2024-11-20T10:32:09,964 Disabling truststore because Python version isn't 3.10+ 2024-11-20T10:32:10,481 Created temporary directory: /tmp/pip-build-tracker-8yswnzkw 2024-11-20T10:32:10,482 Initialized build tracking at /tmp/pip-build-tracker-8yswnzkw 2024-11-20T10:32:10,482 Created build tracker: /tmp/pip-build-tracker-8yswnzkw 2024-11-20T10:32:10,483 Entered build tracker: /tmp/pip-build-tracker-8yswnzkw 2024-11-20T10:32:10,483 Created temporary directory: /tmp/pip-wheel-pfbr796o 2024-11-20T10:32:10,489 Created temporary directory: /tmp/pip-ephem-wheel-cache-bsdtw51a 2024-11-20T10:32:10,534 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-11-20T10:32:10,537 2 location(s) to search for versions of kssdutils: 2024-11-20T10:32:10,537 * https://pypi.org/simple/kssdutils/ 2024-11-20T10:32:10,537 * https://www.piwheels.org/simple/kssdutils/ 2024-11-20T10:32:10,538 Fetching project page and analyzing links: https://pypi.org/simple/kssdutils/ 2024-11-20T10:32:10,538 Getting page https://pypi.org/simple/kssdutils/ 2024-11-20T10:32:10,539 Found index url https://pypi.org/simple/ 2024-11-20T10:32:10,636 Fetched page https://pypi.org/simple/kssdutils/ as application/vnd.pypi.simple.v1+json 2024-11-20T10:32:10,638 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 2024-11-20T10:32:10,638 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 2024-11-20T10:32:10,638 Found link https://files.pythonhosted.org/packages/57/17/dd41697db7220423d0ab77f9f035b9a347edc1edefc2c35d9890178cbe17/kssdutils-1.0.2.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.0.2 2024-11-20T10:32:10,639 Found link https://files.pythonhosted.org/packages/3e/92/7a94130bd54e0e3dd20c1a609aef2f24875b86e9d61752f63b500d3f86f5/kssdutils-1.0.3.tar.gz (from https://pypi.org/simple/kssdutils/), version: 1.0.3 2024-11-20T10:32:10,639 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdutils/ 2024-11-20T10:32:10,639 Getting page https://www.piwheels.org/simple/kssdutils/ 2024-11-20T10:32:10,640 Found index url https://www.piwheels.org/simple/ 2024-11-20T10:32:10,687 Fetched page https://www.piwheels.org/simple/kssdutils/ as text/html 2024-11-20T10:32:10,691 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp311-cp311-linux_armv6l.whl#sha256=85c10f6c3223fb99e39dfddbef722fd2913bd5c63f089283ce23dae20c6a4a4d (from https://www.piwheels.org/simple/kssdutils/) 2024-11-20T10:32:10,691 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.2-cp311-cp311-linux_armv7l.whl#sha256=85c10f6c3223fb99e39dfddbef722fd2913bd5c63f089283ce23dae20c6a4a4d (from https://www.piwheels.org/simple/kssdutils/) 2024-11-20T10:32:10,691 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/) 2024-11-20T10:32:10,692 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/) 2024-11-20T10:32:10,692 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp39-cp39-linux_armv6l.whl#sha256=29a695a62aae6fa18fcad3ae6bfc6bbe19f545f66740fde177ddbf23efa45d15 (from https://www.piwheels.org/simple/kssdutils/) 2024-11-20T10:32:10,692 Skipping link: No binaries permitted for kssdutils: https://www.piwheels.org/simple/kssdutils/kssdutils-1.0.1-cp39-cp39-linux_armv7l.whl#sha256=29a695a62aae6fa18fcad3ae6bfc6bbe19f545f66740fde177ddbf23efa45d15 (from https://www.piwheels.org/simple/kssdutils/) 2024-11-20T10:32:10,692 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/) 2024-11-20T10:32:10,692 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/) 2024-11-20T10:32:10,692 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/) 2024-11-20T10:32:10,693 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/) 2024-11-20T10:32:10,693 Skipping link: not a file: https://www.piwheels.org/simple/kssdutils/ 2024-11-20T10:32:10,693 Skipping link: not a file: https://pypi.org/simple/kssdutils/ 2024-11-20T10:32:10,709 Given no hashes to check 1 links for project 'kssdutils': discarding no candidates 2024-11-20T10:32:10,711 Collecting kssdutils==1.0.2 2024-11-20T10:32:10,713 Created temporary directory: /tmp/pip-unpack-b3a7m98q 2024-11-20T10:32:10,729 Downloading kssdutils-1.0.2.tar.gz (44 kB) 2024-11-20T10:32:10,811 Added kssdutils==1.0.2 from https://files.pythonhosted.org/packages/57/17/dd41697db7220423d0ab77f9f035b9a347edc1edefc2c35d9890178cbe17/kssdutils-1.0.2.tar.gz to build tracker '/tmp/pip-build-tracker-8yswnzkw' 2024-11-20T10:32:10,814 Running setup.py (path:/tmp/pip-wheel-pfbr796o/kssdutils_2b7ac77806964b60a3c95f745186f830/setup.py) egg_info for package kssdutils 2024-11-20T10:32:10,814 Created temporary directory: /tmp/pip-pip-egg-info-uqxwq21e 2024-11-20T10:32:10,815 Preparing metadata (setup.py): started 2024-11-20T10:32:10,816 Running command python setup.py egg_info 2024-11-20T10:32:11,905 running egg_info 2024-11-20T10:32:11,936 creating /tmp/pip-pip-egg-info-uqxwq21e/kssdutils.egg-info 2024-11-20T10:32:11,937 writing /tmp/pip-pip-egg-info-uqxwq21e/kssdutils.egg-info/PKG-INFO 2024-11-20T10:32:11,941 writing dependency_links to /tmp/pip-pip-egg-info-uqxwq21e/kssdutils.egg-info/dependency_links.txt 2024-11-20T10:32:11,943 writing top-level names to /tmp/pip-pip-egg-info-uqxwq21e/kssdutils.egg-info/top_level.txt 2024-11-20T10:32:11,944 writing manifest file '/tmp/pip-pip-egg-info-uqxwq21e/kssdutils.egg-info/SOURCES.txt' 2024-11-20T10:32:12,056 reading manifest file '/tmp/pip-pip-egg-info-uqxwq21e/kssdutils.egg-info/SOURCES.txt' 2024-11-20T10:32:12,058 reading manifest template 'MANIFEST.in' 2024-11-20T10:32:12,064 warning: no files found matching '*.h' under directory 'njheaders' 2024-11-20T10:32:12,064 warning: no files found matching '*.h' under directory 'dnjheaders' 2024-11-20T10:32:12,068 writing manifest file '/tmp/pip-pip-egg-info-uqxwq21e/kssdutils.egg-info/SOURCES.txt' 2024-11-20T10:32:12,157 Preparing metadata (setup.py): finished with status 'done' 2024-11-20T10:32:12,161 Source in /tmp/pip-wheel-pfbr796o/kssdutils_2b7ac77806964b60a3c95f745186f830 