sci-biology:plink-1.90_pre140514:20190703-014455.log

sci-biology:plink-1.90_pre140514:20190703-014455.log (text/plain), 28.92 KB, created by Toralf Förster on 2019-07-03 17:42:17 UTC

 * Package:    sci-biology/plink-1.90_pre140514
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox 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 ...
Package lapack was not found in the pkg-config search path.
Perhaps you should add the directory containing `lapack.pc'
to the PKG_CONFIG_PATH environment variable
Package 'lapack', required by 'virtual:world', not found
Package 'blas', required by 'cblas', not found
make -j1 CXX=x86_64-pc-linux-gnu-g++ 'CFLAGS=-O2 -pipe -march=native' 'ZLIB=-lz ' BLASFLAGS= 
x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native 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  -lm -lpthread -L. -lz 
plink.c: In function ‘int32_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**)’:
plink.c:971:23: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=]
  971 |       sprintf(logbuf, "Error: Invalid .bed file size (expected %" PRId64 " bytes).\n", llyy);
      |                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~
      |                                                                                        |
      |                                                                                        long long int
plink.c: In function ‘int32_t main(int32_t, char**)’:
plink.c:11634:21: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=]
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 ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
 3405 |     freopen("/dev/null", "w", stdout);
      |     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
plink.c:3742:9: warning: ignoring return value of ‘char* getcwd(char*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
 3742 |   getcwd(tbuf, FNAMESIZE);
      |   ~~~~~~^~~~~~~~~~~~~~~~~
plink.c:6146:25: warning: ‘int __builtin_memcmp_eq(const void*, const void*, long unsigned int)’ reading 22 bytes from a region of size 19 [-Wstringop-overflow=]
 6146 |       } else if (!memcmp(argptr2, "lip-scan-window-kb", 22)) {
      |                   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
plink.c:9445:25: warning: ‘int __builtin_memcmp_eq(const void*, const void*, long unsigned int)’ reading 19 bytes from a region of size 16 [-Wstringop-overflow=]
 9445 |       } else if (!memcmp(argptr2, "ead-genome-list", 19)) {
      |                   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from plink_calc.c:73:
plink_calc.c: In function ‘int32_t unrelated_herit_batch(uint32_t, char*, char*, uint32_t, char*, int32_t, Rel_info*)’:
plink_calc.c:2855:22: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=]
 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 ‘LOGPREPRINTFWW’
  737 | #define LOGPREPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0);
      |                                             ^~~~~~~~~~~
plink_calc.c:2878:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
 2878 |         fread(&fxx, 4, 1, grm_binfile);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
plink_calc.c: In function ‘uint32_t rel_cutoff_batch_rbin_emitn(uint32_t, unsigned char*)’:
plink_calc.c:5947:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
 5947 |  fread(&fxx, 4, 1, in_bin_nfile);
      |  ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
plink_calc.c:5949:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
 5949 |  fread(&fxx, 4, 1, in_binfile);
      |  ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
plink_calc.c: In function ‘int32_t rel_cutoff_batch(uint32_t, char*, char*, char*, Rel_info*)’:
plink_calc.c:6480:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
 6480 |        fread(&fxx, 4, 1, in_bin_nfile);
      |        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
plink_calc.c:6482:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
 6482 |        fread(&fxx, 4, 1, in_binfile);
      |        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from plink_cluster.c:1:
plink_cluster.c: In function ‘int32_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*)’:
plink_cluster.c:1177:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=]
 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 ‘LOGPREPRINTFWW’
  737 | #define LOGPREPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0);
      |                                             ^~~~~~~~~~~
In file included from plink_data.c:1:
plink_data.c: In function ‘int32_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)’:
plink_data.c:3476:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 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 ‘LOGPRINTF’
  731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
      |                                        ^~~~~~~~~~~
plink_data.c: In function ‘int32_t generate_dummy(char*, char*, uint32_t, uintptr_t, uintptr_t, double, double)’:
plink_data.c:9636:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=]
 9636 |     printf("Writing dummy .bed (%" PRIu64 " MB)... 0%%", ullii >> 20);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~
      |                                                                |
      |                                                                long long unsigned int
plink_data.c: In function ‘int32_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*)’:
plink_data.c:15194:12: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=]
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 ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
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 ‘LOGPRINTF’
  731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
      |                                        ^~~~~~~~~~~
plink_data.c:15469:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=]
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 ‘LOGPRINTF’
  731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
      |                                        ^~~~~~~~~~~
plink_data.c:15469:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=]
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 ‘LOGPRINTF’
  731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
      |                                        ^~~~~~~~~~~
In file included from plink_family.c:1:
plink_family.c: In function ‘int32_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)’:
plink_family.c:1074:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 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 ‘LOGPRINTF’
  731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
      |                                        ^~~~~~~~~~~
In file included from plink_filter.c:1:
