############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rsubread ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘Rsubread’ ... ** using staged installation @@@@@ The operating system is Linux. ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c HelperFunctions.c -o HelperFunctions.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c LRMbase-index.c -o LRMbase-index.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c LRMchro-event.c -o LRMchro-event.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c LRMfile-io.c -o LRMfile-io.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c LRMhashtable.c -o LRMhashtable.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c LRMhelper.c -o LRMhelper.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c LRMseek-zlib.c -o LRMseek-zlib.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c R_wrapper.c -o R_wrapper.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c RsimReads.c -o RsimReads.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c SNPCalling.c -o SNPCalling.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c aligner.c -o aligner.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c atgcContent.c -o atgcContent.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c build-sam-index.c -o build-sam-index.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c cell-counts.c -o cell-counts.o cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’: cell-counts.c:1622:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized] 1622 | if(search_start>0xffffff00) return; | ^ cell-counts.c:1611:30: note: ‘search_start’ was declared here 1611 | unsigned int search_start, search_end, search_block_id; | ^~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c core-bigtable.c -o core-bigtable.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c core-indel.c -o core-indel.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c core-interface-aligner.c -o core-interface-aligner.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c core-junction.c -o core-junction.o core-junction.c: In function ‘find_donor_receptor’: core-junction.c:2099:25: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) | ^~ core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ | ^~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c core.c -o core.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c detection-calls.c -o detection-calls.o detection-calls.c: In function ‘DTCwrite_annotations’: detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ detection-calls.c:155:109: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c detectionCall.c -o detectionCall.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c exon-algorithms.c -o exon-algorithms.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c exon-align-indel.c -o exon-align-indel.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c exon-align.c -o exon-align.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c flattenAnnotations.c -o flattenAnnotations.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c fullscan.c -o fullscan.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c fusion-align.c -o fusion-align.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c gen_rand_reads.c -o gen_rand_reads.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c gene-algorithms.c -o gene-algorithms.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c gene-value-index.c -o gene-value-index.o gene-value-index.c: In function ‘is_offset_in_chro’: gene-value-index.c:85:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding )) | ^~ In file included from gene-value-index.h:24, from gene-value-index.c:25: subread.h:153:24: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 153 | #define SUBREADprintf msgqu_printf | ^~~~~~~~~~~~ gene-value-index.c:87:41: note: in expansion of macro ‘SUBREADprintf’ 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c hashtable.c -o hashtable.o hashtable.c: In function ‘ArrayListStringJoin’: hashtable.c:51:76: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=] 51 | outpt += snprintf(outbuf + outpt, out_max_len - outpt -1,"%s%s", list->elementList [ x1 ], x1numOfElements-1?",":""); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * void * | %p gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c index-builder.c -o index-builder.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c input-blc.c -o input-blc.o input-blc.c: In function ‘iCache_continuous_read_lanes’: input-blc.c:580:59: warning: unused variable ‘npos’ [-Wunused-variable] 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); | ^~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c input-files.c -o input-files.o input-files.c: In function ‘reduce_SAM_to_BAM’: input-files.c:3244:13: warning: unused variable ‘seq_len’ [-Wunused-variable] 3244 | int seq_len = qual - seq - 1; | ^~~~~~~ input-files.c: In function ‘SAM_pairer_fix_format’: input-files.c:4863:50: warning: variable ‘readname’ set but not used [-Wunused-but-set-variable] 4863 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; | ^~~~~~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c interval_merge.c -o interval_merge.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c long-hashtable.c -o long-hashtable.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c longread-mapping.c -o longread-mapping.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c mergeVCF.c -o mergeVCF.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c processExons.c -o processExons.