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Gentoo's Bugzilla – Attachment 641716 Details for
Bug 725310
sci-biology/plink-1.90_pre140514 does not respect LDFLAGS
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build.log
build.log (text/plain), 30.95 KB, created by
Agostino Sarubbo
on 2020-05-25 13:10:46 UTC
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Description:
build.log
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Creator:
Agostino Sarubbo
Created:
2020-05-25 13:10:46 UTC
Size:
30.95 KB
patch
obsolete
> * Package: sci-biology/plink-1.90_pre140514 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox test userpriv usersandbox >>>> Unpacking source... >>>> Unpacking plink-1.90_pre140514.zip to /var/tmp/portage/sci-biology/plink-1.90_pre140514/work >>>> Source unpacked in /var/tmp/portage/sci-biology/plink-1.90_pre140514/work >>>> Preparing source in /var/tmp/portage/sci-biology/plink-1.90_pre140514/work ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/plink-1.90_pre140514/work ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/plink-1.90_pre140514/work ... >make -j4 CXX=x86_64-pc-linux-gnu-g++ 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches' 'ZLIB=-lz ' 'BLASFLAGS=-llapack -lcblas ' >x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c -o plink -llapack -lcblas -lm -lpthread -L. -lz >plink.c: In function âint32_t plink(char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char**, char*, char*, char*, Two_col_params*, Two_col_params*, char*, char*, char*, char*, Two_col_params*, Two_col_params*, Two_col_params*, Two_col_params*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, char*, double, uint32_t, uint32_t, uint32_t, uint32_t, int32_t, char*, uint32_t, uint32_t, Chrom_info*, Oblig_missing_info*, Family_info*, double, double, uint32_t, uint32_t, double, double, double, double, double, double, double, double, long long unsigned int, long long unsigned int, long long unsigned int, uint32_t, uintptr_t, uint32_t, uintptr_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, double, double, Homozyg_info*, Cluster_info*, uint32_t, uint32_t, Set_info*, Ld_info*, Epi_info*, Clump_info*, Rel_info*, Score_info*, uint32_t, uint32_t, uint32_t, uint32_t, int32_t, int32_t, int32_t, char*, char*, char*, Range_list*, uint32_t, Range_list*, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, double, uint32_t, uint32_t, Range_list*, Range_list*, double, double, uint32_t, double, uint32_t, Aperm_info*, uint32_t, uintptr_t, uint32_t, double, double, Range_list*, uint32_t, uint32_t, uint32_t, Ll_str**)â: >plink.c:971:23: warning: format â%ldâ expects argument of type âlong intâ, but argument 3 has type âlong long intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] > 971 | sprintf(logbuf, "Error: Invalid .bed file size (expected %" PRId64 " bytes).\n", llyy); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ > | | > | long long int >plink.c: In function âint32_t main(int32_t, char**)â: >plink.c:11634:21: warning: format â%ldâ expects argument of type âlong intâ, but argument 3 has type âlong long intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] >11634 | sprintf(logbuf, "%" PRId64 " MB RAM detected; reserving %" PRIdPTR " MB for main workspace.\n", llxx, malloc_size_mb); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ > | | > | long long int >plink.c:3405:12: warning: ignoring return value of âFILE* freopen(const char*, const char*, FILE*)â declared with attribute âwarn_unused_resultâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] > 3405 | freopen("/dev/null", "w", stdout); > | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ >plink.c:3742:9: warning: ignoring return value of âchar* getcwd(char*, size_t)â declared with attribute âwarn_unused_resultâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] > 3742 | getcwd(tbuf, FNAMESIZE); > | ~~~~~~^~~~~~~~~~~~~~~~~ >plink.c:6146:25: warning: âint __builtin_memcmp_eq(const void*, const void*, long unsigned int)â reading 22 bytes from a region of size 19 []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-overflow=-Wstringop-overflow=]8;;] > 6146 | } else if (!memcmp(argptr2, "lip-scan-window-kb", 