sci-biology:subread-1.4.6:20201119-104739.log

sci-biology:subread-1.4.6:20201119-104739.log (text/plain), 42.19 KB, created by Toralf Förster on 2020-11-19 13:10:58 UTC

 * Package:    sci-biology/subread-1.4.6
 * Repository: science
 * Maintainer: [e-mail] [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking subread-1.4.6-source.tar.gz to /var/tmp/portage/sci-biology/subread-1.4.6/work
>>> Source unpacked in /var/tmp/portage/sci-biology/subread-1.4.6/work
>>> Preparing source in /var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source ...
make -j1 -f Makefile.Linux 
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o core.o core.c
core.c: In function ‘print_in_box’:
core.c:89:7: warning: variable ‘is_R_linebreak’ set but not used [-Wunused-but-set-variable]
   89 |  char is_R_linebreak=0, * content, *out_line_buff;
      |       ^~~~~~~~~~~~~~
core.c: In function ‘convert_GZ_to_FQ’:
core.c:759:19: warning: initialization of ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
  759 |  gzFile * rawfp = gzopen(fname, "r");
      |                   ^~~~~~
core.c:770:25: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
  770 |     char * bufr =gzgets(rawfp, linebuff, 3000);
      |                         ^~~~~
      |                         |
      |                         struct gzFile_s **
In file included from /usr/include/zlib.h:34,
                 from sambam-file.h:23,
                 from core.h:47,
                 from core.c:42:
/usr/include/zlib.h:1492:31: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1492 | ZEXTERN char * ZEXPORT gzgets _Z_OF((gzFile file, char *buf, int len));
      |                               ^~~~~
core.c:781:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
  781 |   gzclose(rawfp);
      |           ^~~~~
      |           |
      |           struct gzFile_s **
In file included from /usr/include/zlib.h:34,
                 from sambam-file.h:23,
                 from core.h:47,
                 from core.c:42:
/usr/include/zlib.h:1631:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
 1631 | ZEXTERN int ZEXPORT    gzclose _Z_OF((gzFile file));
      |                                ^~~~~
core.c: In function ‘do_voting’:
core.c:2979:9: warning: variable ‘allsubreads_for_each_gap’ set but not used [-Wunused-but-set-variable]
 2979 |     int allsubreads_for_each_gap [GENE_SLIDING_STEP], noninformative_subreads_for_each_gap[GENE_SLIDING_STEP];
      |         ^~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function ‘split_read_files’:
core.c:3308:4: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3308 |    fgets(read_line_buf, 3000, global_context->input_reads.first_read_file.input_fp);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:3310:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3310 |     fgets(read_line_buf2, 3000, global_context->input_reads.second_read_file.input_fp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:3339:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3339 |     fgets(read_line_buf, 3000, global_context->input_reads.first_read_file.input_fp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:3340:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3340 |     fgets(read_line_buf2, 3000, global_context->input_reads.second_read_file.input_fp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function ‘convert_BAM_to_SAM’:
core.c:702:28: warning: ‘%s’ directive writing up to 299 bytes into a region of size 200 [-Wformat-overflow=]
  702 |   sprintf(temp_file_name, "%s.sam", global_context->config.temp_file_prefix);
      |                            ^~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 304 bytes into a destination of size 200
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:702:28: warning: ‘%s’ directive writing up to 299 bytes into a region of size 200 [-Wformat-overflow=]
  702 |   sprintf(temp_file_name, "%s.sam", global_context->config.temp_file_prefix);
      |                            ^~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 304 bytes into a destination of size 200
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:702:28: warning: ‘%s’ directive writing up to 299 bytes into a region of size 200 [-Wformat-overflow=]
  702 |   sprintf(temp_file_name, "%s.sam", global_context->config.temp_file_prefix);
      |                            ^~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 5 and 304 bytes into a destination of size 200
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function ‘convert_GZ_to_FQ’:
core.c:764:28: warning: ‘%s’ directive writing up to 299 bytes into a region of size 200 [-Wformat-overflow=]
  764 |   sprintf(temp_file_name, "%s-%d.fq", global_context->config.temp_file_prefix, half_n);
      |                            ^~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 6 and 315 bytes into a destination of size 200
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function ‘write_single_fragment’:
core.c:1649:71: warning: ‘%s’ directive output may be truncated writing up to 299 bytes into a region of size 94 [-Wformat-truncation=]
 1649 | (extra_additional_1+strlen(extra_additional_1),100, "\tRG:Z:%s", global_context->config.read_group_id);
      |                                                             ^~

In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:70:10: note: ‘__builtin___snprintf_chk’ output between 7 and 306 bytes into a destination of size 100
   70 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   71 |        __bos (__s), __fmt, __va_arg_pack ());
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:1650:71: warning: ‘%s’ directive output may be truncated writing up to 299 bytes into a region of size 94 [-Wformat-truncation=]