plink_filter.c: In function ‘int32_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*)’:
plink_filter.c:373:13: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
  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 ‘LOGPRINTF’
  731 | #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
      |                                        ^~~~~~~~~~~
plink_filter.c: In function ‘int32_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*)’:
plink_filter.c:1685:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 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 ‘LOGPRINTFWW’
  739 | #define LOGPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); logprintb();
      |                                          ^~~~~~~~~~~
In file included from /usr/include/string.h:494,
                 from plink_common.h:8,
                 from plink_glm.c:1:
In function ‘void* memcpy(void*, const void*, size_t)’,
    inlined from ‘int32_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*)’ at plink_glm.c:7411:8:
/usr/include/bits/string_fortified.h:34:33: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ reading 17 bytes from a region of size 16 [-Wstringop-overflow=]
   34 |   return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void* memcpy(void*, const void*, size_t)’,
    inlined from ‘int32_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*)’ at plink_glm.c:8210:8:
/usr/include/bits/string_fortified.h:34:33: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ reading 17 bytes from a region of size 16 [-Wstringop-overflow=]
   34 |   return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from plink_lasso.c:1:
plink_lasso.c: In function ‘int32_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)’:
plink_lasso.c:902:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=]
  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 ‘LOGPRINTFWW’
  739 | #define LOGPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); logprintb();
      |                                          ^~~~~~~~~~~
In file included from plink_ld.c:1:
plink_ld.c: In function ‘int32_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*)’:
plink_ld.c:7806:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 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 ‘LOGPRINTFWW’
  739 | #define LOGPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); logprintb();
      |                                          ^~~~~~~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccxRreer.o: in function `reml_em_one_trait(double*, double*, double*, double*, double, unsigned int)':
plink_calc.c:(.text+0x8bd8): undefined reference to `cblas_dger'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_calc.c:(.text+0x8c64): undefined reference to `cblas_dsymv'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_calc.c:(.text+0x8c98): undefined reference to `cblas_dsymv'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_calc.c:(.text+0x8cb6): undefined reference to `cblas_ddot'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_calc.c:(.text+0x8cfa): undefined reference to `cblas_dsymv'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_calc.c:(.text+0x8d18): undefined reference to `cblas_ddot'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccxRreer.o: in function `calc_pca(_IO_FILE*, unsigned long, char*, char*, unsigned long long, Rel_info*, unsigned long, unsigned long*, unsigned long, char*, unsigned long, unsigned long*, unsigned long, unsigned long*, unsigned long, unsigned long*, unsigned long, char*, unsigned long, double*, unsigned int, Chrom_info*, double*)':
plink_calc.c:(.text+0x14c26): undefined reference to `dsyevr_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_calc.c:(.text+0x14d9f): undefined reference to `dsyevr_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccEDbkWW.o: in function `mds_plot(char*, char*, unsigned long*, unsigned long, unsigned int*, char*, unsigned int, unsigned int, unsigned long, unsigned int, unsigned int, unsigned int*, unsigned int*, unsigned int, unsigned int, unsigned int, double*)':
plink_cluster.c:(.text+0x665d): undefined reference to `dsyevr_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_cluster.c:(.text+0x67ce): undefined reference to `dsyevr_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccwjTGl5.o: in function `glm_linear_adapt_thread(void*)':
plink_glm.c:(.text+0x5f9f): undefined reference to `dgels_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_glm.c:(.text+0x649a): undefined reference to `dgels_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_glm.c:(.text+0x6609): undefined reference to `dgels_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccwjTGl5.o: in function `glm_linear_maxt_thread(void*)':
plink_glm.c:(.text+0x6f47): undefined reference to `dgels_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_glm.c:(.text+0x7388): undefined reference to `dgels_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccwjTGl5.o:plink_glm.c:(.text+0x7536): more undefined references to `dgels_' follow
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/cc7rOtP4.o: in function `invert_matrix(int, double*, int*, double*)':
plink_matrix.c:(.text+0x16df): undefined reference to `dgetrf_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_matrix.c:(.text+0x16fe): undefined reference to `dgetri_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/cc7rOtP4.o: in function `invert_matrix_trunc_singular(int, double*, int*, double*, int)':
plink_matrix.c:(.text+0x17a7): undefined reference to `dlange_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_matrix.c:(.text+0x1803): undefined reference to `dgetrf_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_matrix.c:(.text+0x18ad): undefined reference to `dgecon_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: plink_matrix.c:(.text+0x18e8): undefined reference to `dgetri_'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/cc7rOtP4.o: in function `col_major_matrix_multiply(int, int, int, double*, double*, double*)':
plink_matrix.c:(.text+0x1940): undefined reference to `cblas_dgemm'
/usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/cc7rOtP4.o: in function `col_major_fmatrix_multiply(int, int, int, float*, float*, float*)':
plink_matrix.c:(.text+0x1980): undefined reference to `cblas_sgemm'
collect2: error: ld returned 1 exit status
make: *** [Makefile:54: plink] Error 1
 * ERROR: sci-biology/plink-1.90_pre140514::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/plink-1.90_pre140514::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/plink-1.90_pre140514::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:plink-1.90_pre140514:20190703-014455.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/plink-1.90_pre140514/work'
 * S: '/var/tmp/portage/sci-biology/plink-1.90_pre140514/work/'