2024-03-15T13:38:22,735 Created temporary directory: /tmp/pip-build-tracker-h0pwnt62 2024-03-15T13:38:22,736 Initialized build tracking at /tmp/pip-build-tracker-h0pwnt62 2024-03-15T13:38:22,736 Created build tracker: /tmp/pip-build-tracker-h0pwnt62 2024-03-15T13:38:22,737 Entered build tracker: /tmp/pip-build-tracker-h0pwnt62 2024-03-15T13:38:22,737 Created temporary directory: /tmp/pip-wheel-7_48b_9b 2024-03-15T13:38:22,741 Created temporary directory: /tmp/pip-ephem-wheel-cache-3ga_fw6p 2024-03-15T13:38:22,769 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-03-15T13:38:22,773 2 location(s) to search for versions of kssdtree: 2024-03-15T13:38:22,773 * https://pypi.org/simple/kssdtree/ 2024-03-15T13:38:22,773 * https://www.piwheels.org/simple/kssdtree/ 2024-03-15T13:38:22,773 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2024-03-15T13:38:22,774 Getting page https://pypi.org/simple/kssdtree/ 2024-03-15T13:38:22,776 Found index url https://pypi.org/simple/ 2024-03-15T13:38:22,828 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2024-03-15T13:38:22,829 Found link https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.1 2024-03-15T13:38:22,829 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2024-03-15T13:38:22,829 Getting page https://www.piwheels.org/simple/kssdtree/ 2024-03-15T13:38:22,830 Found index url https://www.piwheels.org/simple/ 2024-03-15T13:38:23,149 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2024-03-15T13:38:23,152 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv6l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2024-03-15T13:38:23,152 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv7l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2024-03-15T13:38:23,153 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv6l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2024-03-15T13:38:23,153 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv7l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2024-03-15T13:38:23,153 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2024-03-15T13:38:23,154 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2024-03-15T13:38:23,179 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2024-03-15T13:38:23,204 Collecting kssdtree==1.1.1 2024-03-15T13:38:23,208 Created temporary directory: /tmp/pip-unpack-v2xf14zx 2024-03-15T13:38:23,265 Downloading kssdtree-1.1.1.tar.gz (114 kB) 2024-03-15T13:38:23,460 Added kssdtree==1.1.1 from https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-h0pwnt62' 2024-03-15T13:38:23,462 Running setup.py (path:/tmp/pip-wheel-7_48b_9b/kssdtree_8b4ac53aeb004842824659401cf1944f/setup.py) egg_info for package kssdtree 2024-03-15T13:38:23,463 Created temporary directory: /tmp/pip-pip-egg-info-qtptwfd7 2024-03-15T13:38:23,463 Preparing metadata (setup.py): started 2024-03-15T13:38:23,464 Running command python setup.py egg_info 2024-03-15T13:38:24,537 running egg_info 2024-03-15T13:38:24,538 creating /tmp/pip-pip-egg-info-qtptwfd7/kssdtree.egg-info 2024-03-15T13:38:24,562 writing /tmp/pip-pip-egg-info-qtptwfd7/kssdtree.egg-info/PKG-INFO 2024-03-15T13:38:24,565 writing dependency_links to /tmp/pip-pip-egg-info-qtptwfd7/kssdtree.egg-info/dependency_links.txt 2024-03-15T13:38:24,567 writing requirements to /tmp/pip-pip-egg-info-qtptwfd7/kssdtree.egg-info/requires.txt 2024-03-15T13:38:24,569 writing top-level names to /tmp/pip-pip-egg-info-qtptwfd7/kssdtree.egg-info/top_level.txt 2024-03-15T13:38:24,570 writing manifest file '/tmp/pip-pip-egg-info-qtptwfd7/kssdtree.egg-info/SOURCES.txt' 2024-03-15T13:38:24,667 reading manifest file '/tmp/pip-pip-egg-info-qtptwfd7/kssdtree.egg-info/SOURCES.txt' 2024-03-15T13:38:24,669 reading manifest template 'MANIFEST.in' 2024-03-15T13:38:24,686 writing manifest file '/tmp/pip-pip-egg-info-qtptwfd7/kssdtree.egg-info/SOURCES.txt' 2024-03-15T13:38:24,776 Preparing metadata (setup.py): finished with status 'done' 2024-03-15T13:38:24,780 Source in /tmp/pip-wheel-7_48b_9b/kssdtree_8b4ac53aeb004842824659401cf1944f has version 1.1.1, which satisfies requirement kssdtree==1.1.1 from https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz 2024-03-15T13:38:24,781 Removed kssdtree==1.1.1 from https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-h0pwnt62' 2024-03-15T13:38:24,786 Created temporary directory: /tmp/pip-unpack-8yt8xtj3 2024-03-15T13:38:24,786 Created temporary directory: /tmp/pip-unpack-hzmjxlb3 2024-03-15T13:38:24,792 Building wheels for collected packages: kssdtree 2024-03-15T13:38:24,796 Created temporary directory: /tmp/pip-wheel-vtlrfh49 2024-03-15T13:38:24,796 Building wheel for kssdtree (setup.py): started 2024-03-15T13:38:24,797 Destination directory: /tmp/pip-wheel-vtlrfh49 2024-03-15T13:38:24,797 Running command python setup.py bdist_wheel 2024-03-15T13:38:25,830 running bdist_wheel 2024-03-15T13:38:25,924 running build 2024-03-15T13:38:25,925 running build_py 2024-03-15T13:38:25,951 creating build 2024-03-15T13:38:25,951 creating build/lib.linux-armv7l-cpython-39 2024-03-15T13:38:25,953 copying kssdtree.py -> build/lib.linux-armv7l-cpython-39 2024-03-15T13:38:25,956 copying toolutils.py -> build/lib.linux-armv7l-cpython-39 2024-03-15T13:38:25,958 running egg_info 2024-03-15T13:38:26,017 writing kssdtree.egg-info/PKG-INFO 2024-03-15T13:38:26,021 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2024-03-15T13:38:26,024 writing requirements to kssdtree.egg-info/requires.txt 2024-03-15T13:38:26,025 writing top-level names to kssdtree.egg-info/top_level.txt 2024-03-15T13:38:26,052 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-03-15T13:38:26,055 reading manifest template 'MANIFEST.in' 2024-03-15T13:38:26,074 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2024-03-15T13:38:26,077 running build_ext 2024-03-15T13:38:26,600 building 'kssd' extension 2024-03-15T13:38:26,601 creating build/temp.linux-armv7l-cpython-39 2024-03-15T13:38:26,603 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 2024-03-15T13:38:26,762 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-03-15T13:38:26,763 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T13:38:26,763 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-03-15T13:38:26,763 | ^ 2024-03-15T13:38:26,765 co2mco.c: In function ‘co2unitllmco’: 2024-03-15T13:38:26,766 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T13:38:26,766 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-03-15T13:38:26,766 | ^ 2024-03-15T13:38:27,379 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 2024-03-15T13:38:27,679 command_composite.c: In function ‘get_species_abundance’: 2024-03-15T13:38:27,679 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-03-15T13:38:27,679 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-03-15T13:38:27,679 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:27,679 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-03-15T13:38:27,680 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-03-15T13:38:27,680 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:27,680 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:27,680 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-03-15T13:38:27,680 | ^ 2024-03-15T13:38:27,680 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-03-15T13:38:27,681 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-03-15T13:38:27,681 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:27,681 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:27,681 