sci-biology:plink-1.90_pre140514:20161002-193917.log

sci-biology:plink-1.90_pre140514:20161002-193917.log (text/plain), 19.08 KB, created by Toralf Förster on 2016-10-02 21:08:14 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:   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 cblas was not found in the pkg-config search path.
Perhaps you should add the directory containing `cblas.pc'
to the PKG_CONFIG_PATH environment variable
No package 'cblas' found
make -j1 CXX=x86_64-pc-linux-gnu-g++ 'CFLAGS=-march=native -O2 -pipe' ZLIB=-lz BLASFLAGS= 
x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe 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:971:92: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=]
 logbuf, "Error: Invalid .bed file size (expected %" PRId64 " bytes).\n", llyy);
                                                                              ^
plink.c: In function ‘int32_t main(int32_t, char**)’:
plink.c:11634:121: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘long long int’ [-Wformat=]
 ected; reserving %" PRIdPTR " MB for main workspace.\n", llxx, malloc_size_mb);
                                                                              ^
plink.c:3405:38: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
     freopen("/dev/null", "w", stdout);
                                      ^
plink.c:3742:26: warning: ignoring return value of ‘char* getcwd(char*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
   getcwd(tbuf, FNAMESIZE);
                          ^
In file included from plink_calc.c:73:0:
plink_calc.c: In function ‘int32_t unrelated_herit_batch(uint32_t, char*, char*, uint32_t, char*, int32_t, Rel_info*)’:
plink_common.h:737:56: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPREPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0);
                                                        ^
plink_calc.c:2855:7: note: in expansion of macro ‘LOGPREPRINTFWW’
       LOGPREPRINTFWW("Error: --grm-bin expects size of %s to be %" PRIu64 " bytes.\n", grmname, fpos);
       ^~~~~~~~~~~~~~
plink_calc.c:2878:39: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
         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:5947:33: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  fread(&fxx, 4, 1, in_bin_nfile);
                                 ^
plink_calc.c:5949:31: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  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:6480:39: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
        fread(&fxx, 4, 1, in_bin_nfile);
                                       ^
plink_calc.c:6482:37: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
        fread(&fxx, 4, 1, in_binfile);
                                     ^
In file included from plink_cluster.c:1:0:
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_common.h:737:56: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPREPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0);
                                                        ^
plink_cluster.c:1177:5: note: in expansion of macro ‘LOGPREPRINTFWW’
     LOGPREPRINTFWW("Error: --read-dists expects size of %s to be %" PRIu64 " bytes.\n", dist_fname, fpos);
     ^~~~~~~~~~~~~~
In file included from plink_data.c:1:0:
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_common.h:731:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
                                                   ^
plink_data.c:3476:5: note: in expansion of macro ‘LOGPRINTF’
     LOGPRINTF("--set-me-missing: %" PRIu64 " error%s addressed.\n", mendel_error_ct, (mendel_error_ct == 1)? "" : "s");
     ^~~~~~~~~
plink_data.c: In function ‘int32_t generate_dummy(char*, char*, uint32_t, uintptr_t, uintptr_t, double, double)’:
plink_data.c:9636:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=]
     printf("Writing dummy .bed (%" PRIu64 " MB)... 0%%", ullii >> 20);
                                                                     ^
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:15194:138: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘long long unsigned int’ [-Wformat=]
 e log file.\n", position_warning_ct - 3, (position_warning_ct == 4)? "" : "s");
                                                                              ^
In file included from plink_data.c:1:0:
plink_common.h:731:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
                                                   ^
plink_data.c:15469:5: note: in expansion of macro ‘LOGPRINTF’
     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)));
     ^~~~~~~~~
plink_common.h:731:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
                                                   ^
plink_data.c:15469:5: note: in expansion of macro ‘LOGPRINTF’
     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)));
     ^~~~~~~~~
plink_common.h:731:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
                                                   ^
plink_data.c:15469:5: note: in expansion of macro ‘LOGPRINTF’