 1650 | (extra_additional_2+strlen(extra_additional_2),100, "\tRG:Z:%s", global_context->config.read_group_id);
      |                                                             ^~

In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:70:10: note: ‘__builtin___snprintf_chk’ output between 7 and 306 bytes into a destination of size 100
   70 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   71 |        __bos (__s), __fmt, __va_arg_pack ());
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function ‘write_sam_headers’:
core.c:3738:32: warning: ‘%s’ directive output may be truncated writing up to 299 bytes into a region of size 292 [-Wformat-truncation=]
 3738 |    snprintf(obuf,299, "@RG\tID:%s%s",context->config.read_group_id, context->config.read_group_txt);
      |                                ^~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:70:10: note: ‘__builtin___snprintf_chk’ output between 8 and 606 bytes into a destination of size 299
   70 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   71 |        __bos (__s), __fmt, __va_arg_pack ());
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function ‘load_global_context’:
core.c:3857:24: warning: ‘.reads’ directive writing 6 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
 3857 |  sprintf(tmp_fname, "%s.reads", context->config.index_prefix);
      |                        ^~~~~~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 7 and 306 bytes into a destination of size 300
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:3867:25: warning: ‘.00.b.tab’ directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
 3867 |   sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix);
      |                         ^~~~~~~~~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 10 and 309 bytes into a destination of size 300
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:3865:25: warning: ‘.00.c.tab’ directive writing 9 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
 3865 |   sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix);
      |                         ^~~~~~~~~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 10 and 309 bytes into a destination of size 300
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:3878:26: warning: ‘%02d’ directive writing between 2 and 11 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
 3878 |   sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b');
      |                          ^~~~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 10 and 318 bytes into a destination of size 300
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c: In function ‘read_chunk_circles’:
core.c:3448:27: warning: ‘%02d’ directive writing between 2 and 11 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
 3448 |    sprintf(tmp_fname, "%s.%02d.%c.tab", global_context->config.index_prefix, global_context->current_index_block_number,  global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
      |                           ^~~~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 10 and 318 bytes into a destination of size 300
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:3454:27: warning: ‘%02d’ directive writing between 2 and 11 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
 3454 |    sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, global_context->current_index_block_number, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
      |                           ^~~~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 12 and 320 bytes into a destination of size 300
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core.c:3486:27: warning: ‘%02d’ directive writing between 2 and 10 bytes into a region of size between 0 and 299 [-Wformat-overflow=]
 3486 |    sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no,  global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
      |                           ^~~~
core.c:3486:23: note: directive argument in the range [0, 2147483647]
 3486 |    sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no,  global_context->config.space_type == GENE_SPACE_COLOR?'c':'b');
      |                       ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
                 from core.c:26:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 12 and 319 bytes into a destination of size 300
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o core-junction.o core-junction.c
core-junction.c: In function ‘search_events_to_back’:
core-junction.c:390:6: warning: variable ‘move_start’ set but not used [-Wunused-but-set-variable]
  390 |  int move_start = read_tail_pos - SEARCH_MIN_MOVEMENT;
      |      ^~~~~~~~~~
core-junction.c: In function ‘finalise_explain_CIGAR’:
core-junction.c:1670:23: warning: variable ‘tmp_cigar_exonic’ set but not used [-Wunused-but-set-variable]
 1670 |  char tmp_cigar[120], tmp_cigar_exonic[120];
      |                       ^~~~~~~~~~~~~~~~
core-junction.c: In function ‘final_CIGAR_quality’:
core-junction.c:1632:30: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
 1632 |       sprintf(cigar_tiny,"%dS",head_soft_clipped);
      |                              ^
In file included from /usr/include/stdio.h:866,
                 from core-junction.c:21:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-junction.c:1643:30: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
 1643 |       sprintf(cigar_tiny,"%dS",tail_soft_clipped);
      |                              ^
In file included from /usr/include/stdio.h:866,
                 from core-junction.c:21:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 11