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-03-15T13:38:27,681 | ^ 2024-03-15T13:38:27,681 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-03-15T13:38:27,681 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-03-15T13:38:27,682 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:27,682 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:27,682 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-03-15T13:38:27,682 | ^ 2024-03-15T13:38:27,682 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-03-15T13:38:27,682 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-03-15T13:38:27,683 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:27,683 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:27,683 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-03-15T13:38:27,683 | ^ 2024-03-15T13:38:27,683 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-03-15T13:38:27,683 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-03-15T13:38:27,683 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:27,683 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:27,684 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-03-15T13:38:27,684 | ^ 2024-03-15T13:38:27,684 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-03-15T13:38:27,684 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-03-15T13:38:27,684 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:27,918 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 2024-03-15T13:38:28,109 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-03-15T13:38:28,110 command_dist.c:678:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T13:38:28,110 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T13:38:28,111 | ~~^ 2024-03-15T13:38:28,111 | | 2024-03-15T13:38:28,111 | long unsigned int 2024-03-15T13:38:28,111 | %u 2024-03-15T13:38:28,111 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T13:38:28,111 | ~~~~~~~ 2024-03-15T13:38:28,111 | | 2024-03-15T13:38:28,111 | size_t {aka unsigned int} 2024-03-15T13:38:28,112 command_dist.c:678:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T13:38:28,112 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T13:38:28,112 | ~~^ 2024-03-15T13:38:28,112 | | 2024-03-15T13:38:28,112 | long unsigned int 2024-03-15T13:38:28,112 | %u 2024-03-15T13:38:28,112 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T13:38:28,112 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-03-15T13:38:28,113 | ~~~~~~~~~ 2024-03-15T13:38:28,113 | | 2024-03-15T13:38:28,113 | size_t {aka unsigned int} 2024-03-15T13:38:28,113 command_dist.c:678:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-03-15T13:38:28,113 678 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T13:38:28,113 | ~~^ 2024-03-15T13:38:28,113 | | 2024-03-15T13:38:28,114 | long unsigned int 2024-03-15T13:38:28,114 | %u 2024-03-15T13:38:28,114 679 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T13:38:28,114 680 | maplength, (size_t) b * unitsz_distf_mapped); 2024-03-15T13:38:28,114 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:28,114 | | 2024-03-15T13:38:28,114 | unsigned int 2024-03-15T13:38:28,115 command_dist.c:716:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-15T13:38:28,115 716 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-03-15T13:38:28,115 | ^ 2024-03-15T13:38:28,121 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-03-15T13:38:28,122 command_dist.c:864:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T13:38:28,123 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-03-15T13:38:28,123 | ~~^ ~~~~~~~ 2024-03-15T13:38:28,123 | | | 2024-03-15T13:38:28,123 | long unsigned int size_t {aka unsigned int} 2024-03-15T13:38:28,123 | %u 2024-03-15T13:38:28,124 command_dist.c:864:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T13:38:28,124 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-03-15T13:38:28,124 | ~~^ 2024-03-15T13:38:28,124 | | 2024-03-15T13:38:28,124 | long unsigned int 2024-03-15T13:38:28,124 | %u 2024-03-15T13:38:28,125 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-03-15T13:38:28,125 | ~~~~~~~~~ 2024-03-15T13:38:28,125 | | 2024-03-15T13:38:28,125 | size_t {aka unsigned int} 2024-03-15T13:38:28,125 command_dist.c:864:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-03-15T13:38:28,125 864 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-03-15T13:38:28,126 | ~~^ 2024-03-15T13:38:28,126 | | 2024-03-15T13:38:28,126 | long unsigned int 2024-03-15T13:38:28,126 | %u 2024-03-15T13:38:28,126 865 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-03-15T13:38:28,126 866 | (size_t) b * unitsz_distf_mapped); 2024-03-15T13:38:28,126 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:28,127 | | 2024-03-15T13:38:28,127 | unsigned int 2024-03-15T13:38:28,127 command_dist.c:811:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-03-15T13:38:28,128 811 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-03-15T13:38:28,128 | ^~~~~~~ 2024-03-15T13:38:28,128 command_dist.c:810:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-03-15T13:38:28,128 810 | struct stat cbd_fcode_stat; 2024-03-15T13:38:28,128 | ^~~~~~~~~~~~~~ 2024-03-15T13:38:28,128 command_dist.c:809:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-03-15T13:38:28,128 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-03-15T13:38:28,129 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:28,129 command_dist.c:809:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-03-15T13:38:28,129 809 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-03-15T13:38:28,129 | ^~~~~~~~~~~~~~~~~ 2024-03-15T13:38:28,135 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-03-15T13:38:28,136 command_dist.c:1019:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T13:38:28,136 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T13:38:28,136 | ~~^ 2024-03-15T13:38:28,136 | | 2024-03-15T13:38:28,136 | long unsigned int 2024-03-15T13:38:28,136 | %u 2024-03-15T13:38:28,137 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T13:38:28,137 | ~~~~~~~ 2024-03-15T13:38:28,137 | | 2024-03-15T13:38:28,137 | size_t {aka unsigned int} 2024-03-15T13:38:28,137 command_dist.c:1019:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T13:38:28,138 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T13:38:28,138 | ~~^ 2024-03-15T13:38:28,138 | | 2024-03-15T13:38:28,138 | long unsigned int 2024-03-15T13:38:28,138 | %u 2024-03-15T13:38:28,138 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T13:38:28,138 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-03-15T13:38:28,138 | ~~~~~~~~~ 2024-03-15T13:38:28,139 | | 2024-03-15T13:38:28,139 | size_t {aka unsigned int} 2024-03-15T13:38:28,139 command_dist.c:1019:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-03-15T13:38:28,139 1019 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-03-15T13:38:28,140 | ~~^ 2024-03-15T13:38:28,140 | | 2024-03-15T13:38:28,140 | long unsigned int 2024-03-15T13:38:28,140 | %u 2024-03-15T13:38:28,140 1020 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-03-15T13:38:28,140 1021 | maplength, (size_t) b * unitsz_distf_mapped); 2024-03-15T13:38:28,140 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:28,140 | | 2024-03-15T13:38:28,141 | unsigned int 2024-03-15T13:38:28,141 command_dist.c:1035:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:28,141 1035 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-03-15T13:38:28,141 | ^ 2024-03-15T13:38:28,144 command_dist.c: In function ‘mco_co_dist_core’: 2024-03-15T13:38:28,145 command_dist.c:1117:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-15T13:38:28,145 1117 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-03-15T13:38:28,145 | ^ 2024-03-15T13:38:28,150 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-03-15T13:38:28,151 command_dist.c:1240:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:28,151 1240 | for (int rid = 0; rid < ref_num; rid++) 2024-03-15T13:38:28,151 | ^ 2024-03-15T13:38:28,153 command_dist.c:1246:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:28,153 1246 | for (int rid = 0; rid < ref_num; rid++) { 2024-03-15T13:38:28,153 | ^ 2024-03-15T13:38:28,158 command_dist.c: In function ‘dist_print_nobin’: 2024-03-15T13:38:28,159 command_dist.c:1336:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:28,159 1336 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-03-15T13:38:28,159 | ^ 2024-03-15T13:38:28,161 command_dist.c:1357:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:28,161 1357 | for (int rid = 0; rid < ref_num; rid++) { 2024-03-15T13:38:28,161 | ^ 2024-03-15T13:38:28,163 command_dist.c:1381:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:28,163 1381 | for (int rid = 0; rid < ref_num; rid++) 2024-03-15T13:38:28,163 | ^ 2024-03-15T13:38:28,163 command_dist.c:1383:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:28,164 1383 | for (int rid = 0; rid < ref_num; rid++) 2024-03-15T13:38:28,164 | ^ 2024-03-15T13:38:28,414 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-03-15T13:38:28,414 command_dist.c:404:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-03-15T13:38:28,414 404 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-03-15T13:38:28,414 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:28,414 command_dist.c:376:40: note: ‘com_abund_fp’ was declared here 2024-03-15T13:38:28,415 376 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-03-15T13:38:28,415 | ^~~~~~~~~~~~ 2024-03-15T13:38:29,142 command_dist.c: In function ‘get_dim_shuffle’: 2024-03-15T13:38:29,142 command_dist.c:268:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-03-15T13:38:29,142 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-03-15T13:38:29,142 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:29,143 command_dist.c:268:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-03-15T13:38:29,143 268 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-03-15T13:38:29,143 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:29,927 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-03-15T13:38:29,928 command_dist.c:597:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:29,928 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T13:38:29,928 | ^~ ~~~~~~~~~ 2024-03-15T13:38:29,928 command_dist.c:597:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-03-15T13:38:29,928 597 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T13:38:29,929 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:29,929 command_dist.c:626:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T13:38:29,929 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T13:38:29,929 | ^~~~~~~~~~~~~~~ 2024-03-15T13:38:29,929 command_dist.c:626:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-03-15T13:38:29,930 626 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T13:38:29,930 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:29,931 command_dist.c:682:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T13:38:29,931 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-03-15T13:38:29,931 | ^~~~~~~~~~~ 2024-03-15T13:38:29,931 command_dist.c:682:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-03-15T13:38:29,931 682 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-03-15T13:38:29,931 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:29,932 command_dist.c:683:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T13:38:29,932 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-03-15T13:38:29,932 | ^~~~~ 2024-03-15T13:38:29,932 command_dist.c:683:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-03-15T13:38:29,932 683 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-03-15T13:38:29,932 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,140 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-03-15T13:38:30,141 command_dist.c:764:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:30,141 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T13:38:30,141 | ^~ ~~~~~~~~~ 2024-03-15T13:38:30,142 command_dist.c:764:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-03-15T13:38:30,142 764 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T13:38:30,142 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,142 command_dist.c:791:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T13:38:30,143 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T13:38:30,143 | ^~~~~~~~~~~~~~~ 2024-03-15T13:38:30,143 command_dist.c:791:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-03-15T13:38:30,143 791 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T13:38:30,143 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,144 command_dist.c:824:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T13:38:30,144 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-03-15T13:38:30,144 | ^~~~~~~~~~~~~ 2024-03-15T13:38:30,144 command_dist.c:824:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-03-15T13:38:30,144 824 | sprintf(distf, "%s/distance.out", distout_dir); 2024-03-15T13:38:30,144 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,145 command_dist.c:850:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:30,145 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-03-15T13:38:30,146 | ^ 2024-03-15T13:38:30,146 command_dist.c:850:33: note: directive argument in the range [0, 536870912] 2024-03-15T13:38:30,146 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-03-15T13:38:30,146 | ^~~~~~~~~~ 2024-03-15T13:38:30,146 command_dist.c:850:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-03-15T13:38:30,147 850 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-03-15T13:38:30,147 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,147 command_dist.c:852:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:30,147 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-03-15T13:38:30,147 | ^ 2024-03-15T13:38:30,148 command_dist.c:852:28: note: directive argument in the range [0, 536870912] 2024-03-15T13:38:30,148 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-03-15T13:38:30,148 | ^~~~~~~~~~ 2024-03-15T13:38:30,148 command_dist.c:852:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-03-15T13:38:30,148 852 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-03-15T13:38:30,148 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,385 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-03-15T13:38:30,386 command_dist.c:928:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:30,386 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T13:38:30,387 | ^~ ~~~~~~~~~ 2024-03-15T13:38:30,387 command_dist.c:928:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-03-15T13:38:30,387 928 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-03-15T13:38:30,387 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,388 command_dist.c:957:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T13:38:30,388 