has version 1.0.2, which satisfies requirement kssdutils==1.0.2 from https://files.pythonhosted.org/packages/57/17/dd41697db7220423d0ab77f9f035b9a347edc1edefc2c35d9890178cbe17/kssdutils-1.0.2.tar.gz 2024-11-20T10:32:12,162 Removed kssdutils==1.0.2 from https://files.pythonhosted.org/packages/57/17/dd41697db7220423d0ab77f9f035b9a347edc1edefc2c35d9890178cbe17/kssdutils-1.0.2.tar.gz from build tracker '/tmp/pip-build-tracker-8yswnzkw' 2024-11-20T10:32:12,166 Created temporary directory: /tmp/pip-unpack-adnhkb7a 2024-11-20T10:32:12,167 Created temporary directory: /tmp/pip-unpack-sfjnriwj 2024-11-20T10:32:12,167 Building wheels for collected packages: kssdutils 2024-11-20T10:32:12,171 Created temporary directory: /tmp/pip-wheel-1wwtzhdq 2024-11-20T10:32:12,171 Building wheel for kssdutils (setup.py): started 2024-11-20T10:32:12,172 Destination directory: /tmp/pip-wheel-1wwtzhdq 2024-11-20T10:32:12,173 Running command python setup.py bdist_wheel 2024-11-20T10:32:13,184 running bdist_wheel 2024-11-20T10:32:13,319 running build 2024-11-20T10:32:13,319 running build_py 2024-11-20T10:32:13,348 creating build/lib.linux-armv7l-cpython-39 2024-11-20T10:32:13,349 copying kssdutils.py -> build/lib.linux-armv7l-cpython-39 2024-11-20T10:32:13,351 running egg_info 2024-11-20T10:32:13,377 writing kssdutils.egg-info/PKG-INFO 2024-11-20T10:32:13,379 writing dependency_links to kssdutils.egg-info/dependency_links.txt 2024-11-20T10:32:13,381 writing top-level names to kssdutils.egg-info/top_level.txt 2024-11-20T10:32:13,410 reading manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-11-20T10:32:13,413 reading manifest template 'MANIFEST.in' 2024-11-20T10:32:13,418 warning: no files found matching '*.h' under directory 'njheaders' 2024-11-20T10:32:13,418 warning: no files found matching '*.h' under directory 'dnjheaders' 2024-11-20T10:32:13,423 writing manifest file 'kssdutils.egg-info/SOURCES.txt' 2024-11-20T10:32:13,424 running build_ext 2024-11-20T10:32:13,904 building 'kssd' extension 2024-11-20T10:32:13,905 creating build/temp.linux-armv7l-cpython-39 2024-11-20T10:32:13,907 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 2024-11-20T10:32:14,081 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2024-11-20T10:32:14,081 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-20T10:32:14,082 109 | for (unsigned int i = 0; i < comp_num; i++) { 2024-11-20T10:32:14,082 | ^ 2024-11-20T10:32:14,084 co2mco.c: In function ‘co2unitllmco’: 2024-11-20T10:32:14,084 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-20T10:32:14,084 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2024-11-20T10:32:14,085 | ^ 2024-11-20T10:32:14,702 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 2024-11-20T10:32:15,000 command_composite.c: In function ‘get_species_abundance’: 2024-11-20T10:32:15,001 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-20T10:32:15,001 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2024-11-20T10:32:15,001 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,001 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2024-11-20T10:32:15,001 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2024-11-20T10:32:15,001 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,002 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:15,002 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-20T10:32:15,002 | ^ 2024-11-20T10:32:15,002 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-20T10:32:15,002 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2024-11-20T10:32:15,002 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,002 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:15,002 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-20T10:32:15,003 | ^ 2024-11-20T10:32:15,003 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-20T10:32:15,003 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2024-11-20T10:32:15,003 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,003 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:15,003 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-20T10:32:15,004 | ^ 2024-11-20T10:32:15,004 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-20T10:32:15,004 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2024-11-20T10:32:15,004 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,004 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:15,004 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-20T10:32:15,004 | ^ 2024-11-20T10:32:15,004 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2024-11-20T10:32:15,005 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2024-11-20T10:32:15,005 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,005 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:15,005 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-20T10:32:15,005 | ^ 2024-11-20T10:32:15,005 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2024-11-20T10:32:15,005 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2024-11-20T10:32:15,005 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,271 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 2024-11-20T10:32:15,461 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-20T10:32:15,462 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=] 2024-11-20T10:32:15,462 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-20T10:32:15,462 | ~~^ 2024-11-20T10:32:15,462 | | 2024-11-20T10:32:15,462 | long unsigned int 2024-11-20T10:32:15,462 | %u 2024-11-20T10:32:15,462 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-20T10:32:15,462 | ~~~~~~~ 2024-11-20T10:32:15,463 | | 2024-11-20T10:32:15,463 | size_t {aka unsigned int} 2024-11-20T10:32:15,463 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=] 2024-11-20T10:32:15,463 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-20T10:32:15,463 | ~~^ 2024-11-20T10:32:15,463 | | 2024-11-20T10:32:15,463 | long unsigned int 2024-11-20T10:32:15,463 | %u 2024-11-20T10:32:15,464 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-20T10:32:15,464 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-20T10:32:15,464 | ~~~~~~~~~ 2024-11-20T10:32:15,464 | | 2024-11-20T10:32:15,464 | size_t {aka unsigned int} 2024-11-20T10:32:15,464 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-20T10:32:15,464 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-20T10:32:15,465 | ~~^ 2024-11-20T10:32:15,465 | | 2024-11-20T10:32:15,465 | long unsigned int 2024-11-20T10:32:15,465 | %u 2024-11-20T10:32:15,465 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-20T10:32:15,465 679 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-20T10:32:15,465 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,465 | | 2024-11-20T10:32:15,466 | unsigned int 2024-11-20T10:32:15,466 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-20T10:32:15,467 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2024-11-20T10:32:15,467 | ^ 2024-11-20T10:32:15,473 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-20T10:32:15,474 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=] 2024-11-20T10:32:15,474 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-20T10:32:15,474 | ~~^ ~~~~~~~ 2024-11-20T10:32:15,474 | | | 2024-11-20T10:32:15,475 | long unsigned int size_t {aka unsigned int} 2024-11-20T10:32:15,475 | %u 2024-11-20T10:32:15,475 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=] 2024-11-20T10:32:15,476 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-20T10:32:15,476 | ~~^ 2024-11-20T10:32:15,476 | | 2024-11-20T10:32:15,476 | long unsigned int 2024-11-20T10:32:15,476 | %u 2024-11-20T10:32:15,476 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-20T10:32:15,476 | ~~~~~~~~~ 2024-11-20T10:32:15,476 | | 2024-11-20T10:32:15,477 | size_t {aka unsigned int} 2024-11-20T10:32:15,477 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-20T10:32:15,477 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2024-11-20T10:32:15,477 | ~~^ 2024-11-20T10:32:15,477 | | 2024-11-20T10:32:15,477 | long unsigned int 2024-11-20T10:32:15,478 | %u 2024-11-20T10:32:15,478 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2024-11-20T10:32:15,478 865 | (size_t) b * unitsz_distf_mapped); 2024-11-20T10:32:15,478 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,478 | | 2024-11-20T10:32:15,478 | unsigned int 2024-11-20T10:32:15,479 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2024-11-20T10:32:15,479 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2024-11-20T10:32:15,479 | ^~~~~~~ 2024-11-20T10:32:15,480 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2024-11-20T10:32:15,480 809 | struct stat cbd_fcode_stat; 2024-11-20T10:32:15,480 | ^~~~~~~~~~~~~~ 2024-11-20T10:32:15,480 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2024-11-20T10:32:15,480 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-20T10:32:15,480 | ^~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,481 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2024-11-20T10:32:15,481 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2024-11-20T10:32:15,481 | ^~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,486 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-20T10:32:15,488 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=] 2024-11-20T10:32:15,488 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-20T10:32:15,488 | ~~^ 2024-11-20T10:32:15,488 | | 2024-11-20T10:32:15,488 | long unsigned int 2024-11-20T10:32:15,488 | %u 2024-11-20T10:32:15,488 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-20T10:32:15,489 | ~~~~~~~ 2024-11-20T10:32:15,489 | | 2024-11-20T10:32:15,489 | size_t {aka unsigned int} 2024-11-20T10:32:15,490 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=] 2024-11-20T10:32:15,490 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-20T10:32:15,490 | ~~^ 2024-11-20T10:32:15,490 | | 2024-11-20T10:32:15,490 | long unsigned int 2024-11-20T10:32:15,490 | %u 2024-11-20T10:32:15,490 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-20T10:32:15,490 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-20T10:32:15,491 | ~~~~~~~~~ 2024-11-20T10:32:15,491 | | 2024-11-20T10:32:15,491 | size_t {aka unsigned int} 2024-11-20T10:32:15,491 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2024-11-20T10:32:15,491 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2024-11-20T10:32:15,492 | ~~^ 2024-11-20T10:32:15,492 | | 2024-11-20T10:32:15,492 | long unsigned int 2024-11-20T10:32:15,492 | %u 2024-11-20T10:32:15,492 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2024-11-20T10:32:15,492 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2024-11-20T10:32:15,492 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,492 | | 2024-11-20T10:32:15,493 | unsigned int 2024-11-20T10:32:15,493 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2024-11-20T10:32:15,493 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2024-11-20T10:32:15,493 | ^ 2024-11-20T10:32:15,496 command_dist.c: In function ‘mco_co_dist_core’: 2024-11-20T10:32:15,497 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-20T10:32:15,497 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2024-11-20T10:32:15,497 | ^ 2024-11-20T10:32:15,503 command_dist.c: In function ‘koc_dist_print_nobin’: 2024-11-20T10:32:15,504 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-20T10:32:15,504 1239 | for (int rid = 0; rid < ref_num; rid++) 2024-11-20T10:32:15,504 | ^ 2024-11-20T10:32:15,506 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-20T10:32:15,506 1245 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-20T10:32:15,506 | ^ 2024-11-20T10:32:15,512 command_dist.c: In function ‘dist_print_nobin’: 