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-junction.c: In function ‘write_fusion_final_results’:
core-junction.c:2471:41: warning: ‘.fusion.txt’ directive output may be truncated writing 11 bytes into a region of size between 1 and 300 [-Wformat-truncation=]
 2471 |  snprintf(fn2, MAX_FILE_NAME_LENGTH, "%s.fusion.txt", global_context->config.output_prefix);
      |                                         ^~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
                 from core-junction.c:21:
/usr/include/bits/stdio2.h:70:10: note: ‘__builtin___snprintf_chk’ output between 12 and 311 bytes into a destination of size 300
   70 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   71 |        __bos (__s), __fmt, __va_arg_pack ());
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-junction.c: In function ‘write_junction_final_results’:
core-junction.c:2516:41: warning: ‘.junction.bed’ directive output may be truncated writing 13 bytes into a region of size between 1 and 300 [-Wformat-truncation=]
 2516 |  snprintf(fn2, MAX_FILE_NAME_LENGTH, "%s.junction.bed", global_context->config.output_prefix);
      |                                         ^~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
                 from core-junction.c:21:
/usr/include/bits/stdio2.h:70:10: note: ‘__builtin___snprintf_chk’ output between 14 and 313 bytes into a destination of size 300
   70 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   71 |        __bos (__s), __fmt, __va_arg_pack ());
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o core-indel.o core-indel.c
core-indel.c: In function ‘find_new_indels’:
core-indel.c:1317:9: warning: variable ‘best_j’ set but not used [-Wunused-but-set-variable]
 1317 |     int best_j=0, best_score=-99999, is_ambiguous_indel= 0;
      |         ^~~~~~
core-indel.c: In function ‘full_indel_alignment’:
core-indel.c:2659:41: warning: variable ‘best_right’ set but not used [-Wunused-but-set-variable]
 2659 |    int best_edge_score = -1, best_left, best_right;
      |                                         ^~~~~~~~~~
core-indel.c:2659:30: warning: variable ‘best_left’ set but not used [-Wunused-but-set-variable]
 2659 |    int best_edge_score = -1, best_left, best_right;
      |                              ^~~~~~~~~
core-indel.c: In function ‘find_potential_ultralong_indels’:
core-indel.c:2764:24: warning: variable ‘best_c2_location’ set but not used [-Wunused-but-set-variable]
 2764 |   int best_match = -1, best_c2_location = -1;
      |                        ^~~~~~~~~~~~~~~~
core-indel.c: In function ‘finalise_pileup_file’:
core-indel.c:3042:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3042 |   fread(&read_len, sizeof(short), 1, tmp_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3043:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3043 |   fread(read_text, sizeof(char), read_len, tmp_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3044:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3044 |   fread(qual_text, sizeof(char), read_len, tmp_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3121:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3121 |   fread(&read_len, sizeof(short), 1, tmp_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3122:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3122 |   fread(read_text, sizeof(char), read_len, tmp_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3123:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3123 |   fread(qual_text, sizeof(char), read_len, tmp_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c: In function ‘finalise_pileup_file_by_debrujin’:
core-indel.c:3478:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3478 |   fread(&read_len, sizeof(short), 1, tmp_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3479:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3479 |   fread(read_text, sizeof(char), read_len, tmp_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3480:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 3480 |   fread(qual_text, sizeof(char), read_len, tmp_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c: In function ‘write_indel_final_results’:
core-indel.c:1521:41: warning: ‘.indel’ directive output may be truncated writing 6 bytes into a region of size between 1 and 300 [-Wformat-truncation=]
 1521 |  snprintf(fn2, MAX_FILE_NAME_LENGTH, "%s.indel", global_context->config.output_prefix);
      |                                         ^~~~~~
In file included from /usr/include/stdio.h:866,
                 from subread.h:25,
                 from gene-value-index.h:24,
                 from core-indel.c:28:
/usr/include/bits/stdio2.h:70:10: note: ‘__builtin___snprintf_chk’ output between 7 and 306 bytes into a destination of size 300
   70 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   71 |        __bos (__s), __fmt, __va_arg_pack ());
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c: In function ‘write_local_reassembly’:
core-indel.c:1722:32: warning: ‘-’ directive writing 1 byte into a region of size between 0 and 299 [-Wformat-overflow=]
 1722 |   sprintf(temp_file_name,"%s@%s-%04u.bin", global_context -> config.temp_file_prefix, chro_name , chro_offset / BASE_BLOCK_LENGTH );
      |                                ^
In file included from /usr/include/stdio.h:866,
                 from subread.h:25,
                 from gene-value-index.h:24,
                 from core-indel.c:28:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 11 or more bytes (assuming 310) into a destination of size 300
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c: In function ‘finalise_long_insertions_by_hashtable’:
core-indel.c:3513:23: warning: ‘.reassembly.fa’ directive writing 14 bytes into a region of size between 1 and 300 [-Wformat-overflow=]
 3513 |  sprintf(tmp_fname,"%s.reassembly.fa", global_context->config.output_prefix);
      |                       ^~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:866,
                 from subread.h:25,
                 from gene-value-index.h:24,
                 from core-indel.c:28:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 15 and 314 bytes into a destination of size 300
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
core-indel.c:3525:33: warning: ‘-’ directive writing 1 byte into a region of size between 0 and 299 [-Wformat-overflow=]
 3525 |    sprintf(temp_file_name,"%s@%s-%04u.bin", global_context -> config.temp_file_prefix, global_context -> chromosome_table.read_names+chro_i*MAX_CHROMOSOME_NAME_LEN , block_no );
      |                                 ^
In file included from /usr/include/stdio.h:866,
                 from subread.h:25,
                 from gene-value-index.h:24,
                 from core-indel.c:28:
/usr/include/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 11 or more bytes (assuming 310) into a destination of size 300
   38 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   39 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o sambam-file.o sambam-file.c
sambam-file.c: In function ‘PBam_get_next_zchunk’:
sambam-file.c:324:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  324 |  fread(&ID1, 1, 1, bam_fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:325:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  325 |  fread(&ID2, 1, 1, bam_fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:326:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  326 |  fread(&CM, 1, 1, bam_fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:327:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  327 |  fread(&FLG, 1, 1, bam_fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:336:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  336 |  fread(&XLEN,1, 2, bam_fp );
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:344:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  344 |   fread(&SI1, 1, 1, bam_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:345:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  345 |   fread(&SI2, 1, 1, bam_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:346:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  346 |   fread(&SLEN, 1, 2, bam_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:350:4: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  350 |    fread(&BSIZE_MID, 1,2 , bam_fp);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:362:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  362 |   fread(buffer, 1, CDATA_READING, bam_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sambam-file.c:366:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  366 |   fread(&real_len, 4, 1, bam_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:519,
                 from sambam-file.c:30:
In function ‘strncpy’,
    inlined from ‘PBam_chunk_headers’ at sambam-file.c:467:6:
/usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 100 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o sublog.o sublog.c
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o gene-algorithms.o gene-algorithms.c
gene-algorithms.c: In function ‘show_cigar’:
gene-algorithms.c:747:6: warning: variable ‘last_end’ set but not used [-Wunused-but-set-variable]
  747 |  int last_end=0, last_offset = 0, cursor = 0;
      |      ^~~~~~~~
gene-algorithms.c:746:9: warning: variable ‘is_error’ set but not used [-Wunused-but-set-variable]
  746 |  int i, is_error = 0;
      |         ^~~~~~~~
gene-algorithms.c: In function ‘match_chro_indel’:
gene-algorithms.c:1159:28: warning: variable ‘last_section_indels’ set but not used [-Wunused-but-set-variable]
 1159 |  int last_section_end = 0, last_section_indels=0;
      |                            ^~~~~~~~~~~~~~~~~~~
gene-algorithms.c: In function ‘miltime’:
gene-algorithms.c:1541:2: warning: ‘ftime’ is deprecated [-Wdeprecated-declarations]
 1541 |  ftime(&trp);
      |  ^~~~~
In file included from gene-algorithms.c:32:
/usr/include/sys/timeb.h:39:12: note: declared here
   39 | extern int ftime (struct timeb *__timebuf)
      |            ^~~~~
gene-algorithms.c: In function ‘search_DP_branch’:
gene-algorithms.c:1703:6: warning: variable ‘table_mask2_j_1’ set but not used [-Wunused-but-set-variable]
 1703 |  int table_mask2_j_1 = 0, table_mask2_i_1 = 0;
      |      ^~~~~~~~~~~~~~~
gene-algorithms.c: In function ‘final_mapping_quality’:
gene-algorithms.c:2344:7: warning: variable ‘is_match_begin’ set but not used [-Wunused-but-set-variable]
 2344 |   int is_match_begin = 0;
      |       ^~~~~~~~~~~~~~
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o hashtable.o hashtable.c
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o input-files.o input-files.c
input-files.c: In function ‘geinput_next_char’:
input-files.c:442:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  442 |     fgets(out_buf, 1999,input->input_fp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function ‘sort_SAM_finalise’:
input-files.c:2188:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2188 |     fread(&read_name_len, 2,1 , bbfp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:2194:6: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2194 |      fread(read_name, 1, read_name_len, bbfp);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:2197:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2197 |     fread(&read_len,2,1,bbfp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:2203:6: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2203 |      fread(new_line_mem, 1, read_len, bbfp);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:2256:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2256 |     fread(&read_name_len, 2,1 , bbfp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:2262:6: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2262 |      fread(read_name_buf, 1, read_name_len, bbfp);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:2266:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2266 |     fread(&read_len, 2,1 , bbfp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c:2269:6: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2269 |      fread(read_line_buf, 1, read_len, bbfp);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
input-files.c: In function ‘is_SAM_unsorted’:
input-files.c:2651:33: warning: ‘read_name[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2651 |  for(field_cursor = 0; read_name[field_cursor] ; field_cursor++)
      |                        ~~~~~~~~~^~~~~~~~~~~~~~
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o sorted-hashtable.o sorted-hashtable.c
sorted-hashtable.c: In function ‘gehash_load’:
sorted-hashtable.c:1249:2: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1249 |  fread(magic_chars,1,8,fp);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1272:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1272 |     fread(&option_key, 2, 1, fp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1275:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1275 |     fread(&option_length, 2, 1, fp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1278:6: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 1278 |      fread(&(the_table -> index_gap),2,1,fp);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o gene-value-index.o gene-value-index.c
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o exon-algorithms.o exon-algorithms.c
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o HelperFunctions.o HelperFunctions.c
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o interval_merge.o interval_merge.c
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -O2 -pipe -march=native -fno-diagnostics-color    -c -o long-hashtable.o long-hashtable.c
gcc   -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\""1.4.6"\"  -D_FILE_OFFSET_BITS=64 -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0  -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o  -lpthread -lz -lm   -DMAKE_FOR_EXON -D MAKE_STANDALONE 
readSummary.c: In function ‘readSummary’:
readSummary.c:2708:9: warning: variable ‘curchr_name’ set but not used [-Wunused-but-set-variable]
 2708 |  char * curchr_name;
      |         ^~~~~~~~~~~
readSummary.c:2707:15: warning: variable ‘curpos’ set but not used [-Wunused-but-set-variable]
 2707 |  long curchr, curpos;
      |               ^~~~~~
readSummary.c:2707:7: warning: variable ‘curchr’ set but not used [-Wunused-but-set-variable]
 2707 |  long curchr, curpos;
      |       ^~~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: core.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: multiple definition of `replica_index'; /var/tmp/portage/sci-biology/subread-1.4.6/temp/ccHgWVyy.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: core-junction.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: multiple definition of `replica_index'; /var/tmp/portage/sci-biology/subread-1.4.6/temp/ccHgWVyy.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: core-indel.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: multiple definition of `replica_index'; /var/tmp/portage/sci-biology/subread-1.4.6/temp/ccHgWVyy.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: sambam-file.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: multiple definition of `replica_index'; /var/tmp/portage/sci-biology/subread-1.4.6/temp/ccHgWVyy.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: gene-algorithms.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: multiple definition of `replica_index'; /var/tmp/portage/sci-biology/subread-1.4.6/temp/ccHgWVyy.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: input-files.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: multiple definition of `replica_index'; /var/tmp/portage/sci-biology/subread-1.4.6/temp/ccHgWVyy.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: sorted-hashtable.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: multiple definition of `replica_index'; /var/tmp/portage/sci-biology/subread-1.4.6/temp/ccHgWVyy.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: gene-value-index.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: multiple definition of `replica_index'; /var/tmp/portage/sci-biology/subread-1.4.6/temp/ccHgWVyy.o:/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src/gene-algorithms.h:63: first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile.Linux:40: featureCounts] Error 1
 * ERROR: sci-biology/subread-1.4.6::science failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/subread-1.4.6::science'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/subread-1.4.6::science'`.
 * The complete build log is located at '/var/log/portage/sci-biology:subread-1.4.6:20201119-104739.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/subread-1.4.6/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/subread-1.4.6/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source/src'
 * S: '/var/tmp/portage/sci-biology/subread-1.4.6/work/subread-1.4.6-source'