T05:00:26,957 adding 'kssdutils-1.0.1.dist-info/WHEEL' 2024-11-19T05:00:26,958 adding 'kssdutils-1.0.1.dist-info/dependency_links.txt' 2024-11-19T05:00:26,959 adding 'kssdutils-1.0.1.dist-info/top_level.txt' 2024-11-19T05:00:26,960 adding 'kssdutils-1.0.1.dist-info/RECORD' 2024-11-19T05:00:26,963 removing build/bdist.linux-armv7l/wheel 2024-11-19T05:00:27,818 Building wheel for kssdutils (setup.py): finished with status 'done' 2024-11-19T05:00:28,611 Created wheel for kssdutils: filename=kssdutils-1.0.1-cp39-cp39-linux_armv7l.whl size=179740 sha256=29a695a62aae6fa18fcad3ae6bfc6bbe19f545f66740fde177ddbf23efa45d15 2024-11-19T05:00:28,614 Stored in directory: /tmp/pip-ephem-wheel-cache-gy1aou6j/wheels/53/a5/d2/06fcdf8cedf0fdec41f9611772dca86e39e2aaa7b420045c87 2024-11-19T05:00:28,641 Successfully built kssdutils 2024-11-19T05:00:28,655 Removed build tracker: '/tmp/pip-build-tracker-gu_hbf5g'