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T13:38:30,388 | ^~~~~~~~~~~~~~~ 2024-03-15T13:38:30,388 command_dist.c:957:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-03-15T13:38:30,389 957 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-03-15T13:38:30,389 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,389 command_dist.c:991:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T13:38:30,390 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-03-15T13:38:30,390 | ^~~~~~~~~~~~~ 2024-03-15T13:38:30,390 command_dist.c:991:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-03-15T13:38:30,390 991 | sprintf(distf, "%s/distance.out", distout_dir); 2024-03-15T13:38:30,390 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,391 command_dist.c:1023:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T13:38:30,392 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-03-15T13:38:30,392 | ^~~~~~~~~~~ 2024-03-15T13:38:30,392 command_dist.c:1023:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-03-15T13:38:30,392 1023 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-03-15T13:38:30,392 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,393 command_dist.c:1024:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-03-15T13:38:30,393 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-03-15T13:38:30,393 | ^~~~~ 2024-03-15T13:38:30,394 command_dist.c:1024:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-03-15T13:38:30,394 1024 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-03-15T13:38:30,394 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,641 command_dist.c: In function ‘combine_queries’: 2024-03-15T13:38:30,642 command_dist.c:1493:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T13:38:30,642 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-03-15T13:38:30,642 | ^ 2024-03-15T13:38:30,643 command_dist.c:1493:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T13:38:30,643 1493 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-03-15T13:38:30,643 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,644 command_dist.c:1500:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T13:38:30,644 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-03-15T13:38:30,644 | ^ 2024-03-15T13:38:30,645 command_dist.c:1500:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T13:38:30,645 1500 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-03-15T13:38:30,645 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:30,647 command_dist.c:1604:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:30,647 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-03-15T13:38:30,647 | ^~ ~~~~~~~~ 2024-03-15T13:38:30,648 command_dist.c:1604:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-03-15T13:38:30,648 1604 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-03-15T13:38:30,648 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,125 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 2024-03-15T13:38:31,291 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 2024-03-15T13:38:31,435 command_set.c: In function ‘sketch_operate’: 2024-03-15T13:38:31,435 command_set.c:179:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-03-15T13:38:31,435 179 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-03-15T13:38:31,435 | ^ 2024-03-15T13:38:31,445 command_set.c: In function ‘combin_subset_pans’: 2024-03-15T13:38:31,446 command_set.c:458:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-03-15T13:38:31,446 458 | free(co_dstat_fpath); 2024-03-15T13:38:31,446 | ^~~~~~~~~~~~~~ 2024-03-15T13:38:31,447 In file included from kssdheaders/global_basic.h:159, 2024-03-15T13:38:31,447 from command_set.c:15: 2024-03-15T13:38:31,447 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-03-15T13:38:31,448 565 | extern void free (void *__ptr) __THROW; 2024-03-15T13:38:31,448 | ~~~~~~^~~~~ 2024-03-15T13:38:31,452 command_set.c: In function ‘grouping_genomes’: 2024-03-15T13:38:31,453 command_set.c:563:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-03-15T13:38:31,453 563 | free(co_dstat_fpath); 2024-03-15T13:38:31,453 | ^~~~~~~~~~~~~~ 2024-03-15T13:38:31,453 In file included from kssdheaders/global_basic.h:159, 2024-03-15T13:38:31,454 from command_set.c:15: 2024-03-15T13:38:31,454 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-03-15T13:38:31,454 565 | extern void free (void *__ptr) __THROW; 2024-03-15T13:38:31,454 | ~~~~~~^~~~~ 2024-03-15T13:38:31,570 command_set.c: In function ‘sketch_union’: 2024-03-15T13:38:31,570 command_set.c:72:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T13:38:31,570 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:31,570 | ^ 2024-03-15T13:38:31,571 command_set.c:72:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T13:38:31,571 72 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:31,571 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,571 command_set.c:83:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,572 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-03-15T13:38:31,572 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:31,572 command_set.c:83:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T13:38:31,572 83 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-03-15T13:38:31,572 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,573 command_set.c:93:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,573 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-03-15T13:38:31,573 | ^~ ~~~~~~~~~~ 2024-03-15T13:38:31,573 command_set.c:93:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-03-15T13:38:31,574 93 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-03-15T13:38:31,574 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,686 command_set.c: In function ‘sketch_operate’: 2024-03-15T13:38:31,687 command_set.c:154:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,687 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-03-15T13:38:31,687 | ^~ ~~~~~~~~~~ 2024-03-15T13:38:31,687 command_set.c:154:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-03-15T13:38:31,687 154 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-03-15T13:38:31,688 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,688 command_set.c:156:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,688 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-03-15T13:38:31,688 | ^~ ~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,688 command_set.c:156:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-03-15T13:38:31,689 156 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-03-15T13:38:31,689 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,689 command_set.c:166:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,690 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-03-15T13:38:31,690 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:31,690 command_set.c:166:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T13:38:31,690 166 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-03-15T13:38:31,690 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,691 command_set.c:170:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,691 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-03-15T13:38:31,691 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:31,691 command_set.c:170:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T13:38:31,691 170 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-03-15T13:38:31,692 