     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)));
     ^~~~~~~~~
In file included from plink_family.c:1:0:
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_common.h:731:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
                                                   ^
plink_family.c:1074:3: note: in expansion of macro ‘LOGPRINTF’
   LOGPRINTF("--me/--mendel: %" PRIu64 " Mendel error%s detected.\n", tot_error_ct, (tot_error_ct == 1)? "" : "s");
   ^~~~~~~~~
In file included from plink_filter.c:1:0:
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_common.h:731:51: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTF(...) sprintf(logbuf, __VA_ARGS__); logprintb();
                                                   ^
plink_filter.c:373:3: note: in expansion of macro ‘LOGPRINTF’
   LOGPRINTF("--oblig-missing: %" PRIu64 " call%s confirmed missing.\n", tot_missing, (tot_missing == 1)? "" : "s");
   ^~~~~~~~~
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_common.h:739:53: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); logprintb();
                                                     ^
plink_filter.c:1685:5: note: in expansion of macro ‘LOGPRINTFWW’
     LOGPRINTFWW("Warning: %" PRIu64 " het. haploid genotype%s present (see %s.hh ).\n", hethap_ct, (hethap_ct == 1LLU)? "" : "s", outname);
     ^~~~~~~~~~~
In file included from plink_lasso.c:1:0:
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_common.h:739:53: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); logprintb();
                                                     ^
plink_lasso.c:902:3: note: in expansion of macro ‘LOGPRINTFWW’
   LOGPRINTFWW("--lasso report written to %s. Total iterations: %" PRIu64 ".\n", outname, iter_tot);
   ^~~~~~~~~~~
In file included from plink_ld.c:1:0:
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_common.h:739:53: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’ [-Wformat=]
 #define LOGPRINTFWW(...) sprintf(logbuf, __VA_ARGS__); wordwrap(logbuf, 0); logprintb();
                                                     ^
plink_ld.c:7806:3: note: in expansion of macro ‘LOGPRINTFWW’
   LOGPRINTFWW("%" PRIu64 " valid tests performed, summary written to %s .\n", tests_expected - tests_thrown_out, outname);
   ^~~~~~~~~~~
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/cc35VU39.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+0x65b0): undefined reference to `dsyevr_'
plink_cluster.c:(.text+0x6718): undefined reference to `dsyevr_'
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccW9ym51.o: In function `glm_linear_adapt_thread(void*)':
plink_glm.c:(.text+0x640b): undefined reference to `dgels_'
plink_glm.c:(.text+0x690d): undefined reference to `dgels_'
plink_glm.c:(.text+0x6a57): undefined reference to `dgels_'
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccW9ym51.o: In function `glm_linear_maxt_thread(void*)':
plink_glm.c:(.text+0x72e3): undefined reference to `dgels_'
plink_glm.c:(.text+0x75a5): undefined reference to `dgels_'
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccW9ym51.o:plink_glm.c:(.text+0x77e1): more undefined references to `dgels_' follow
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccEIW9y5.o: In function `reml_em_one_trait(double*, double*, double*, double*, double, unsigned int)':
plink_calc.c:(.text+0x8070): undefined reference to `cblas_dger'
plink_calc.c:(.text+0x8102): undefined reference to `cblas_dsymv'
plink_calc.c:(.text+0x8132): undefined reference to `cblas_dsymv'
plink_calc.c:(.text+0x8150): undefined reference to `cblas_ddot'
plink_calc.c:(.text+0x8190): undefined reference to `cblas_dsymv'
plink_calc.c:(.text+0x81ae): undefined reference to `cblas_ddot'
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccEIW9y5.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+0x13c4e): undefined reference to `dsyevr_'
plink_calc.c:(.text+0x13da6): undefined reference to `dsyevr_'
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccBxzfHL.o: In function `invert_matrix(int, double*, int*, double*)':
plink_matrix.c:(.text+0x14aa): undefined reference to `dgetrf_'
plink_matrix.c:(.text+0x14cb): undefined reference to `dgetri_'
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccBxzfHL.o: In function `invert_matrix_trunc_singular(int, double*, int*, double*, int)':
plink_matrix.c:(.text+0x155a): undefined reference to `dlange_'
plink_matrix.c:(.text+0x15b3): undefined reference to `dgetrf_'
plink_matrix.c:(.text+0x1658): undefined reference to `dgecon_'
plink_matrix.c:(.text+0x1695): undefined reference to `dgetri_'
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccBxzfHL.o: In function `col_major_matrix_multiply(int, int, int, double*, double*, double*)':
plink_matrix.c:(.text+0x16f0): undefined reference to `cblas_dgemm'
/var/tmp/portage/sci-biology/plink-1.90_pre140514/temp/ccBxzfHL.o: In function `col_major_fmatrix_multiply(int, int, int, float*, float*, float*)':
plink_matrix.c:(.text+0x1730): 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_pre140514:20161002-193917.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/'