2024-11-20T10:32:15,513 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-20T10:32:15,513 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2024-11-20T10:32:15,513 | ^ 2024-11-20T10:32:15,515 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-20T10:32:15,515 1356 | for (int rid = 0; rid < ref_num; rid++) { 2024-11-20T10:32:15,515 | ^ 2024-11-20T10:32:15,516 command_dist.c:1380:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-20T10:32:15,516 1380 | for (int rid = 0; rid < ref_num; rid++) 2024-11-20T10:32:15,516 | ^ 2024-11-20T10:32:15,517 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2024-11-20T10:32:15,517 1382 | for (int rid = 0; rid < ref_num; rid++) 2024-11-20T10:32:15,517 | ^ 2024-11-20T10:32:15,772 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2024-11-20T10:32:15,772 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2024-11-20T10:32:15,772 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2024-11-20T10:32:15,772 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:15,772 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2024-11-20T10:32:15,773 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2024-11-20T10:32:15,773 | ^~~~~~~~~~~~ 2024-11-20T10:32:16,495 command_dist.c: In function ‘get_dim_shuffle’: 2024-11-20T10:32:16,495 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2024-11-20T10:32:16,495 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-20T10:32:16,495 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:16,496 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2024-11-20T10:32:16,496 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2024-11-20T10:32:16,496 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,284 command_dist.c: In function ‘mco_cbd_co_dist’: 2024-11-20T10:32:17,284 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:17,285 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-20T10:32:17,285 | ^~ ~~~~~~~~~ 2024-11-20T10:32:17,285 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-20T10:32:17,285 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-20T10:32:17,285 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,286 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-20T10:32:17,286 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-20T10:32:17,286 | ^~~~~~~~~~~~~~~ 2024-11-20T10:32:17,286 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-20T10:32:17,286 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-20T10:32:17,286 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,287 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-20T10:32:17,287 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-20T10:32:17,288 | ^~~~~~~~~~~ 2024-11-20T10:32:17,288 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-20T10:32:17,288 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-20T10:32:17,288 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,288 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-20T10:32:17,288 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-20T10:32:17,288 | ^~~~~ 2024-11-20T10:32:17,289 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-20T10:32:17,289 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-20T10:32:17,289 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,495 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2024-11-20T10:32:17,496 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:17,496 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-20T10:32:17,496 | ^~ ~~~~~~~~~ 2024-11-20T10:32:17,496 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-20T10:32:17,496 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-20T10:32:17,497 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,497 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-20T10:32:17,497 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-20T10:32:17,497 | ^~~~~~~~~~~~~~~ 2024-11-20T10:32:17,498 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-20T10:32:17,498 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-20T10:32:17,498 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,498 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-20T10:32:17,498 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-20T10:32:17,499 | ^~~~~~~~~~~~~ 2024-11-20T10:32:17,499 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-20T10:32:17,499 823 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-20T10:32:17,499 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,500 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:17,500 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-20T10:32:17,500 | ^ 2024-11-20T10:32:17,501 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2024-11-20T10:32:17,501 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-20T10:32:17,501 | ^~~~~~~~~~ 2024-11-20T10:32:17,501 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-20T10:32:17,501 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2024-11-20T10:32:17,501 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,502 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:17,502 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-20T10:32:17,502 | ^ 2024-11-20T10:32:17,502 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2024-11-20T10:32:17,503 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-20T10:32:17,503 | ^~~~~~~~~~ 2024-11-20T10:32:17,503 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2024-11-20T10:32:17,503 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2024-11-20T10:32:17,503 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,739 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2024-11-20T10:32:17,740 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:17,740 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-20T10:32:17,740 | ^~ ~~~~~~~~~ 2024-11-20T10:32:17,740 