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,692 command_set.c:175:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,692 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-03-15T13:38:31,692 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:31,693 command_set.c:175:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T13:38:31,693 175 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-03-15T13:38:31,693 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,694 command_set.c:188:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,694 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-03-15T13:38:31,694 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:31,695 command_set.c:188:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T13:38:31,695 188 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-03-15T13:38:31,695 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,695 command_set.c:193:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T13:38:31,695 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:31,696 | ^ 2024-03-15T13:38:31,696 command_set.c:193:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T13:38:31,696 193 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:31,696 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,846 command_set.c: In function ‘uniq_sketch_union’: 2024-03-15T13:38:31,847 command_set.c:235:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T13:38:31,847 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:31,847 | ^ 2024-03-15T13:38:31,847 command_set.c:235:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T13:38:31,847 235 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:31,848 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,848 command_set.c:248:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,848 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-03-15T13:38:31,849 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:31,849 command_set.c:248:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T13:38:31,849 248 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-03-15T13:38:31,849 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,850 command_set.c:260:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,850 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-03-15T13:38:31,850 | ^~ ~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,851 command_set.c:260:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-03-15T13:38:31,851 260 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-03-15T13:38:31,851 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,976 command_set.c: In function ‘combin_pans’: 2024-03-15T13:38:31,976 command_set.c:298:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,977 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T13:38:31,977 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:31,977 command_set.c:298:25: note: directive argument in the range [0, 1073741823] 2024-03-15T13:38:31,977 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T13:38:31,977 | ^~~~~~~~~~ 2024-03-15T13:38:31,978 command_set.c:298:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-03-15T13:38:31,978 298 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T13:38:31,978 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,979 command_set.c:301:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:31,979 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T13:38:31,979 | ^~ ~~~~~~~~~~ 2024-03-15T13:38:31,979 command_set.c:301:25: note: directive argument in the range [0, 1073741823] 2024-03-15T13:38:31,979 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T13:38:31,980 | ^~~~~~~~~~ 2024-03-15T13:38:31,980 command_set.c:301:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-03-15T13:38:31,980 301 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T13:38:31,980 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:31,981 command_set.c:343:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T13:38:31,982 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:31,982 | ^ 2024-03-15T13:38:31,982 command_set.c:343:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T13:38:31,982 343 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:31,982 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,165 command_set.c: In function ‘combin_subset_pans’: 2024-03-15T13:38:32,166 command_set.c:470:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:32,166 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-03-15T13:38:32,167 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:32,167 command_set.c:470:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T13:38:32,167 470 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-03-15T13:38:32,167 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,168 command_set.c:476:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:32,168 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-03-15T13:38:32,168 | ^~ ~~~~~~~~~~ 2024-03-15T13:38:32,169 command_set.c:476:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T13:38:32,169 476 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-03-15T13:38:32,169 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,170 command_set.c:482:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:32,170 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T13:38:32,170 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:32,171 command_set.c:482:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T13:38:32,171 482 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T13:38:32,171 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,173 command_set.c:513:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:32,173 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T13:38:32,173 | ^~ ~~~~~~~~~~ 2024-03-15T13:38:32,174 command_set.c:513:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T13:38:32,174 513 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T13:38:32,174 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,175 command_set.c:524:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T13:38:32,175 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:32,175 | ^ 2024-03-15T13:38:32,175 command_set.c:524:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T13:38:32,176 524 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:32,176 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,383 command_set.c: In function ‘grouping_genomes’: 2024-03-15T13:38:32,384 command_set.c:575:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:32,384 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-03-15T13:38:32,384 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:32,385 command_set.c:575:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T13:38:32,385 575 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-03-15T13:38:32,385 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,386 command_set.c:581:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:32,386 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-03-15T13:38:32,386 | ^~ ~~~~~~~~~~ 2024-03-15T13:38:32,387 command_set.c:581:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T13:38:32,387 581 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-03-15T13:38:32,387 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,389 command_set.c:613:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:32,389 