22)) { > | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >plink.c:9445:25: warning: âint __builtin_memcmp_eq(const void*, const void*, long unsigned int)â reading 19 bytes from a region of size 16 []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-overflow=-Wstringop-overflow=]8;;] > 9445 | } else if (!memcmp(argptr2, "ead-genome-list", 19)) { > | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >In file included from plink_calc.c:73: >plink_calc.c: In function âint32_t unrelated_herit_batch(uint32_t, char*, char*, uint32_t, char*, int32_t, Rel_info*)â: >plink_calc.c:2855:22: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 4 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] > 2855 | LOGPREPRINTFWW("Error: --grm-bin expects size of %s to be %" PRIu64 " bytes.\n", grmname, fpos); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ > | | > | long long unsigned int >plink_common.h:737:45: note: in definition of macro âLOGPREPRINTFWWâ > 737 | #define LOGPREPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); > | ^~~~~~~~~~~ >plink_calc.c:2878:14: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] > 2878 | fread(&fxx, 4, 1, grm_binfile); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ >plink_calc.c: In function âuint32_t rel_cutoff_batch_rbin_emitn(uint32_t, unsigned char*)â: >plink_calc.c:5947:7: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] > 5947 | fread(&fxx, 4, 1, in_bin_nfile); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ >plink_calc.c:5949:7: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] > 5949 | fread(&fxx, 4, 1, in_binfile); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ >plink_calc.c: In function âint32_t rel_cutoff_batch(uint32_t, char*, char*, char*, Rel_info*)â: >plink_calc.c:6480:13: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] > 6480 | fread(&fxx, 4, 1, in_bin_nfile); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ >plink_calc.c:6482:13: warning: ignoring return value of âsize_t fread(void*, size_t, size_t, FILE*)â declared with attribute âwarn_unused_resultâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] > 6482 | fread(&fxx, 4, 1, in_binfile); > | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ >In file included from plink_cluster.c:1: >plink_cluster.c: In function âint32_t read_dists(char*, char*, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, uintptr_t, uint32_t*, uint32_t*, uint32_t, uint32_t, double*, uint32_t, double*, uint32_t*)â: >plink_cluster.c:1177:20: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 4 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] > 1177 | LOGPREPRINTFWW("Error: --read-dists expects size of %s to be %" PRIu64 " bytes.\n", dist_fname, fpos); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ > | | > | long long unsigned int >plink_common.h:737:45: note: in definition of macro âLOGPREPRINTFWWâ > 737 | #define LOGPREPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); > | ^~~~~~~~~~~ >In file included from plink_data.c:1: >plink_data.c: In function âint32_t make_bed(FILE*, uintptr_t, char*, uint32_t, char*, char*, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, double*, uint32_t*, char**, uintptr_t*, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, char*, uintptr_t, char*, uintptr_t, uintptr_t*, uintptr_t*, uintptr_t*, uintptr_t*, uintptr_t*, double*, char*, uint32_t, uint32_t*, long long unsigned int, uint32_t, uint32_t, Two_col_params*, char*, char*, char*, uintptr_t, uint32_t*, uint32_t*, char*, uintptr_t, uint32_t, Chrom_info*, uint32_t)â: >plink_data.c:3476:15: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 3 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] > 3476 | LOGPRINTF("--set-me-missing: %" PRIu64 " error%s addressed.\n", mendel_error_ct, (mendel_error_ct == 1)? "" : "s"); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ > | | > | long long unsigned int >plink_common.h:731:40: note: in definition of macro âLOGPRINTFâ > 731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb(); > | ^~~~~~~~~~~ >plink_data.c: In function âint32_t generate_dummy(char*, char*, uint32_t, uintptr_t, uintptr_t, double, double)â: >plink_data.c:9636:12: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 2 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] > 9636 | printf("Writing dummy .bed (%" PRIu64 " MB)... 