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2024-11-20T10:32:17,741 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2024-11-20T10:32:17,741 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,741 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-20T10:32:17,742 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-20T10:32:17,742 | ^~~~~~~~~~~~~~~ 2024-11-20T10:32:17,742 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2024-11-20T10:32:17,742 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2024-11-20T10:32:17,742 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,743 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-20T10:32:17,743 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-20T10:32:17,743 | ^~~~~~~~~~~~~ 2024-11-20T10:32:17,744 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-20T10:32:17,744 990 | sprintf(distf, "%s/distance.out", distout_dir); 2024-11-20T10:32:17,744 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,745 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-20T10:32:17,745 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-20T10:32:17,745 | ^~~~~~~~~~~ 2024-11-20T10:32:17,746 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2024-11-20T10:32:17,746 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2024-11-20T10:32:17,746 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:17,746 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2024-11-20T10:32:17,746 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-20T10:32:17,747 | ^~~~~ 2024-11-20T10:32:17,747 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-20T10:32:17,747 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2024-11-20T10:32:17,747 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:18,001 command_dist.c: In function ‘combine_queries’: 2024-11-20T10:32:18,002 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-20T10:32:18,002 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-20T10:32:18,002 | ^ 2024-11-20T10:32:18,003 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-20T10:32:18,003 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2024-11-20T10:32:18,003 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:18,004 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-20T10:32:18,004 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-20T10:32:18,004 | ^ 2024-11-20T10:32:18,005 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-20T10:32:18,005 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2024-11-20T10:32:18,005 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:18,007 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:18,007 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-20T10:32:18,007 | ^~ ~~~~~~~~ 2024-11-20T10:32:18,008 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2024-11-20T10:32:18,008 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2024-11-20T10:32:18,008 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:18,476 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 2024-11-20T10:32:18,644 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 2024-11-20T10:32:18,791 command_set.c: In function ‘sketch_operate’: 2024-11-20T10:32:18,791 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2024-11-20T10:32:18,792 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2024-11-20T10:32:18,792 | ^ 2024-11-20T10:32:18,801 command_set.c: In function ‘combin_subset_pans’: 2024-11-20T10:32:18,801 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-20T10:32:18,802 457 | free(co_dstat_fpath); 2024-11-20T10:32:18,802 | ^~~~~~~~~~~~~~ 2024-11-20T10:32:18,802 In file included from kssdheaders/global_basic.h:159, 2024-11-20T10:32:18,802 from command_set.c:15: 2024-11-20T10:32:18,802 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-20T10:32:18,802 565 | extern void free (void *__ptr) __THROW; 2024-11-20T10:32:18,803 | ~~~~~~^~~~~ 2024-11-20T10:32:18,806 command_set.c: In function ‘grouping_genomes’: 2024-11-20T10:32:18,807 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2024-11-20T10:32:18,807 562 | free(co_dstat_fpath); 2024-11-20T10:32:18,807 | ^~~~~~~~~~~~~~ 2024-11-20T10:32:18,807 In file included from kssdheaders/global_basic.h:159, 2024-11-20T10:32:18,807 from command_set.c:15: 2024-11-20T10:32:18,807 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2024-11-20T10:32:18,807 565 | extern void free (void *__ptr) __THROW; 2024-11-20T10:32:18,808 | ~~~~~~^~~~~ 2024-11-20T10:32:18,922 command_set.c: In function ‘sketch_union’: 2024-11-20T10:32:18,923 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-20T10:32:18,923 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:18,923 | ^ 2024-11-20T10:32:18,923 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-20T10:32:18,923 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:18,924 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:18,924 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:18,924 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-20T10:32:18,924 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:18,924 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-20T10:32:18,924 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-20T10:32:18,924 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:18,925 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:18,925 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-20T10:32:18,925 | ^~ ~~~~~~~~~~ 2024-11-20T10:32:18,925 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-20T10:32:18,925 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2024-11-20T10:32:18,925 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,036 command_set.c: In function ‘sketch_operate’: 2024-11-20T10:32:19,036 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,036 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-20T10:32:19,036 | ^~ ~~~~~~~~~~ 2024-11-20T10:32:19,037 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2024-11-20T10:32:19,037 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2024-11-20T10:32:19,037 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,037 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,037 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-20T10:32:19,037 | ^~ ~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,037 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-20T10:32:19,037 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2024-11-20T10:32:19,038 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,038 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,038 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-20T10:32:19,038 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:19,038 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-20T10:32:19,038 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-20T10:32:19,038 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,038 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,039 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-20T10:32:19,039 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:19,039 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-20T10:32:19,039 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2024-11-20T10:32:19,039 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,039 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,039 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-20T10:32:19,039 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:19,040 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-20T10:32:19,040 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2024-11-20T10:32:19,040 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,040 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,040 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-20T10:32:19,040 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:19,040 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-20T10:32:19,041 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2024-11-20T10:32:19,041 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,041 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-20T10:32:19,041 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:19,041 | ^ 2024-11-20T10:32:19,041 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-20T10:32:19,041 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:19,041 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,194 command_set.c: In function ‘uniq_sketch_union’: 2024-11-20T10:32:19,195 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-20T10:32:19,195 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:19,195 | ^ 2024-11-20T10:32:19,195 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-20T10:32:19,195 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:19,196 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,196 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,196 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-20T10:32:19,196 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:19,196 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-20T10:32:19,196 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2024-11-20T10:32:19,197 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,197 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,197 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-20T10:32:19,197 | ^~ ~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,197 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2024-11-20T10:32:19,197 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2024-11-20T10:32:19,197 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,322 command_set.c: In function ‘combin_pans’: 2024-11-20T10:32:19,322 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,322 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-20T10:32:19,322 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:19,322 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2024-11-20T10:32:19,323 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-20T10:32:19,323 | ^~~~~~~~~~ 2024-11-20T10:32:19,323 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2024-11-20T10:32:19,323 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-20T10:32:19,323 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,323 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,323 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-20T10:32:19,323 | ^~ ~~~~~~~~~~ 2024-11-20T10:32:19,324 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2024-11-20T10:32:19,324 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-20T10:32:19,324 | ^~~~~~~~~~ 2024-11-20T10:32:19,324 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2024-11-20T10:32:19,324 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-20T10:32:19,324 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,324 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-20T10:32:19,324 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:19,325 | ^ 2024-11-20T10:32:19,325 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-20T10:32:19,325 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:19,325 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,507 command_set.c: In function ‘combin_subset_pans’: 2024-11-20T10:32:19,508 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,508 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-20T10:32:19,508 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:19,508 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-20T10:32:19,508 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-20T10:32:19,508 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,509 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,509 