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T13:38:32,389 | ^~ ~~~~~~~~~~~ 2024-03-15T13:38:32,390 command_set.c:613:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-03-15T13:38:32,390 613 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-03-15T13:38:32,390 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,391 command_set.c:635:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-03-15T13:38:32,392 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T13:38:32,392 | ^~ ~~~~~~~~~~ 2024-03-15T13:38:32,392 command_set.c:635:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-03-15T13:38:32,392 635 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-03-15T13:38:32,393 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,393 command_set.c:646:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-03-15T13:38:32,394 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:32,394 | ^ 2024-03-15T13:38:32,394 command_set.c:646:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-03-15T13:38:32,395 646 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-03-15T13:38:32,395 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:32,667 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 2024-03-15T13:38:32,943 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 2024-03-15T13:38:33,088 global_basic.c: In function ‘organize_infile_list’: 2024-03-15T13:38:33,088 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-03-15T13:38:33,088 195 | while (isspace(*buf)) buf++; 2024-03-15T13:38:33,089 | ^~~~~~~ 2024-03-15T13:38:33,089 global_basic.c:201:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T13:38:33,089 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-03-15T13:38:33,089 | ~~^ 2024-03-15T13:38:33,089 | | 2024-03-15T13:38:33,090 | long unsigned int 2024-03-15T13:38:33,090 | %u 2024-03-15T13:38:33,090 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-03-15T13:38:33,090 | ~~~~~~~~~~~ 2024-03-15T13:38:33,090 | | 2024-03-15T13:38:33,090 | size_t {aka unsigned int} 2024-03-15T13:38:33,090 global_basic.c:233:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2024-03-15T13:38:33,091 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-03-15T13:38:33,091 | ~~^ 2024-03-15T13:38:33,091 | | 2024-03-15T13:38:33,091 | long unsigned int 2024-03-15T13:38:33,091 | %u 2024-03-15T13:38:33,092 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-03-15T13:38:33,092 | ~~~~~~~~~~~ 2024-03-15T13:38:33,092 | | 2024-03-15T13:38:33,092 | size_t {aka unsigned int} 2024-03-15T13:38:33,793 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 2024-03-15T13:38:33,945 iseq2comem.c: In function ‘reads2mco’: 2024-03-15T13:38:33,945 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,945 156 | if (base > TL) { 2024-03-15T13:38:33,946 | ^ 2024-03-15T13:38:33,946 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,946 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T13:38:33,946 | ^~ 2024-03-15T13:38:33,946 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,946 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T13:38:33,947 | ^ 2024-03-15T13:38:33,947 iseq2comem.c: In function ‘fasta2co’: 2024-03-15T13:38:33,947 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,947 239 | if (base > TL) { 2024-03-15T13:38:33,948 | ^ 2024-03-15T13:38:33,948 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,948 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T13:38:33,948 | ^~ 2024-03-15T13:38:33,948 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,948 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T13:38:33,949 | ^ 2024-03-15T13:38:33,949 iseq2comem.c: In function ‘fastq2co’: 2024-03-15T13:38:33,949 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-03-15T13:38:33,949 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-03-15T13:38:33,949 | ^~ 2024-03-15T13:38:33,950 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,950 318 | if (base > TL) { 2024-03-15T13:38:33,950 | ^ 2024-03-15T13:38:33,950 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,951 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T13:38:33,951 | ^~ 2024-03-15T13:38:33,951 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,951 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T13:38:33,951 | ^ 2024-03-15T13:38:33,951 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,952 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-03-15T13:38:33,952 | ^ 2024-03-15T13:38:33,953 iseq2comem.c: In function ‘fastq2koc’: 2024-03-15T13:38:33,953 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,953 402 | if (base > TL) { 2024-03-15T13:38:33,953 | ^ 2024-03-15T13:38:33,954 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,954 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T13:38:33,954 | ^~ 2024-03-15T13:38:33,954 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,954 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T13:38:33,954 | ^ 2024-03-15T13:38:33,959 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-03-15T13:38:33,959 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,959 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T13:38:33,960 | ^~ 2024-03-15T13:38:33,960 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:33,960 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-03-15T13:38:33,960 | ^ 2024-03-15T13:38:35,119 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 2024-03-15T13:38:35,183 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 2024-03-15T13:38:35,304 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 2024-03-15T13:38:35,616 pykssd.c: In function ‘py_dist_dispatch’: 2024-03-15T13:38:35,616 pykssd.c:304:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-03-15T13:38:35,617 304 | int state1 = dist_dispatch(&dist_opt_val1); 2024-03-15T13:38:35,617 | ^~~~~~ 2024-03-15T13:38:35,617 pykssd.c:361:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-03-15T13:38:35,617 361 | int state2 = dist_dispatch(&dist_opt_val2); 2024-03-15T13:38:35,617 | ^~~~~~ 2024-03-15T13:38:35,618 pykssd.c:480:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-03-15T13:38:35,618 480 | int state4 = dist_dispatch(&dist_opt_val4); 2024-03-15T13:38:35,618 | ^~~~~~ 2024-03-15T13:38:35,756 pykssd.c: In function ‘rename_file’: 2024-03-15T13:38:35,757 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-03-15T13:38:35,757 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-03-15T13:38:35,757 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-03-15T13:38:35,757 pykssd.c:41:15: note: length computed here 2024-03-15T13:38:35,757 41 | int len = strlen(p1); 2024-03-15T13:38:35,757 | ^~~~~~~~~~ 2024-03-15T13:38:36,122 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 2024-03-15T13:38:36,276 building 'nj' extension 2024-03-15T13:38:36,277 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 -Injheaders -I/usr/include/python3.9 -c align.c -o build/temp.linux-armv7l-cpython-39/align.o 2024-03-15T13:38:36,681 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 -Injheaders -I/usr/include/python3.9 -c buildtree.c -o build/temp.linux-armv7l-cpython-39/buildtree.o 2024-03-15T13:38:36,806 buildtree.c: In function ‘UPGMA_buildtree’: 2024-03-15T13:38:36,807 buildtree.c:716:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:36,807 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-03-15T13:38:36,807 | ^~ 2024-03-15T13:38:36,807 buildtree.c:716:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:36,807 