Running phase: unpackPhase unpacking source archive /nix/store/97nwzkrxz4ir9rp6b1nrar5mrnp3l0ha-source source root is source Running phase: patchPhase applying patch /nix/store/fixzrdsv39b2b3zvj3d8c264640w0gbq-allocate-enough-memory.patch patching file kssd.c Running phase: updateAutotoolsGnuConfigScriptsPhase Running phase: configurePhase no configure script, doing nothing Running phase: buildPhase build flags: SHELL=/nix/store/11ciq72n4fdv8rw6wgjgasfv4mjs1jrw-bash-5.2p37/bin/bash gcc -std=gnu11 -Wall -Wno-unused-result -O3 -ggdb -lz -fopenmp *.c -o ./kssd -lm command_composite.c: In function 'get_species_abundance': command_composite.c:158:27: warning: '.' directive writing 1 byte into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 158 | sprintf(tmpfname,"%s/%s.%d",composite_opt->refdir,skch_prefix,c); | ^ command_composite.c:158:21: note: directive argument in the range [-2147483641, 2147483646] 158 | sprintf(tmpfname,"%s/%s.%d",composite_opt->refdir,skch_prefix,c); | ^~~~~~~~~~ In file included from /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/stdio.h:970, from /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/argp.h:23, from command_composite.h:17, from command_composite.c:15: In function 'sprintf', inlined from 'get_species_abundance' at command_composite.c:158:4: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 4 or more bytes (assuming 269) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_composite.c: In function 'get_species_abundance': command_composite.c:164:27: warning: '.' directive writing 1 byte into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 164 | sprintf(tmpfname,"%s/%s.%d",composite_opt->refdir,idx_prefix,c); | ^ command_composite.c:164:21: note: directive argument in the range [-2147483641, 2147483646] 164 | sprintf(tmpfname,"%s/%s.%d",composite_opt->refdir,idx_prefix,c); | ^~~~~~~~~~ In function 'sprintf', inlined from 'get_species_abundance' at command_composite.c:164:4: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 4 or more bytes (assuming 269) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_composite.c: In function 'get_species_abundance': command_composite.c:170:27: warning: '.' directive writing 1 byte into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 170 | sprintf(tmpfname,"%s/%s.%d",composite_opt->qrydir,skch_prefix,c); | ^ command_composite.c:170:21: note: directive argument in the range [-2147483641, 2147483646] 170 | sprintf(tmpfname,"%s/%s.%d",composite_opt->qrydir,skch_prefix,c); | ^~~~~~~~~~ In function 'sprintf', inlined from 'get_species_abundance' at command_composite.c:170:4: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 4 or more bytes (assuming 269) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_composite.c: In function 'get_species_abundance': command_composite.c:176:29: warning: '.' directive writing 1 byte into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 176 | sprintf(tmpfname,"%s/%s.%d",composite_opt->qrydir,idx_prefix,c); | ^ command_composite.c:176:23: note: directive argument in the range [-2147483641, 2147483646] 176 | sprintf(tmpfname,"%s/%s.%d",composite_opt->qrydir,idx_prefix,c); | ^~~~~~~~~~ In function 'sprintf', inlined from 'get_species_abundance' at command_composite.c:176:6: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 4 or more bytes (assuming 269) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_composite.c: In function 'get_species_abundance': command_composite.c:182:27: warning: '.' directive writing 1 byte into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 182 | sprintf(tmpfname,"%s/%s.%d.a",composite_opt->qrydir,skch_prefix,c); | ^ command_composite.c:182:21: note: directive argument in the range [-2147483641, 2147483646] 182 | sprintf(tmpfname,"%s/%s.%d.a",composite_opt->qrydir,skch_prefix,c); | ^~~~~~~~~~~~ In function 'sprintf', inlined from 'get_species_abundance' at command_composite.c:182:4: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 271) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_composite.c: In function 'get_species_abundance': command_composite.c:131:63: warning: '%s' directive argument is null [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 131 | if (qry_dstat_fpath == NULL) err(errno,"cannot find %s under %s ",co_dstat, qry_dstat_fpath); | ^~ command_composite.c:129:63: warning: '%s' directive argument is null [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 129 | if (ref_dstat_fpath == NULL) err(errno,"cannot find %s under %s ",co_dstat, ref_dstat_fpath); | ^~ command_dist.c: In function 'run_stageI': command_dist.c:368:2: warning: this 'for' clause does not guard... [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmisleading-indentation-Wmisleading-indentation8;;] 368 | for(int i = 0; i< co_dstat_wrout.infile_num; i++) | ^~~ command_dist.c:370:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 370 | fclose(coutfp); | ^~~~~~ command_dist.c: In function 'mco_cbdco_nobin_dist': command_dist.c:709:52: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-Wformat=8;;] 709 | if( comp_sz % page_sz != 0 ) err(errno,"comp_sz %d is not multiple of page_sz %d ",comp_sz,page_sz ); | ~^ ~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld command_dist.c:714:11: warning: unused variable 'fco_pos' [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unused-variable-Wunused-variable8;;] 714 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1) ); | ^~~~~~~ command_dist.c:713:15: warning: unused variable 'cbd_fcode_stat' [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unused-variable-Wunused-variable8;;] 713 | struct stat cbd_fcode_stat; | ^~~~~~~~~~~~~~ command_dist.c:712:28: warning: unused variable 'cbd_fcode_comp_index_fp' [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unused-variable-Wunused-variable8;;] 712 | FILE *cbd_fcode_comp_fp,*cbd_fcode_comp_index_fp; | ^~~~~~~~~~~~~~~~~~~~~~~ command_dist.c:712:9: warning: unused variable 'cbd_fcode_comp_fp' [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unused-variable-Wunused-variable8;;] 712 | FILE *cbd_fcode_comp_fp,*cbd_fcode_comp_index_fp; | ^~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbd_koc_compatible_dist': command_dist.c:857:52: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-Wformat=8;;] 857 | if( comp_sz % page_sz != 0 ) err(errno,"comp_sz %d is not multiple of page_sz %d ",comp_sz,page_sz ); | ~^ ~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld command_dist.c: In function 'run_stageI._omp_fn.1': command_dist.c:338:6: warning: 'com_abund_fp' may be used uninitialized [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized8;;] 338 | fwrite(tmp_mem, sizeof(unsigned short)*tmpkmerct, 1 , com_abund_fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ command_dist.c:310:33: note: 'com_abund_fp' was declared here 310 | FILE *com_cofp,*indexfp, *com_abund_fp; | ^~~~~~~~~~~~ command_dist.c: In function 'get_dim_shuffle': command_dist.c:213:31: warning: '%s' directive writing up to 264 bytes into a region of size 256 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 213 | sprintf(shuf_infile_name,"%s.shuf",shuf_infile_name_prefix); | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ In file included from /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/stdio.h:970, from /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/argp.h:23, from global_basic.h:53, from command_dist.h:17, from command_dist.c:15: In function 'sprintf', inlined from 'get_dim_shuffle' at command_dist.c:213:5: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 270 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbd_co_dist': command_dist.c:523:34: warning: '%s' directive writing 13 bytes into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 523 | sprintf(refmco_dstat_fpath,"%s/%s",refmco_dname,mco_dstat); | ^~ ~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbd_co_dist' at command_dist.c:523:3: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 15 and 270 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbd_co_dist': command_dist.c:552:21: warning: '/sharedk_ct.dat' directive writing 15 bytes into a region of size between 1 and 256 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 552 | sprintf(onedist,"%s/sharedk_ct.dat",distout_dir); | ^~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbd_co_dist' at command_dist.c:552:2: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 271 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbd_co_dist': command_dist.c:599:31: warning: '/mco.index.' directive writing 11 bytes into a region of size between 1 and 256 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 599 | sprintf(mco_index_fcode,"%s/mco.index.%d",refmco_dname,j); | ^~~~~~~~~~~ command_dist.c:599:28: note: directive argument in the range [-2147483641, 2147483646] 599 | sprintf(mco_index_fcode,"%s/mco.index.%d",refmco_dname,j); | ^~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbd_co_dist' at command_dist.c:599:4: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 13 and 278 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbd_co_dist': command_dist.c:600:28: warning: '/mco.' directive writing 5 bytes into a region of size between 1 and 256 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 600 | sprintf(mco_fcode,"%s/mco.%d",refmco_dname,j); | ^~~~~ command_dist.c:600:25: note: directive argument in the range [-2147483641, 2147483646] 600 | sprintf(mco_fcode,"%s/mco.%d",refmco_dname,j); | ^~~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbd_co_dist' at command_dist.c:600:7: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 272 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbdco_nobin_dist': command_dist.c:673:34: warning: '%s' directive writing 13 bytes into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 673 | sprintf(refmco_dstat_fpath,"%s/%s",refmco_dname,mco_dstat); | ^~ ~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbdco_nobin_dist' at command_dist.c:673:3: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 15 and 270 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbdco_nobin_dist': command_dist.c:700:22: warning: '/sharedk_ct.dat' directive writing 15 bytes into a region of size between 1 and 256 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 