* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Linux.
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c HelperFunctions.c -o HelperFunctions.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c R_wrapper.c -o R_wrapper.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c SNPCalling.c -o SNPCalling.o
SNPCalling.c: In function ‘read_tmp_block’:
SNPCalling.c:275:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&SNP_rec, sizeof(SNP_rec),1 , tmp_fp);
^
SNPCalling.c:294:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_rec, sizeof(read_rec), 1, tmp_fp);
^
SNPCalling.c:295:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
SNPCalling.c:296:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read, sizeof(char), read_len, tmp_fp);
^
SNPCalling.c:297:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(qual, sizeof(char), read_len, tmp_fp);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c aligner.c -o aligner.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c atgcContent.c -o atgcContent.o
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:73:7: warning: unused variable ‘data_ready’ [-Wunused-variable]
int data_ready=1;
^
atgcContent.c:71:7: warning: unused variable ‘offset’ [-Wunused-variable]
int offset;
^
atgcContent.c:70:7: warning: unused variable ‘readlen’ [-Wunused-variable]
int readlen;
^
atgcContent.c:68:11: warning: unused variable ‘z’ [-Wunused-variable]
ssize_t z;
^
atgcContent.c:67:10: warning: unused variable ‘len’ [-Wunused-variable]
size_t len = 0;
^
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:109:11: warning: unused variable ‘z’ [-Wunused-variable]
ssize_t z;
^
atgcContent.c:108:10: warning: unused variable ‘len’ [-Wunused-variable]
size_t len = 0;
^
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:85:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MAX_LINE_LENGTH, fin);
^
atgcContent.c: In function ‘atgcContent’:
atgcContent.c:111:7: warning: ‘readlen’ may be used uninitialized in this function [-Wmaybe-uninitialized]
int readlen;
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c build-sam-index.c -o build-sam-index.o
build-sam-index.c: In function ‘transfer_SAM_to_position_table’:
build-sam-index.c:364:47: warning: variable ‘is_anchor_certain’ set but not used [-Wunused-but-set-variable]
int read_len, is_repeated, mapping_quality, is_anchor_certain=1;
^
build-sam-index.c: In function ‘transform_pillup_to_index’:
build-sam-index.c:125:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&record, sizeof(record), 1, pile_fp);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c core-bigtable.c -o core-bigtable.o
core-bigtable.c: In function ‘bigtable_readonly_result’:
core-bigtable.c:70:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(write_ptr, loadjunc?sizeof(subjunc_result_t):sizeof(mapping_result_t), 1, global_context -> bigtable_cache_file_fp);
^
core-bigtable.c: In function ‘bigtable_retrieve_cache’:
core-bigtable.c:227:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> big_margin_data , sizeof(short) * 3 * global_context -> config.big_margin_record_size , 1, global_context -> bigtable_cache_file_fp );
^
core-bigtable.c:228:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> alignment_res , sizeof(mapping_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp );
^
core-bigtable.c:231:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread( current_cache -> subjunc_res , sizeof(subjunc_result_t) * global_context -> config.multi_best_reads , 1, global_context -> bigtable_cache_file_fp);
^
core-bigtable.c:237:5: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(global_context -> bigtable_cache_file_fp), new_file_size);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c core-indel.c -o core-indel.o
core-indel.c: In function ‘find_new_indels’:
core-indel.c:1589:9: warning: variable ‘best_j’ set but not used [-Wunused-but-set-variable]
int best_j=0, best_score=-99999, is_ambiguous_indel= 0;
^
core-indel.c: In function ‘full_indel_alignment’:
core-indel.c:2936:41: warning: variable ‘best_right’ set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^
core-indel.c:2936:30: warning: variable ‘best_left’ set but not used [-Wunused-but-set-variable]
int best_edge_score = -1, best_left, best_right;
^
core-indel.c: In function ‘find_potential_ultralong_indels’:
core-indel.c:3035:24: warning: variable ‘best_c2_location’ set but not used [-Wunused-but-set-variable]
int best_match = -1, best_c2_location = -1;
^
core-indel.c: In function ‘finalise_pileup_file’:
core-indel.c:3313:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
core-indel.c:3314:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3315:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3392:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
core-indel.c:3393:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3394:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c: In function ‘finalise_pileup_file_by_debrujin’:
core-indel.c:3756:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
core-indel.c:3757:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read_text, sizeof(char), read_len, tmp_fp);
^
core-indel.c:3758:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c core-junction.c -o core-junction.o
core-junction.c: In function ‘copy_vote_to_alignment_res’:
core-junction.c:945:12: warning: variable ‘current_piece_minor_score’ set but not used [-Wunused-but-set-variable]
int i,j, current_piece_minor_score = 0;
^
core-junction.c: In function ‘find_donor_receptor’:
core-junction.c:1996:8: warning: variable ‘sp2s’ set but not used [-Wunused-but-set-variable]
char sp2s[200];
^
core-junction.c: In function ‘finalise_explain_CIGAR’:
core-junction.c:3119:10: warning: variable ‘is_front_search’ set but not used [-Wunused-but-set-variable]
int is_front_search = 0;
^
core-junction.c:3255:94: warning: variable ‘total_coverage_length’ set but not used [-Wunused-but-set-variable]
int final_qual = 0, applied_mismatch = 0, non_clipped_length = 0, total_indel_length = 0, total_coverage_length = 0, final_MATCH = 0, chromosomal_length = 0;
^
core-junction.c:3235:28: warning: variable ‘isCigarOK’ set but not used [-Wunused-but-set-variable]
int mismatch_bases = 0, isCigarOK = 0;
^
core-junction.c:3049:23: warning: variable ‘tmp_cigar_exonic’ set but not used [-Wunused-but-set-variable]
char tmp_cigar[120], tmp_cigar_exonic[120];
^
core-junction.c: In function ‘find_translocation_brk_PQR’:
core-junction.c:5635:23: warning: variable ‘candBrkPlist’ set but not used [-Wunused-but-set-variable]
chromosome_event_t * candBrkPlist [_PQR_LIST_SIZE];
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c core.c -o core.o
core.c: In function ‘print_in_box’:
core.c:158:7: warning: variable ‘is_R_linebreak’ set but not used [-Wunused-but-set-variable]
char is_R_linebreak=0, * content, *out_line_buff;
^
core.c: In function ‘convert_GZ_to_FQ’:
core.c:853:19: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
gzFile * rawfp = gzopen(fname, "r");
^
core.c:864:25: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
char * bufr =gzgets(rawfp, linebuff, 3000);
^
In file included from subread.h:26:0,
from core.c:43:
/usr/include/zlib.h:1372:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
core.c:875:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(rawfp);
^
In file included from subread.h:26:0,
from core.c:43:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
core.c: In function ‘calc_tlen’:
core.c:1548:16: warning: variable ‘section_start’ set but not used [-Wunused-but-set-variable]
unsigned int section_start = smaller_head_pos, section_end = 0;
^
core.c: In function ‘do_iteration_one’:
core.c:2174:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
int ret;
^
core.c: In function ‘write_realignments_for_fragment’:
core.c:2386:21: warning: variable ‘raw_r2’ set but not used [-Wunused-but-set-variable]
mapping_result_t * raw_r2 = NULL;
^
core.c:2383:21: warning: variable ‘raw_r1’ set but not used [-Wunused-but-set-variable]
mapping_result_t * raw_r1 = NULL;
^
core.c: In function ‘do_iteration_two’:
core.c:2452:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
int ret;
^
core.c: In function ‘do_voting’:
core.c:3021:9: warning: variable ‘allsubreads_for_each_gap’ set but not used [-Wunused-but-set-variable]
int allsubreads_for_each_gap [GENE_SLIDING_STEP], noninformative_subreads_for_each_gap[GENE_SLIDING_STEP];
^
core.c:2940:6: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
int ret, xk1;
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c detectionCall.c -o detectionCall.o
detectionCall.c: In function ‘build_ir_data_structure_map’:
detectionCall.c:176:28: warning: unused variable ‘read_entrezid’ [-Wunused-variable]