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2024-03-15T13:38:36,807 | ^~ 2024-03-15T13:38:37,366 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 -Injheaders -I/usr/include/python3.9 -c cluster.c -o build/temp.linux-armv7l-cpython-39/cluster.o 2024-03-15T13:38:37,687 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 -Injheaders -I/usr/include/python3.9 -c distancemat.c -o build/temp.linux-armv7l-cpython-39/distancemat.o 2024-03-15T13:38:37,804 distancemat.c: In function ‘clone_DistanceMatrix’: 2024-03-15T13:38:37,805 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T13:38:37,805 226 | for( i=0; i < dest->size; i++) { 2024-03-15T13:38:37,805 | ^ 2024-03-15T13:38:37,805 distancemat.c: In function ‘empty_DistanceMatrix’: 2024-03-15T13:38:37,805 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T13:38:37,805 260 | for( i=0; i < mat->size; i++) { 2024-03-15T13:38:37,806 | ^ 2024-03-15T13:38:37,806 distancemat.c: In function ‘print_DistanceMatrix’: 2024-03-15T13:38:37,806 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T13:38:37,806 349 | for(row=0; row < mat->size; row++) { 2024-03-15T13:38:37,806 | ^ 2024-03-15T13:38:37,807 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2024-03-15T13:38:37,807 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2024-03-15T13:38:37,807 410 | while(c = fgetc(handle)) { 2024-03-15T13:38:37,807 | ^ 2024-03-15T13:38:38,142 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 -Injheaders -I/usr/include/python3.9 -c pynj.c -o build/temp.linux-armv7l-cpython-39/pynj.o 2024-03-15T13:38:38,507 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 -Injheaders -I/usr/include/python3.9 -c sequence.c -o build/temp.linux-armv7l-cpython-39/sequence.o 2024-03-15T13:38:38,699 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 -Injheaders -I/usr/include/python3.9 -c tree.c -o build/temp.linux-armv7l-cpython-39/tree.o 2024-03-15T13:38:39,389 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 -Injheaders -I/usr/include/python3.9 -c util.c -o build/temp.linux-armv7l-cpython-39/util.o 2024-03-15T13:38:39,554 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/align.o build/temp.linux-armv7l-cpython-39/buildtree.o build/temp.linux-armv7l-cpython-39/cluster.o build/temp.linux-armv7l-cpython-39/distancemat.o build/temp.linux-armv7l-cpython-39/pynj.o build/temp.linux-armv7l-cpython-39/sequence.o build/temp.linux-armv7l-cpython-39/tree.o build/temp.linux-armv7l-cpython-39/util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so 2024-03-15T13:38:39,668 building 'dnj' extension 2024-03-15T13:38:39,669 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c bytescale.c -o build/temp.linux-armv7l-cpython-39/bytescale.o -fopenmp 2024-03-15T13:38:39,734 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 -Idnjheaders -I/usr/include/python3.9 -c dnj.c -o build/temp.linux-armv7l-cpython-39/dnj.o -fopenmp 2024-03-15T13:38:39,854 dnj.c: In function ‘minQpair’: 2024-03-15T13:38:39,854 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,854 70 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,855 | ^~~ 2024-03-15T13:38:39,855 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,855 126 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,856 | ^~~ 2024-03-15T13:38:39,856 dnj.c: In function ‘maxQpair’: 2024-03-15T13:38:39,856 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,856 157 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,856 | ^~~ 2024-03-15T13:38:39,857 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,857 213 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,857 | ^~~ 2024-03-15T13:38:39,857 dnj.c: In function ‘UPGMApair’: 2024-03-15T13:38:39,857 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,857 237 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,858 | ^~~ 2024-03-15T13:38:39,858 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,858 284 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,858 | ^~~ 2024-03-15T13:38:39,858 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,859 291 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,859 | ^~~ 2024-03-15T13:38:39,859 dnj.c: In function ‘minQrow’: 2024-03-15T13:38:39,860 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,860 374 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,860 | ^~~ 2024-03-15T13:38:39,861 dnj.c: In function ‘maxQrow’: 2024-03-15T13:38:39,861 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,861 435 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,861 | ^~~ 2024-03-15T13:38:39,862 dnj.c: In function ‘UPGMArow’: 2024-03-15T13:38:39,862 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,862 488 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,862 | ^~~ 2024-03-15T13:38:39,863 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,863 494 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,863 | ^~~ 2024-03-15T13:38:39,864 dnj.c: In function ‘minQ_thread’: 2024-03-15T13:38:39,864 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:39,864 553 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:39,864 | ^~~ 2024-03-15T13:38:41,025 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 -Idnjheaders -I/usr/include/python3.9 -c filebuff.c -o build/temp.linux-armv7l-cpython-39/filebuff.o -fopenmp 2024-03-15T13:38:41,130 filebuff.c: In function ‘BuffgzFileBuff’: 2024-03-15T13:38:41,130 filebuff.c:99:47: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:41,131 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2024-03-15T13:38:41,131 | ^~ 2024-03-15T13:38:41,413 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 -Idnjheaders -I/usr/include/python3.9 -c hclust.c -o build/temp.linux-armv7l-cpython-39/hclust.o -fopenmp 2024-03-15T13:38:41,531 hclust.c: In function ‘minQ’: 2024-03-15T13:38:41,532 hclust.c:364:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:41,532 364 | while(++i < Q->n) { 2024-03-15T13:38:41,532 | ^ 2024-03-15T13:38:41,532 hclust.c:377:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:41,532 377 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:41,532 | ^~~ 2024-03-15T13:38:41,532 hclust.c: In function ‘maxQ’: 2024-03-15T13:38:41,533 hclust.c:394:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-03-15T13:38:41,533 394 | while(++i < Q->n) { 2024-03-15T13:38:41,533 | ^ 2024-03-15T13:38:41,533 hclust.c:407:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:41,533 407 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:41,533 | ^~~ 2024-03-15T13:38:43,588 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 -Idnjheaders -I/usr/include/python3.9 -c matrix.c -o build/temp.linux-armv7l-cpython-39/matrix.o -fopenmp 2024-03-15T13:38:43,707 matrix.c: In function ‘ltdMatrix_popArrange’: 2024-03-15T13:38:43,707 matrix.c:538:9: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-03-15T13:38:43,707 538 | if(pos != n) { 2024-03-15T13:38:43,707 | ^~ 2024-03-15T13:38:44,450 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 -Idnjheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2024-03-15T13:38:44,513 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 -Idnjheaders -I/usr/include/python3.9 -c nj.c -o build/temp.linux-armv7l-cpython-39/nj.o -fopenmp 2024-03-15T13:38:44,628 nj.c: In function ‘initQ’: 2024-03-15T13:38:44,629 nj.c:243:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:44,629 243 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:44,629 | ^~~ 2024-03-15T13:38:44,630 nj.c: In function ‘initQ_MN’: 