0%%", ullii >> 20); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ > | | > | long long unsigned int >plink_data.c: In function âint32_t merge_datasets(char*, char*, char*, char*, char*, char*, char*, char*, char*, long long unsigned int, uint32_t, uint32_t, long long unsigned int, Chrom_info*)â: >plink_data.c:15194:12: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 2 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] >15194 | printf("%" PRIu64 " more multiple-position warning%s: see log file.\n", position_warning_ct - 3, (position_warning_ct == 4)? "" : "s"); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ > | | > | long long unsigned int >In file included from plink_data.c:1: >plink_data.c:15469:15: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 3 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] >15469 | LOGPRINTF("%" PRIu64 " overlapping variants, %" PRIu64 " genotyped in both filesets.\n%" PRIu64 " concordant, for a concordance rate of %g.\n", diff_total_overlap, diff_not_both_genotyped, diff_not_both_genotyped - diff_discordant, 1.0 - (((double)diff_discordant) / ((double)diff_not_both_genotyped))); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ > | | > | long long unsigned int >plink_common.h:731:40: note: in definition of macro âLOGPRINTFâ > 731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb(); > | ^~~~~~~~~~~ >plink_data.c:15469:15: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 4 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] >15469 | LOGPRINTF("%" PRIu64 " overlapping variants, %" PRIu64 " genotyped in both filesets.\n%" PRIu64 " concordant, for a concordance rate of %g.\n", diff_total_overlap, diff_not_both_genotyped, diff_not_both_genotyped - diff_discordant, 1.0 - (((double)diff_discordant) / ((double)diff_not_both_genotyped))); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ > | | > | long long unsigned int >plink_common.h:731:40: note: in definition of macro âLOGPRINTFâ > 731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb(); > | ^~~~~~~~~~~ >plink_data.c:15469:15: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 5 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] >15469 | LOGPRINTF("%" PRIu64 " overlapping variants, %" PRIu64 " genotyped in both filesets.\n%" PRIu64 " concordant, for a concordance rate of %g.\n", diff_total_overlap, diff_not_both_genotyped, diff_not_both_genotyped - diff_discordant, 1.0 - (((double)diff_discordant) / ((double)diff_not_both_genotyped))); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > | | > | long long unsigned int >plink_common.h:731:40: note: in definition of macro âLOGPRINTFâ > 731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb(); > | ^~~~~~~~~~~ >In file included from plink_family.c:1: >plink_family.c: In function âint32_t mendel_error_scan(Family_info*, FILE*, uintptr_t, char*, char*, uint32_t, uint32_t, uint32_t, uintptr_t, uintptr_t*, uintptr_t*, uintptr_t*, char*, uintptr_t, char**, uintptr_t, uintptr_t, uintptr_t*, uintptr_t*, uintptr_t*, uintptr_t*, uintptr_t*, char*, uintptr_t, char*, uintptr_t, char*, uintptr_t, uint32_t, uint32_t, Chrom_info*, uint32_t)â: >plink_family.c:1074:13: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 3 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] > 1074 | LOGPRINTF("--me/--mendel: %" PRIu64 " Mendel error%s detected.\n", tot_error_ct, (tot_error_ct == 1)? "" : "s"); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ > | | > | long long unsigned int >plink_common.h:731:40: note: in definition of macro âLOGPRINTFâ > 731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb(); > | ^~~~~~~~~~~ >In file included from plink_filter.c:1: >plink_filter.c: In function âint32_t load_oblig_missing(FILE*, uintptr_t, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, char*, uintptr_t, uintptr_t, uint32_t*, uintptr_t, uintptr_t*, uintptr_t*, Chrom_info*, Oblig_missing_info*)â: >plink_filter.c:373:13: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 3 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] > 373 | LOGPRINTF("--oblig-missing: %" PRIu64 " call%s confirmed missing.