int read_start, read_end, read_entrezid, read_n, read_gc, read_at;
^
detectionCall.c: In function ‘simplify_SAM_file’:
detectionCall.c:214:9: warning: unused variable ‘z’ [-Wunused-variable]
size_t z;
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function ‘build_ir_data_structure’:
detectionCallAnnotation.c:117:28: warning: unused variable ‘read_length’ [-Wunused-variable]
int read_start, read_end, read_length;
^
detectionCallAnnotation.c: In function ‘breakIntegenicRegion’:
detectionCallAnnotation.c:152:43: warning: unused variable ‘read_length’ [-Wunused-variable]
int read_entrezid, read_start, read_end, read_length;
^
detectionCallAnnotation.c:152:6: warning: unused variable ‘read_entrezid’ [-Wunused-variable]
int read_entrezid, read_start, read_end, read_length;
^
detectionCallAnnotation.c: In function ‘calculateExonGCContent’:
detectionCallAnnotation.c:196:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, sizeof(line), fseq);
^
detectionCallAnnotation.c: In function ‘calculateIRGCContent’:
detectionCallAnnotation.c:283:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, sizeof(line), fseq);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c exon-align-indel.c -o exon-align-indel.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c exon-align.c -o exon-align.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c fullscan.c -o fullscan.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c fusion-align.c -o fusion-align.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c: In function ‘show_cigar’:
gene-algorithms.c:771:6: warning: variable ‘last_end’ set but not used [-Wunused-but-set-variable]
int last_end=0, last_offset = 0, cursor = 0;
^
gene-algorithms.c:770:9: warning: variable ‘is_error’ set but not used [-Wunused-but-set-variable]
int i, is_error = 0;
^
gene-algorithms.c: In function ‘match_chro_indel’:
gene-algorithms.c:1183:28: warning: variable ‘last_section_indels’ set but not used [-Wunused-but-set-variable]
int last_section_end = 0, last_section_indels=0;
^
gene-algorithms.c: In function ‘search_DP_branch’:
gene-algorithms.c:1732:6: warning: variable ‘table_mask2_j_1’ set but not used [-Wunused-but-set-variable]
int table_mask2_j_1 = 0, table_mask2_i_1 = 0;
^
gene-algorithms.c: In function ‘final_mapping_quality’:
gene-algorithms.c:2373:7: warning: variable ‘is_match_begin’ set but not used [-Wunused-but-set-variable]
int is_match_begin = 0;
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c gene-value-index.c -o gene-value-index.o
gene-value-index.c: In function ‘gvindex_load’:
gene-value-index.c:149:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
int read_length;
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c index-builder.c -o index-builder.o
index-builder.c: In function ‘scan_gene_index’:
index-builder.c:458:19: warning: variable ‘table_no’ set but not used [-Wunused-but-set-variable]
int file_number, table_no, i ,j;
^
index-builder.c: In function ‘main_buildindex’:
index-builder.c:1179:2: warning: ignoring return value of ‘mkstemp’, declared with attribute warn_unused_result [-Wunused-result]
mkstemp(tmp_fa_file);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c input-files.c -o input-files.o
input-files.c: In function ‘SAM_pairer_get_next_read_BIN’:
input-files.c:2754:11: warning: variable ‘ref_name’ set but not used [-Wunused-but-set-variable]
char ref_name[MAX_CHROMOSOME_NAME_LEN];
^
input-files.c: In function ‘fix_write_block’:
input-files.c:4297:23: warning: variable ‘retbam’ set but not used [-Wunused-but-set-variable]
int x1, bam_len = 0, retbam;
^
input-files.c: In function ‘SAM_nosort_run_once’:
input-files.c:4755:9: warning: variable ‘ref_name’ set but not used [-Wunused-but-set-variable]
char ref_name[MAX_CHROMOSOME_NAME_LEN];
^
input-files.c: In function ‘geinput_next_char’:
input-files.c:523:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(out_buf, 1999,input->input_fp);
^
input-files.c: In function ‘SAM_pairer_writer_reset’:
input-files.c:3406:2: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(bam_main -> bam_fp), 0);
^
input-files.c: In function ‘SAM_pairer_osr_next_name’:
input-files.c:3613:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3625:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c: In function ‘SAM_pairer_osr_next_bin’:
input-files.c:3635:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3639:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3642:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(bin, 1, rlen, fp);
^
input-files.c: In function ‘fix_load_next_block’:
input-files.c:4273:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(bam_buf, 1, bsize - xlen - 19, in);
^
input-files.c: In function ‘sort_SAM_finalise’:
input-files.c:5067:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:5073:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read_name, 1, read_name_len, bbfp);
^
input-files.c:5076:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,2,1,bbfp);
^
input-files.c:5082:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(new_line_mem, 1, read_len, bbfp);
^
input-files.c:5135:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:5141:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read_name_buf, 1, read_name_len, bbfp);
^
input-files.c:5145:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, 2,1 , bbfp);
^
input-files.c:5148:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read_line_buf, 1, read_len, bbfp);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c interval_merge.c -o interval_merge.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c long-hashtable.c -o long-hashtable.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c mergeVCF.c -o mergeVCF.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c processExons.c -o processExons.o
processExons.c: In function ‘find_chr’:
processExons.c:237:10: warning: unused variable ‘pt’ [-Wunused-variable]
char *pt = strcpy(gene_array[gene_pos].chr_array[current_chr_index].id,chr_id);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c propmapped.c -o propmapped.o
propmapped.c: In function ‘prop_PE’:
propmapped.c:349:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,1,1,fp);
^
propmapped.c:352:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read_name,read_len,1,fp);
^
propmapped.c:356:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&flags,1, sizeof(short), fp);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c qualityScores.c -o qualityScores.o
qualityScores.c: In function ‘finalise_qs_context’:
qualityScores.c:82:12: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c: In function ‘rewind_qs_file’:
qualityScores.c:275:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c:282:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
qualityScores.c: In function ‘start_qs_context’:
qualityScores.c:313:29: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c read-repair.c -o read-repair.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c readSummary.c -o readSummary.o
readSummary.c: In function ‘calc_junctions_from_cigar’:
readSummary.c:347:15: warning: variable ‘right_boundary’ set but not used [-Wunused-but-set-variable]
unsigned int right_boundary = 0;
^
readSummary.c: In function ‘calc_total_frag_len’:
readSummary.c:1804:15: warning: variable ‘merged_section_indel_positions’ set but not used [-Wunused-but-set-variable]
unsigned int merged_section_indel_positions[ MAXIMUM_INSERTION_IN_SECTION * 3 ][ MAXIMUM_INSERTION_IN_SECTION ];
^
readSummary.c:1802:16: warning: variable ‘merged_section_belong_R2’ set but not used [-Wunused-but-set-variable]
unsigned char merged_section_belong_R2[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
^
readSummary.c:1801:16: warning: variable ‘merged_section_belong_R1’ set but not used [-Wunused-but-set-variable]
unsigned char merged_section_belong_R1[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
^
readSummary.c:1799:15: warning: variable ‘merged_section_start_positions’ set but not used [-Wunused-but-set-variable]
unsigned int merged_section_start_positions[ MAXIMUM_INSERTION_IN_SECTION * 3 ];
^
readSummary.c: In function ‘readSummary’:
readSummary.c:4442:9: warning: variable ‘curchr_name’ set but not used [-Wunused-but-set-variable]
char * curchr_name, * fasta_contigs_fname;
^
readSummary.c:4441:15: warning: variable ‘curpos’ set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c:4441:7: warning: variable ‘curchr’ set but not used [-Wunused-but-set-variable]
long curchr, curpos;
^
readSummary.c: In function ‘load_feature_info’:
readSummary.c:927:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(file_line, MAX_LINE_LENGTH, fp);
^
