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###
### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD INSTALL Rsubread
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* installing to library ‘/home/biocbuild/bbs-3.3-bioc/R/library’
* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Linux.
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c HelperFunctions.c -o HelperFunctions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c R_wrapper.c -o R_wrapper.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c SNPCalling.c -o SNPCalling.o
SNPCalling.c: In function ‘read_tmp_block’:
SNPCalling.c:256:9: 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:275:9: 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:276:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, sizeof(short), 1, tmp_fp);
^
SNPCalling.c:277:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read, sizeof(char), read_len, tmp_fp);
^
SNPCalling.c:278:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(qual, sizeof(char), read_len, tmp_fp);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c aligner.c -o aligner.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c atgcContent.c -o atgcContent.o
atgcContent.c: In function ‘retrieve_sequence’:
atgcContent.c:85:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MAX_LINE_LENGTH, fin);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c build-sam-index.c -o build-sam-index.o
build-sam-index.c: In function ‘transform_pillup_to_index’:
build-sam-index.c:125:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&record, sizeof(record), 1, pile_fp);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c core-bigtable.c -o core-bigtable.o
core-bigtable.c: In function ‘bigtable_readonly_result’:
core-bigtable.c:70:9: 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:219:12: 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:220:12: 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:223:14: 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:229:14: 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 -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c core-indel.c -o core-indel.o
core-indel.c: In function ‘finalise_pileup_file’:
core-indel.c:3291:8: 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:3292:8: 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:3293:8: 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:3370:8: 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:3371:8: 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:3372:8: 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:3734:8: 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:3735:8: 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:3736:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(qual_text, sizeof(char), read_len, tmp_fp);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c core-interface-aligner.c -o core-interface-aligner.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c core-junction.c -o core-junction.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c core.c -o core.o
core.c: In function ‘convert_GZ_to_FQ’:
core.c:781:19: warning: initialization from incompatible pointer type [enabled by default]
gzFile * rawfp = gzopen(fname, "r");
^
core.c:792:5: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [enabled by default]
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’ but argument is of type ‘struct gzFile_s **’
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
core.c:803:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(rawfp);
^
In file included from subread.h:26:0,
from core.c:43:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c detectionCall.c -o detectionCall.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c: In function ‘calculateExonGCContent’:
detectionCallAnnotation.c:196:8: 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:283:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
fgets(line, sizeof(line), fseq);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c exon-algorithms.c -o exon-algorithms.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c exon-align-indel.c -o exon-align-indel.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c exon-align.c -o exon-align.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c fullscan.c -o fullscan.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c fusion-align.c -o fusion-align.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c gene-algorithms.c -o gene-algorithms.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c gene-value-index.c -o gene-value-index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c hashtable.c -o hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c index-builder.c -o index-builder.o
index-builder.c: In function ‘main_buildindex’:
index-builder.c:1166:9: warning: ignoring return value of ‘mkstemp’, declared with attribute warn_unused_result [-Wunused-result]
mkstemp(tmp_fa_file);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c input-files.c -o input-files.o
input-files.c: In function ‘geinput_next_char’:
input-files.c:505:10: 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:3189:11: 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:3361:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3373:8: 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:3383:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3387:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&rlen, 1, 2, fp);
^
input-files.c:3390:7: 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:3750:9: 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:4419:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:4425:11: 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:4428:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,2,1,bbfp);
^
input-files.c:4434:11: 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:4487:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_name_len, 2,1 , bbfp);
^
input-files.c:4493:11: 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:4497:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len, 2,1 , bbfp);
^
input-files.c:4500:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read_line_buf, 1, read_len, bbfp);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c interval_merge.c -o interval_merge.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c long-hashtable.c -o long-hashtable.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c mergeVCF.c -o mergeVCF.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c processExons.c -o processExons.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c propmapped.c -o propmapped.o
propmapped.c: In function ‘prop_PE’:
propmapped.c:346:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&read_len,1,1,fp);
^
propmapped.c:349:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(read_name,read_len,1,fp);
^
propmapped.c:353:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&flags,1, sizeof(short), fp);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c qualityScores.c -o qualityScores.o
qualityScores.c: In function ‘finalise_qs_context’:
qualityScores.c:82:4: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ but argument is of type ‘struct gzFile_s **’
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
qualityScores.c: In function ‘rewind_qs_file’:
qualityScores.c:275:3: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [enabled by default]
gzclose(qs_context -> gzfq_reader);
^
In file included from qualityScores.c:24:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile’ 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 [enabled by default]
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 [enabled by default]
qs_context -> gzfq_reader = gzopen(qs_context->input_name, "rb");
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c readSummary.c -o readSummary.o
readSummary.c: In function ‘load_feature_info’:
readSummary.c:868:8: 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:1458:12: warning: ignoring return value of ‘ftruncate’, declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(global_context -> SAM_output_fp), 0);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c removeDupReads.c -o removeDupReads.o
removeDupReads.c: In function ‘parse_base_blocks’:
removeDupReads.c:87:10: 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:96:10: 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 -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c sam2bed.c -o sam2bed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c sambam-file.c -o sambam-file.o
sambam-file.c: In function ‘PBam_get_next_zchunk’:
sambam-file.c:325:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&ID1, 1, 1, bam_fp);
^
sambam-file.c:326:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&ID2, 1, 1, bam_fp);
^
sambam-file.c:327:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&CM, 1, 1, bam_fp);
^
sambam-file.c:328:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&FLG, 1, 1, bam_fp);
^
sambam-file.c:337:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&XLEN,1, 2, bam_fp );
^
sambam-file.c:345:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&SI1, 1, 1, bam_fp);
^
sambam-file.c:346:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&SI2, 1, 1, bam_fp);
^
sambam-file.c:347:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&SLEN, 1, 2, bam_fp);
^
sambam-file.c:351:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&BSIZE_MID, 1,2 , bam_fp);
^
sambam-file.c:363:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(buffer, 1, CDATA_READING, bam_fp);
^
sambam-file.c:367:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&real_len, 4, 1, bam_fp);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c seek-zlib.c -o seek-zlib.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o
sorted-hashtable.c: In function ‘gehash_load’:
sorted-hashtable.c:1267:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(magic_chars,1,8,fp);
^
sorted-hashtable.c:1290:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&option_key, 2, 1, fp);
^
sorted-hashtable.c:1293:10: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&option_length, 2, 1, fp);
^
sorted-hashtable.c:1296:11: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread(&(the_table -> index_gap),2,1,fp);
^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.21.0\"" -fpic -g -O2 -c sublog.c -o sublog.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-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 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-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/R/library/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)