* Package: sci-biology/subread-1.4.6 * Repository: science * Maintainer: mmokrejs@fold.natur.cuni.cz sci-biology@gentoo.org * 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'