readSummary.c: In function ‘process_pairer_reset’:
readSummary.c:1555:3: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(global_context -> SAM_output_fp), 0);
^
readSummary.c: In function ‘load_feature_info’:
readSummary.c:865:10: warning: ‘token_temp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
char * token_temp, *chro_name;
^
readSummary.c:929:10: warning: ‘token_temp’ may be used uninitialized in this function [-Wmaybe-uninitialized]
char * token_temp;
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c removeDupReads.c -o removeDupReads.o
removeDupReads.c: In function ‘parse_base_blocks’:
removeDupReads.c:88:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_record, sizeof(base_block_temp_read_t), 1, block_fp);
^
removeDupReads.c:97:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_record, sizeof(base_block_temp_read_t), 1, block_fp);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c sam2bed.c -o sam2bed.o
sam2bed.c: In function ‘sam2bed’:
sam2bed.c:43:7: warning: unused variable ‘i’ [-Wunused-variable]
int i, readlen, chr_start, chr_end, flag, mqs;
^
sam2bed.c:40:10: warning: variable ‘tok’ set but not used [-Wunused-but-set-variable]
char * tok;
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c sambam-file.c -o sambam-file.o
sambam-file.c: In function ‘PBam_get_next_zchunk’:
sambam-file.c:352:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&ID1, 1, 1, bam_fp);
^
sambam-file.c:353:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&ID2, 1, 1, bam_fp);
^
sambam-file.c:354:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&CM, 1, 1, bam_fp);
^
sambam-file.c:355:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&FLG, 1, 1, bam_fp);
^
sambam-file.c:364:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&XLEN,1, 2, bam_fp );
^
sambam-file.c:372:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&SI1, 1, 1, bam_fp);
^
sambam-file.c:373:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&SI2, 1, 1, bam_fp);
^
sambam-file.c:374:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&SLEN, 1, 2, bam_fp);
^
sambam-file.c:378:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&BSIZE_MID, 1,2 , bam_fp);
^
sambam-file.c:390:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, 1, CDATA_READING, bam_fp);
^
sambam-file.c:394:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&real_len, 4, 1, bam_fp);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c seek-zlib.c -o seek-zlib.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o
sorted-hashtable.c: In function ‘load_int32’:
sorted-hashtable.c:1237:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
int read_length;
^
sorted-hashtable.c: In function ‘load_int64’:
sorted-hashtable.c:1246:6: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
int read_length;
^
sorted-hashtable.c: In function ‘gehash_load’:
sorted-hashtable.c:1290:9: warning: variable ‘read_length’ set but not used [-Wunused-but-set-variable]
int i, read_length;
^
sorted-hashtable.c: In function ‘gehash_load_option’:
sorted-hashtable.c:1264:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^
sorted-hashtable.c:1269:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^
sorted-hashtable.c:1272:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^
sorted-hashtable.c:1276:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(result ,option_length,1,fp);
^
sorted-hashtable.c: In function ‘gehash_load’:
sorted-hashtable.c:1303:2: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^
sorted-hashtable.c:1326:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^
sorted-hashtable.c:1329:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^
sorted-hashtable.c:1332:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> index_gap),2,1,fp);
^
sorted-hashtable.c:1334:6: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> padding),2,1,fp);
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.23.4\"" -fpic -g -O2 -Wall -c sublog.c -o sublog.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o Rsubread.so HelperFunctions.o R_wrapper.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o fullscan.o fusion-align.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o interval_merge.o long-hashtable.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/Rsubread.Rcheck/Rsubread/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsubread)