700 | sprintf(onedist,"%s/sharedk_ct.dat",distout_dir); | ^~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbdco_nobin_dist' at command_dist.c:700:3: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 271 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbdco_nobin_dist': command_dist.c:725:21: warning: '/distance.out' directive writing 13 bytes into a region of size between 1 and 256 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 725 | sprintf(distf, "%s/distance.out", distout_dir); | ^~~~~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbdco_nobin_dist' at command_dist.c:725:3: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 269 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbdco_nobin_dist': command_dist.c:749:33: warning: '.' directive writing 1 byte into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 749 | sprintf(mco_index_fcode,"%s/%s.%d",refmco_dname,mco_idx_prefix,j); | ^ command_dist.c:749:27: note: directive argument in the range [-2147483641, 2147483646] 749 | sprintf(mco_index_fcode,"%s/%s.%d",refmco_dname,mco_idx_prefix,j); | ^~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbdco_nobin_dist' at command_dist.c:749:3: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 4 or more bytes (assuming 269) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbdco_nobin_dist': command_dist.c:751:27: warning: '.' directive writing 1 byte into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 751 | sprintf(mco_fcode,"%s/%s.%d",refmco_dname,mco_gids_prefix,j); | ^ command_dist.c:751:21: note: directive argument in the range [-2147483641, 2147483646] 751 | sprintf(mco_fcode,"%s/%s.%d",refmco_dname,mco_gids_prefix,j); | ^~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbdco_nobin_dist' at command_dist.c:751:3: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 4 or more bytes (assuming 269) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbd_koc_compatible_dist': command_dist.c:819:34: warning: '%s' directive writing 13 bytes into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 819 | sprintf(refmco_dstat_fpath,"%s/%s",refmco_dname,mco_dstat); | ^~ ~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbd_koc_compatible_dist' at command_dist.c:819:3: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 15 and 270 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbd_koc_compatible_dist': command_dist.c:848:22: warning: '/sharedk_ct.dat' directive writing 15 bytes into a region of size between 1 and 256 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 848 | sprintf(onedist,"%s/sharedk_ct.dat",distout_dir); | ^~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbd_koc_compatible_dist' at command_dist.c:848:3: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 271 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbd_koc_compatible_dist': command_dist.c:874:21: warning: '/distance.out' directive writing 13 bytes into a region of size between 1 and 256 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 874 | sprintf(distf, "%s/distance.out", distout_dir); | ^~~~~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbd_koc_compatible_dist' at command_dist.c:874:3: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 269 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbd_koc_compatible_dist': command_dist.c:903:34: warning: '/mco.index.' directive writing 11 bytes into a region of size between 1 and 256 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 903 | sprintf(mco_index_fcode,"%s/mco.index.%d",refmco_dname,j); | ^~~~~~~~~~~ command_dist.c:903:31: note: directive argument in the range [-2147483641, 2147483646] 903 | sprintf(mco_index_fcode,"%s/mco.index.%d",refmco_dname,j); | ^~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbd_koc_compatible_dist' at command_dist.c:903:7: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 13 and 278 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'mco_cbd_koc_compatible_dist': command_dist.c:904:28: warning: '/mco.' directive writing 5 bytes into a region of size between 1 and 256 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 904 | sprintf(mco_fcode,"%s/mco.%d",refmco_dname,j); | ^~~~~ command_dist.c:904:25: note: directive argument in the range [-2147483641, 2147483646] 904 | sprintf(mco_fcode,"%s/mco.%d",refmco_dname,j); | ^~~~~~~~~~~ In function 'sprintf', inlined from 'mco_cbd_koc_compatible_dist' at command_dist.c:904:7: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 272 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'combine_queries': command_dist.c:1336:37: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 1336 | sprintf(one_kmerct_list_name,"%s/%s",co_dir,kmerct_list_fname); | ^ In function 'sprintf', inlined from 'combine_queries' at command_dist.c:1336:2: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'combine_queries': command_dist.c:1343:36: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 1343 | sprintf(one_infilename_name,"%s/%s",co_dir,fname_fname); | ^ In function 'sprintf', inlined from 'combine_queries' at command_dist.c:1343:2: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_dist.c: In function 'combine_queries': command_dist.c:1448:28: warning: '%s' directive writing 12 bytes into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 1448 | sprintf(one_stat_name,"%s/%s",co_dir,co_dstat); | ^~ ~~~~~~~~ In function 'sprintf', inlined from 'combine_queries' at command_dist.c:1448:2: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 14 and 269 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_reverse.c: In function 'co_reverse2kmer._omp_fn.1': command_reverse.c:296:26: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 296 | sprintf(fullname,"%s/%s",opt_val->outdir,filename); | ^ In file included from /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/stdio.h:970, from /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/argp.h:23, from global_basic.h:53, from command_reverse.h:17, from command_reverse.c:15: In function 'sprintf', inlined from 'co_reverse2kmer._omp_fn.1' at command_reverse.c:296:3: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 2 or more bytes (assuming 257) into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ command_set.c: In function 'cmd_set': command_set.c:203:3: warning: this 'if' clause does not guard... [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmisleading-indentation-Wmisleading-indentation8;;] 203 | if(set_opt.operation == 2) | ^~ command_set.c:205:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 205 | if(set_opt.operation == 3) | ^~ command_set.c:213:46: error: implicit declaration of function 'combin_subset_pans' [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wimplicit-function-declaration-Wimplicit-function-declaration8;;] 213 | else if (set_opt.subsetf[0]!='\0') return combin_subset_pans(set_opt.subsetf); | ^~~~~~~~~~~~~~~~~~ command_set.c: In function 'organize_taxf': command_set.c:552:63: warning: format '%s' expects argument of type 'char *', but argument 5 has type 'int' [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-Wformat=8;;] 552 | err(errno,"organize_taxf(): %dth line %s is not full read %s, exceed PATHLEN %d ",i,tmpstr,PATHLEN); | ~^ | | | char * | %d command_set.c:552:82: warning: format '%d' expects a matching 'int' argument [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-Wformat=8;;] 552 | err(errno,"organize_taxf(): %dth line %s is not full read %s, exceed PATHLEN %d ",i,tmpstr,PATHLEN); | ~^ | | | int command_set.c: In function 'combin_subset_pans': command_set.c:609:7: warning: passing argument 1 of 'free' discards 'const' qualifier from pointer target type [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wdiscarded-qualifiers-Wdiscarded-qualifiers8;;] 609 | free(co_dstat_fpath); | ^~~~~~~~~~~~~~ In file included from global_basic.h:153, from command_set.c:16: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/stdlib.h:687:25: note: expected 'void *' but argument is of type 'const char *' 687 | extern void free (void *__ptr) __THROW; | ~~~~~~^~~~~ command_shuffle.c: In function 'write_dim_shuffle_file': command_shuffle.c:176:26: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 176 | sprintf(outfile,"%s.shuf",outfile_prefix); | ^ In file included from /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/stdio.h:970, from /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/argp.h:23, from command_shuffle.h:35, from command_shuffle.c:15: In function 'sprintf', inlined from 'write_dim_shuffle_file' at command_shuffle.c:176:2: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 6 and 257 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ global_basic.c: In function 'fpathopen': global_basic.c:136:2: warning: this 'if' clause does not guard... [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmisleading-indentation-Wmisleading-indentation8;;] 136 | if(! ( ( stat(dpath, &s) == 0 ) && S_ISDIR(s.st_mode) ) ) | ^~ global_basic.c:138:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 138 | FILE *fp; | ^~~~ global_basic.c: In function 'organize_infile_frm_arg': global_basic.c:231:28: warning: '%s' directive writing up to 255 bytes into a region of size between 0 and 255 [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wformat-overflow-Wformat-overflow=8;;] 231 | sprintf(fullpath, "%s/%s", remaining_args[i], dirent->d_name); | ^~ In file included from /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/stdio.h:970, from /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/argp.h:23, from global_basic.h:53, from global_basic.c:15: In function 'sprintf', inlined from 'organize_infile_frm_arg' at global_basic.c:231:6: /nix/store/1ycjq6h047qqwp3fm9sbl805xnrxlh2h-glibc-2.40-66-dev/include/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 512 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ iseq2comem.c: In function 'fastq2co': iseq2comem.c:336:6: warning: this 'else' clause does not guard... [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmisleading-indentation-Wmisleading-indentation8;;] 336 | else co[n] = (drtuple << CT_BIT) + 1LLU; | ^~~~ iseq2comem.c:337:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 337 | if( keycount > hashlimit) | ^~ make: *** [Makefile:4: all] Error 1