2024-03-15T13:38:44,631 nj.c:358:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:44,631 358 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:44,631 | ^~~ 2024-03-15T13:38:44,634 nj.c: In function ‘minD’: 2024-03-15T13:38:44,634 nj.c:559:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:44,635 559 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:44,635 | ^~~ 2024-03-15T13:38:44,636 nj.c: In function ‘maxD’: 2024-03-15T13:38:44,636 nj.c:642:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:44,636 642 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:44,636 | ^~~ 2024-03-15T13:38:44,639 nj.c: In function ‘minPair’: 2024-03-15T13:38:44,640 nj.c:826:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2024-03-15T13:38:44,640 826 | pos <<= sizeof(unsigned) * 8; 2024-03-15T13:38:44,640 | ^~~ 2024-03-15T13:38:46,656 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 -Idnjheaders -I/usr/include/python3.9 -c nwck.c -o build/temp.linux-armv7l-cpython-39/nwck.o -fopenmp 2024-03-15T13:38:47,124 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 -Idnjheaders -I/usr/include/python3.9 -c pherror.c -o build/temp.linux-armv7l-cpython-39/pherror.o -fopenmp 2024-03-15T13:38:47,211 pherror.c: In function ‘cfread’: 2024-03-15T13:38:47,211 pherror.c:58:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2024-03-15T13:38:47,211 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2024-03-15T13:38:47,211 | ^~ 2024-03-15T13:38:47,302 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 -Idnjheaders -I/usr/include/python3.9 -c phy.c -o build/temp.linux-armv7l-cpython-39/phy.o -fopenmp 2024-03-15T13:38:48,217 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 -Idnjheaders -I/usr/include/python3.9 -c pydnj.c -o build/temp.linux-armv7l-cpython-39/pydnj.o -fopenmp 2024-03-15T13:38:48,516 In file included from pydnj.c:11: 2024-03-15T13:38:48,516 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2024-03-15T13:38:48,516 20 | #define _XOPEN_SOURCE 600 2024-03-15T13:38:48,516 | 2024-03-15T13:38:48,516 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2024-03-15T13:38:48,517 from /usr/include/limits.h:26, 2024-03-15T13:38:48,517 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:195, 2024-03-15T13:38:48,517 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/syslimits.h:7, 2024-03-15T13:38:48,517 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:34, 2024-03-15T13:38:48,517 from /usr/include/python3.9/Python.h:11, 2024-03-15T13:38:48,517 from pydnj.c:1: 2024-03-15T13:38:48,517 /usr/include/features.h:207: note: this is the location of the previous definition 2024-03-15T13:38:48,518 207 | # define _XOPEN_SOURCE 700 2024-03-15T13:38:48,518 | 2024-03-15T13:38:48,531 pydnj.c: In function ‘py_build’: 2024-03-15T13:38:48,531 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2024-03-15T13:38:48,531 165 | p = omp_get_num_procs(); 2024-03-15T13:38:48,531 | ^~~~~~~~~~~~~~~~~ 2024-03-15T13:38:48,712 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 -Idnjheaders -I/usr/include/python3.9 -c qseqs.c -o build/temp.linux-armv7l-cpython-39/qseqs.o -fopenmp 2024-03-15T13:38:48,900 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 -Idnjheaders -I/usr/include/python3.9 -c str.c -o build/temp.linux-armv7l-cpython-39/str.o -fopenmp 2024-03-15T13:38:49,009 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 -Idnjheaders -I/usr/include/python3.9 -c tmp.c -o build/temp.linux-armv7l-cpython-39/tmp.o -fopenmp 2024-03-15T13:38:49,198 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 -Idnjheaders -I/usr/include/python3.9 -c vector.c -o build/temp.linux-armv7l-cpython-39/vector.o -fopenmp 2024-03-15T13:38:49,350 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/bytescale.o build/temp.linux-armv7l-cpython-39/dnj.o build/temp.linux-armv7l-cpython-39/filebuff.o build/temp.linux-armv7l-cpython-39/hclust.o build/temp.linux-armv7l-cpython-39/matrix.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/nj.o build/temp.linux-armv7l-cpython-39/nwck.o build/temp.linux-armv7l-cpython-39/pherror.o build/temp.linux-armv7l-cpython-39/phy.o build/temp.linux-armv7l-cpython-39/pydnj.o build/temp.linux-armv7l-cpython-39/qseqs.o build/temp.linux-armv7l-cpython-39/str.o build/temp.linux-armv7l-cpython-39/tmp.o build/temp.linux-armv7l-cpython-39/vector.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -fopenmp 2024-03-15T13:38:49,519 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-03-15T13:38:49,520 !! 2024-03-15T13:38:49,520 ******************************************************************************** 2024-03-15T13:38:49,520 Please avoid running ``setup.py`` directly. 2024-03-15T13:38:49,520 Instead, use pypa/build, pypa/installer or other 2024-03-15T13:38:49,520 standards-based tools. 2024-03-15T13:38:49,521 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-03-15T13:38:49,521 ******************************************************************************** 2024-03-15T13:38:49,521 !! 2024-03-15T13:38:49,521 self.initialize_options() 2024-03-15T13:38:49,543 installing to build/bdist.linux-armv7l/wheel 2024-03-15T13:38:49,543 running install 2024-03-15T13:38:49,569 running install_lib 2024-03-15T13:38:49,592 creating build/bdist.linux-armv7l 2024-03-15T13:38:49,592 creating build/bdist.linux-armv7l/wheel 2024-03-15T13:38:49,594 copying build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-03-15T13:38:49,598 copying build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-03-15T13:38:49,606 copying build/lib.linux-armv7l-cpython-39/kssdtree.py -> build/bdist.linux-armv7l/wheel 2024-03-15T13:38:49,608 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2024-03-15T13:38:49,619 copying build/lib.linux-armv7l-cpython-39/toolutils.py -> build/bdist.linux-armv7l/wheel 2024-03-15T13:38:49,621 running install_egg_info 2024-03-15T13:38:49,650 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/kssdtree-1.1.1-py3.9.egg-info 2024-03-15T13:38:49,661 running install_scripts 2024-03-15T13:38:49,678 creating build/bdist.linux-armv7l/wheel/kssdtree-1.1.1.dist-info/WHEEL 2024-03-15T13:38:49,681 creating '/tmp/pip-wheel-vtlrfh49/kssdtree-1.1.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-03-15T13:38:49,798 adding 'dnj.cpython-39-arm-linux-gnueabihf.so' 2024-03-15T13:38:49,892 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2024-03-15T13:38:49,897 adding 'kssdtree.py' 2024-03-15T13:38:49,919 adding 'nj.cpython-39-arm-linux-gnueabihf.so' 2024-03-15T13:38:49,922 adding 'toolutils.py' 2024-03-15T13:38:49,924 adding 'kssdtree-1.1.1.dist-info/METADATA' 2024-03-15T13:38:49,925 adding 'kssdtree-1.1.1.dist-info/WHEEL' 2024-03-15T13:38:49,926 adding 'kssdtree-1.1.1.dist-info/dependency_links.txt' 2024-03-15T13:38:49,927 adding 'kssdtree-1.1.1.dist-info/top_level.txt' 2024-03-15T13:38:49,928 adding 'kssdtree-1.1.1.dist-info/RECORD' 2024-03-15T13:38:49,936 removing build/bdist.linux-armv7l/wheel 2024-03-15T13:38:50,074 Building wheel for kssdtree (setup.py): finished with status 'done' 2024-03-15T13:38:50,080 Created wheel for kssdtree: filename=kssdtree-1.1.1-cp39-cp39-linux_armv7l.whl size=376305 sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 2024-03-15T13:38:50,082 Stored in directory: /tmp/pip-ephem-wheel-cache-3ga_fw6p/wheels/90/dc/3a/4a660d0b409851f5c71a211971f6550adb5c17ae0d39bffa0b 2024-03-15T13:38:50,092 Successfully built kssdtree 2024-03-15T13:38:50,103 Removed build tracker: '/tmp/pip-build-tracker-h0pwnt62'