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-20T10:32:19,509 | ^~ ~~~~~~~~~~ 2024-11-20T10:32:19,509 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-20T10:32:19,509 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-20T10:32:19,509 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,509 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,510 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-20T10:32:19,510 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:19,510 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-20T10:32:19,510 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-20T10:32:19,510 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,511 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,512 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-20T10:32:19,512 | ^~ ~~~~~~~~~~ 2024-11-20T10:32:19,512 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-20T10:32:19,512 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-20T10:32:19,512 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,512 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-20T10:32:19,512 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:19,512 | ^ 2024-11-20T10:32:19,513 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-20T10:32:19,513 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:19,513 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,714 command_set.c: In function ‘grouping_genomes’: 2024-11-20T10:32:19,714 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,714 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-20T10:32:19,714 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:19,715 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-20T10:32:19,715 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2024-11-20T10:32:19,715 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,715 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,715 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-20T10:32:19,715 | ^~ ~~~~~~~~~~ 2024-11-20T10:32:19,716 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-20T10:32:19,716 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2024-11-20T10:32:19,716 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,717 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,718 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-20T10:32:19,718 | ^~ ~~~~~~~~~~~ 2024-11-20T10:32:19,718 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2024-11-20T10:32:19,718 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2024-11-20T10:32:19,718 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,719 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2024-11-20T10:32:19,719 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-20T10:32:19,719 | ^~ ~~~~~~~~~~ 2024-11-20T10:32:19,719 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2024-11-20T10:32:19,719 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2024-11-20T10:32:19,720 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,720 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2024-11-20T10:32:19,720 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:19,720 | ^ 2024-11-20T10:32:19,720 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2024-11-20T10:32:19,721 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2024-11-20T10:32:19,721 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:19,993 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 2024-11-20T10:32:20,271 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 2024-11-20T10:32:20,422 global_basic.c: In function ‘organize_infile_list’: 2024-11-20T10:32:20,422 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2024-11-20T10:32:20,422 195 | while (isspace(*buf)) buf++; 2024-11-20T10:32:20,422 | ^~~~~~~ 2024-11-20T10:32:20,423 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=] 2024-11-20T10:32:20,423 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-20T10:32:20,423 | ~~^ 2024-11-20T10:32:20,424 | | 2024-11-20T10:32:20,424 | long unsigned int 2024-11-20T10:32:20,424 | %u 2024-11-20T10:32:20,424 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-20T10:32:20,424 | ~~~~~~~~~~~ 2024-11-20T10:32:20,424 | | 2024-11-20T10:32:20,424 | size_t {aka unsigned int} 2024-11-20T10:32:20,426 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=] 2024-11-20T10:32:20,426 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2024-11-20T10:32:20,426 | ~~^ 2024-11-20T10:32:20,426 | | 2024-11-20T10:32:20,426 | long unsigned int 2024-11-20T10:32:20,426 | %u 2024-11-20T10:32:20,427 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2024-11-20T10:32:20,427 | ~~~~~~~~~~~ 2024-11-20T10:32:20,427 | | 2024-11-20T10:32:20,427 | size_t {aka unsigned int} 2024-11-20T10:32:21,100 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 2024-11-20T10:32:21,253 iseq2comem.c: In function ‘reads2mco’: 2024-11-20T10:32:21,254 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,254 156 | if (base > TL) { 2024-11-20T10:32:21,254 | ^ 2024-11-20T10:32:21,254 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,254 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-20T10:32:21,254 | ^~ 2024-11-20T10:32:21,255 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,255 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-20T10:32:21,255 | ^ 2024-11-20T10:32:21,256 iseq2comem.c: In function ‘fasta2co’: 2024-11-20T10:32:21,256 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,256 239 | if (base > TL) { 2024-11-20T10:32:21,256 | ^ 2024-11-20T10:32:21,256 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,257 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-20T10:32:21,257 | ^~ 2024-11-20T10:32:21,257 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,257 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-20T10:32:21,257 | ^ 2024-11-20T10:32:21,257 