\n", tot_missing, (tot_missing == 1)? "" : "s"); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ > | | > | long long unsigned int >plink_common.h:731:40: note: in definition of macro âLOGPRINTFâ > 731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb(); > | ^~~~~~~~~~~ >plink_filter.c: In function âint32_t calc_freqs_and_hwe(FILE*, char*, char*, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, uintptr_t*, int32_t, int32_t, double*, uintptr_t**, uintptr_t, uint32_t, uint32_t, uint32_t, double, uintptr_t*, uintptr_t*, int32_t**, int32_t**, int32_t**, int32_t**, int32_t**, int32_t**, int32_t**, int32_t**, int32_t**, int32_t**, int32_t**, uintptr_t**, uint32_t*, uint32_t*, uint32_t*, uint32_t, uintptr_t*, double**, double, Chrom_info*, Oblig_missing_info*, uintptr_t*, uintptr_t*, uint32_t, uint32_t*)â: >plink_filter.c:1685:17: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 3 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] > 1685 | LOGPRINTFWW("Warning: %" PRIu64 " het. haploid genotype%s present (see %s.hh ).\n", hethap_ct, (hethap_ct == 1LLU)? "" : "s", outname); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ > | | > | long long unsigned int >plink_common.h:739:42: note: in definition of macro âLOGPRINTFWWâ > 739 | #define LOGPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); logprintb(); > | ^~~~~~~~~~~ >In file included from /usr/include/string.h:495, > from plink_common.h:8, > from plink_glm.c:1: >In function âvoid* memcpy(void*, const void*, size_t)â, > inlined from âint32_t glm_linear_nosnp(pthread_t*, FILE*, uintptr_t, char*, char*, uint32_t, double, uint32_t, uint32_t, Range_list*, Range_list*, double, double, double, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, uintptr_t*, char*, char*, Chrom_info*, uintptr_t, uintptr_t, uintptr_t*, uint32_t, uint32_t*, uint32_t*, uint32_t, uint32_t, uintptr_t*, double*, uintptr_t, char*, uintptr_t, uintptr_t*, double*, uintptr_t*, uintptr_t*, uint32_t, uint32_t, Set_info*)â at plink_glm.c:7411:8: >/usr/include/bits/string_fortified.h:34:33: warning: âvoid* __builtin_memcpy(void*, const void*, long unsigned int)â reading 17 bytes from a region of size 16 []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-overflow=-Wstringop-overflow=]8;;] > 34 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); > | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >In function âvoid* memcpy(void*, const void*, size_t)â, > inlined from âint32_t glm_logistic_nosnp(pthread_t*, FILE*, uintptr_t, char*, char*, uint32_t, double, uint32_t, uint32_t, Range_list*, Range_list*, double, double, double, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, uintptr_t*, char*, char*, Chrom_info*, uintptr_t, uintptr_t, uintptr_t*, uint32_t, uint32_t*, uint32_t*, uint32_t, uint32_t, uintptr_t*, uintptr_t*, uintptr_t, char*, uintptr_t, uintptr_t*, double*, uintptr_t*, uintptr_t*, uint32_t, uint32_t, Set_info*)â at plink_glm.c:8210:8: >/usr/include/bits/string_fortified.h:34:33: warning: âvoid* __builtin_memcpy(void*, const void*, long unsigned int)â reading 17 bytes from a region of size 16 []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-overflow=-Wstringop-overflow=]8;;] > 34 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); > | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >In file included from plink_lasso.c:1: >plink_lasso.c: In function âint32_t lasso(pthread_t*, FILE*, uintptr_t, char*, char*, uintptr_t, uintptr_t*, uintptr_t, char*, uintptr_t, char**, uintptr_t*, uint32_t, Chrom_info*, uintptr_t, uintptr_t, double, double, Range_list*, long long unsigned int, uintptr_t*, uintptr_t*, double*, uintptr_t, char*, uintptr_t, uintptr_t*, double*, uintptr_t*, uint32_t)â: >plink_lasso.c:902:15: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 4 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] > 902 | LOGPRINTFWW("--lasso report written to %s. Total iterations: %" PRIu64 ".