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c propmapped.c -o propmapped.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c qualityScores.c -o qualityScores.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c read-repair.c -o read-repair.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c readSummary.c -o readSummary.o readSummary.c: In function ‘sort_junc_feature_make_gaps’: readSummary.c:858:47: warning: format ‘%s’ expects argument of type ‘char *’, but argument 5 has type ‘void *’ [-Wformat=] 858 | fprintf(stderr,"POS %d %d of %s\n", min_start,max_stop,k); | ~^ ~ | | | | char * void * | %p readSummary.c: In function ‘sort_junc_feature’: readSummary.c:870:49: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=] 870 | fprintf(stderr,"MERGED GeneBodyTree = %ld\n", global_context -> junction_GenebodyTree_table -> numOfElements); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int srInt_64 {aka long long int} | %lld readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3840:58: warning: variable ‘assignment_target_number’ set but not used [-Wunused-but-set-variable] 3840 | srInt_64 assignment_target_number = tmp_voter_id; | ^~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘fc_thread_merge_results’: readSummary.c:3910:32: warning: unused variable ‘sample_i’ [-Wunused-variable] 3910 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ readSummary.c: In function ‘determine_jcount_gene_transcript_report’: readSummary.c:5460:29: warning: unused variable ‘this_exons’ [-Wunused-variable] 5460 | int this_exons=0; | ^~~~~~~~~~ readSummary.c:5469:29: warning: unused variable ‘this_exons’ [-Wunused-variable] 5469 | int this_exons=0; | ^~~~~~~~~~ readSummary.c: In function ‘fc_write_final_junctions’: readSummary.c:5591:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable] 5591 | int unique_junctions = 0; | ^~~~~~~~~~~~~~~~ readSummary.c:5575:20: warning: unused variable ‘ky_i2’ [-Wunused-variable] 5575 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5575:13: warning: unused variable ‘ky_i1’ [-Wunused-variable] 5575 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5573:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable] 5573 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail; | ^~~~~~~~~~~~~~ readSummary.c: In function ‘readSummary’: readSummary.c:5787:52: warning: variable ‘scrna_total_BAM_no’ set but not used [-Wunused-but-set-variable] 5787 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; | ^~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘register_junc_feature.part.0’: readSummary.c:876:35: warning: array subscript ‘fc_junction_exon_in_transcript_t[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=] 876 | new_item -> transcript_id = HashTableGetKey(global_context -> junction_transcript_table, transcript_id); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:875:55: note: object of size 8 allocated by ‘calloc’ 875 | fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:878:43: warning: array subscript ‘fc_junction_exon_in_transcript_t[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=] 878 | new_item -> transcript_id = strdup(transcript_id); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:875:55: note: object of size 8 allocated by ‘calloc’ 875 | fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:884:83: warning: array subscript ‘fc_junction_exon_in_transcript_t[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=] 884 | HashTablePut(global_context -> junction_transcript_table, new_item->transcript_id, new_txp); | ~~~~~~~~^~~~~~~~~~~~~~~ readSummary.c:875:55: note: object of size 8 allocated by ‘calloc’ 875 | fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:890:32: warning: array subscript ‘fc_junction_exon_in_transcript_t[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=] 890 | new_item -> chro_start = start; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ readSummary.c:875:55: note: object of size 8 allocated by ‘calloc’ 875 | fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:891:31: warning: array subscript ‘fc_junction_exon_in_transcript_t[0]’ is partly outside array bounds of ‘unsigned char[8]’ [-Warray-bounds=] 891 | new_item -> chro_stop = stop; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ readSummary.c:875:55: note: object of size 8 allocated by ‘calloc’ 875 | fc_junction_exon_in_transcript_t * new_item = calloc(sizeof(sizeof(fc_junction_exon_in_transcript_t)),1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3773:66: warning: ‘longest_overlap_score’ may be used uninitialized [-Wmaybe-uninitialized] 3773 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:3542:51: note: ‘longest_overlap_score’ was declared here 3542 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c removeDupReads.c -o removeDupReads.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c sam2bed.c -o sam2bed.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c sambam-file.c -o sambam-file.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c seek-zlib.c -o seek-zlib.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c sorted-hashtable.c -o sorted-hashtable.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c sublog.c -o sublog.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.21.1\"" -fpic -g -O2 -Wall -c tx-unique.c -o tx-unique.o gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.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 tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-Rsubread/00new/Rsubread/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rsubread)