iseq2comem.c: In function ‘fastq2co’: 2024-11-20T10:32:21,258 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2024-11-20T10:32:21,258 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2024-11-20T10:32:21,258 | ^~ 2024-11-20T10:32:21,259 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,259 318 | if (base > TL) { 2024-11-20T10:32:21,259 | ^ 2024-11-20T10:32:21,259 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,259 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-20T10:32:21,259 | ^~ 2024-11-20T10:32:21,260 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,260 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-20T10:32:21,260 | ^ 2024-11-20T10:32:21,260 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,260 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2024-11-20T10:32:21,261 | ^ 2024-11-20T10:32:21,262 iseq2comem.c: In function ‘fastq2koc’: 2024-11-20T10:32:21,262 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,262 402 | if (base > TL) { 2024-11-20T10:32:21,262 | ^ 2024-11-20T10:32:21,262 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,263 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-20T10:32:21,263 | ^~ 2024-11-20T10:32:21,263 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,263 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-20T10:32:21,263 | ^ 2024-11-20T10:32:21,268 iseq2comem.c: In function ‘mt_shortreads2koc’: 2024-11-20T10:32:21,268 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,268 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-20T10:32:21,269 | ^~ 2024-11-20T10:32:21,269 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2024-11-20T10:32:21,269 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2024-11-20T10:32:21,269 | ^ 2024-11-20T10:32:22,436 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 2024-11-20T10:32:22,500 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 2024-11-20T10:32:22,622 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 pykssd.c -o build/temp.linux-armv7l-cpython-39/pykssd.o -fopenmp 2024-11-20T10:32:22,937 pykssd.c: In function ‘py_dist_dispatch’: 2024-11-20T10:32:22,937 pykssd.c:329:13: warning: unused variable ‘state1’ [-Wunused-variable] 2024-11-20T10:32:22,938 329 | int state1 = dist_dispatch(&dist_opt_val1); 2024-11-20T10:32:22,938 | ^~~~~~ 2024-11-20T10:32:22,938 pykssd.c:386:13: warning: unused variable ‘state2’ [-Wunused-variable] 2024-11-20T10:32:22,938 386 | int state2 = dist_dispatch(&dist_opt_val2); 2024-11-20T10:32:22,938 | ^~~~~~ 2024-11-20T10:32:22,939 pykssd.c:510:13: warning: unused variable ‘state4’ [-Wunused-variable] 2024-11-20T10:32:22,940 510 | int state4 = dist_dispatch(&dist_opt_val4); 2024-11-20T10:32:22,940 | ^~~~~~ 2024-11-20T10:32:23,083 pykssd.c: In function ‘rename_file’: 2024-11-20T10:32:23,083 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2024-11-20T10:32:23,084 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2024-11-20T10:32:23,084 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2024-11-20T10:32:23,084 pykssd.c:41:15: note: length computed here 2024-11-20T10:32:23,084 41 | int len = strlen(p1); 2024-11-20T10:32:23,084 | ^~~~~~~~~~ 2024-11-20T10:32:23,507 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 2024-11-20T10:32:23,683 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-11-20T10:32:23,683 !! 2024-11-20T10:32:23,684 ******************************************************************************** 2024-11-20T10:32:23,684 Please avoid running ``setup.py`` directly. 2024-11-20T10:32:23,684 Instead, use pypa/build, pypa/installer or other 2024-11-20T10:32:23,684 standards-based tools. 2024-11-20T10:32:23,684 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-11-20T10:32:23,684 ******************************************************************************** 2024-11-20T10:32:23,684 !! 2024-11-20T10:32:23,685 self.initialize_options() 2024-11-20T10:32:23,710 installing to build/bdist.linux-armv7l/wheel 2024-11-20T10:32:23,711 running install 2024-11-20T10:32:23,737 running install_lib 2024-11-20T10:32:23,764 creating build/bdist.linux-armv7l/wheel 2024-11-20T10:32:23,766 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2024-11-20T10:32:23,778 copying build/lib.linux-armv7l-cpython-39/kssdutils.py -> build/bdist.linux-armv7l/wheel/. 2024-11-20T10:32:23,784 running install_egg_info 2024-11-20T10:32:23,817 Copying kssdutils.egg-info to build/bdist.linux-armv7l/wheel/./kssdutils-1.0.2-py3.9.egg-info 2024-11-20T10:32:23,827 running install_scripts 2024-11-20T10:32:23,879 creating build/bdist.linux-armv7l/wheel/kssdutils-1.0.2.dist-info/WHEEL 2024-11-20T10:32:23,883 creating '/tmp/pip-wheel-1wwtzhdq/kssdutils-1.0.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-11-20T10:32:23,977 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2024-11-20T10:32:23,982 adding 'kssdutils.py' 2024-11-20T10:32:23,984 adding 'kssdutils-1.0.2.dist-info/METADATA' 2024-11-20T10:32:23,985 adding 'kssdutils-1.0.2.dist-info/WHEEL' 2024-11-20T10:32:23,987 adding 'kssdutils-1.0.2.dist-info/dependency_links.txt' 2024-11-20T10:32:23,988 adding 'kssdutils-1.0.2.dist-info/top_level.txt' 2024-11-20T10:32:23,989 adding 'kssdutils-1.0.2.dist-info/RECORD' 2024-11-20T10:32:23,994 removing build/bdist.linux-armv7l/wheel 2024-11-20T10:32:24,123 Building wheel for kssdutils (setup.py): finished with status 'done' 2024-11-20T10:32:24,128 Created wheel for kssdutils: filename=kssdutils-1.0.2-cp39-cp39-linux_armv7l.whl size=179764 sha256=809195defd92c452797e9a87d99cfa8217c9ca4800c4a57d3e669846368160b1 2024-11-20T10:32:24,129 Stored in directory: /tmp/pip-ephem-wheel-cache-bsdtw51a/wheels/bc/83/ac/65289e14b8c365e186dd9cd8a2be562e5b56ca4743f4a0161b 2024-11-20T10:32:24,139 Successfully built kssdutils 2024-11-20T10:32:24,149 Removed build tracker: '/tmp/pip-build-tracker-8yswnzkw'