\n", outname, iter_tot); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ > | | > | long long unsigned int >plink_common.h:739:42: note: in definition of macro âLOGPRINTFWWâ > 739 | #define LOGPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); logprintb(); > | ^~~~~~~~~~~ >In file included from plink_ld.c:1: >plink_ld.c: In function âint32_t epistasis_report(pthread_t*, Epi_info*, FILE*, uintptr_t, uintptr_t, uintptr_t, uintptr_t*, uintptr_t*, char*, uintptr_t, uint32_t*, uint32_t, uint32_t, Chrom_info*, uintptr_t, uintptr_t*, uint32_t, uint32_t, uintptr_t*, double*, uint32_t, uint32_t, char*, char*, Set_info*)â: >plink_ld.c:7806:15: warning: format â%luâ expects argument of type âlong unsigned intâ, but argument 3 has type âlong long unsigned intâ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] > 7806 | LOGPRINTFWW("%" PRIu64 " valid tests performed, summary written to %s .\n", tests_expected - tests_thrown_out, outname); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > | | > | long long unsigned int >plink_common.h:739:42: note: in definition of macro âLOGPRINTFWWâ > 739 | #define LOGPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); logprintb(); > | ^~~~~~~~~~~ >>>> Source compiled. >>>> Test phase: sci-biology/plink-1.90_pre140514 >>>> Completed testing sci-biology/plink-1.90_pre140514 > >>>> Install sci-biology/plink-1.90_pre140514 into /var/tmp/portage/sci-biology/plink-1.90_pre140514/image/ >>>> Completed installing sci-biology/plink-1.90_pre140514 into /var/tmp/portage/sci-biology/plink-1.90_pre140514/image/ > > * Final size of build directory: 6036 KiB (5.8 MiB) > * Final size of installed tree: 1748 KiB (1.7 MiB) > > > * QA Notice: Files built without respecting LDFLAGS have been detected > * Please include the following list of files in your report: > * /usr/bin/p-link > >strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version > /usr/bin/p-link >>>> Done. > > > >emerge --info: >Portage 2.3.100 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r3, 5.4.0-1009-aws x86_64) >================================================================= >System uname: Linux-5.4.0-1009-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7 >KiB Mem: 16011344 total, 1832892 free >KiB Swap: 0 total, 0 free >Timestamp of repository gentoo: Mon, 25 May 2020 12:35:49 +0000 >sh bash 5.0_p17 >ld GNU ld (Gentoo 2.34 p4) 2.34.0 >app-shells/bash: 5.0_p17::gentoo >dev-lang/perl: 5.30.2-r2::gentoo >dev-lang/python: 2.7.18::gentoo, 3.7.7-r2::gentoo, 3.8.3::gentoo >sys-apps/baselayout: 2.7::gentoo >sys-apps/openrc: 0.42.1::gentoo >sys-apps/sandbox: 2.18::gentoo >sys-devel/autoconf: 2.69-r5::gentoo >sys-devel/automake: 1.16.2::gentoo >sys-devel/binutils: 2.34-r1::gentoo >sys-devel/gcc: 10.1.0::gentoo >sys-devel/gcc-config: 2.3::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.3::gentoo >sys-kernel/linux-headers: 5.6::gentoo (virtual/os-headers) >sys-libs/glibc: 2.31-r3::gentoo >Repositories: > >gentoo > location: /usr/portage > sync-type: rsync > sync-uri: rsync://rsync.gentoo.org/gentoo-portage > priority: -1000 > sync-rsync-verify-metamanifest: yes > sync-rsync-verify-jobs: 1 > sync-rsync-verify-max-age: 24 > sync-rsync-extra-opts: > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="*" >CBUILD="x86_64-pc-linux-gnu" >CC="x86_64-pc-linux-gnu-gcc" >CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >CHOST="x86_64-pc-linux-gnu" >CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" >CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" >CXX="x86_64-pc-linux-gnu-g++" >CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >DISTDIR="/usr/portage/distfiles" >EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k" >ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" >FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" >FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="C.UTF-8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" >MAKEOPTS="-j4" >PKGDIR="/root/.packages" >PORTAGE_CONFIGROOT="/" >PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" >PORTAGE_TMPDIR="/var/tmp" >USE="acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" >Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS >
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bug 725310
: 641716