############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Rsubread ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘Rsubread’ ... ** this is package ‘Rsubread’ version ‘2.25.0’ ** using staged installation @@@@@ The operating system is Linux. ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c HelperFunctions.c -o HelperFunctions.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMbase-index.c -o LRMbase-index.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMchro-event.c -o LRMchro-event.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMfile-io.c -o LRMfile-io.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMhashtable.c -o LRMhashtable.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMhelper.c -o LRMhelper.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMseek-zlib.c -o LRMseek-zlib.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c R_wrapper.c -o R_wrapper.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c RsimReads.c -o RsimReads.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c SNPCalling.c -o SNPCalling.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c aligner.c -o aligner.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c atgcContent.c -o atgcContent.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c build-sam-index.c -o build-sam-index.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c cell-counts.c -o cell-counts.o cell-counts.c: In function ‘cellCounts_write_junction_sumtable’: cell-counts.c:1174:16: warning: unused variable ‘params’ [-Wunused-variable] 1174 | void * params [5]; | ^~~~~~ cell-counts.c: In function ‘cellCounts_add_or_update_chroEvent_in_table’: cell-counts.c:1257:23: warning: variable ‘new_details’ set but not used [-Wunused-but-set-variable] 1257 | chroEvent_t * new_details = NULL; | ^~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_copy_txn_to_juncs’: cell-counts.c:1311:28: warning: variable ‘last_start’ set but not used [-Wunused-but-set-variable] 1311 | int last_end = -1, last_start = -1; | ^~~~~~~~~~ cell-counts.c: In function ‘cellCounts_register_junc_feature’: cell-counts.c:1517:30: warning: unused variable ‘sample_i’ [-Wunused-variable] 1517 | int xk1, edge_tab_i, sample_i; | ^~~~~~~~ cell-counts.c: In function ‘cellCounts_vote_and_add_count’: cell-counts.c:2797:139: warning: unused variable ‘testi’ [-Wunused-variable] 2797 | char * sample_seq=NULL, *sample_qual=NULL, *BC_qual=NULL, *BC_seq=NULL, *UMI_seq=NULL, *UMI_qual=NULL, *lane_str=NULL, *RG=NULL, *testi; | ^~~~~ cell-counts.c: In function ‘cellCounts_convert_stack_to_cigar_str’: cell-counts.c:3360:37: warning: unused variable ‘thread_context’ [-Wunused-variable] 3360 | cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no; | ^~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_end_build_candidature_from_stacks’: cell-counts.c:3441:29: warning: unused variable ‘cigar_rlen’ [-Wunused-variable] 3441 | int cigar_rlen = cellCounts_reduce_Cigar(cigar_end5,final_cigar); | ^~~~~~~~~~ cell-counts.c:3408:29: warning: unused variable ‘x_candidate’ [-Wunused-variable] 3408 | int x_3end, x_5end, x_candidate; | ^~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_tree_iterative_search’: cell-counts.c:3620:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable] 3620 | int read_for_testing_len = edge_region_end - edge_region_start +1; | ^~~~~~~~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_explain_one_alignment’: cell-counts.c:3726:139: warning: unused variable ‘testi’ [-Wunused-variable] 3726 | char * sample_seq=NULL, *sample_qual=NULL, *BC_qual=NULL, *BC_seq=NULL, *UMI_seq=NULL, *UMI_qual=NULL, *lane_str=NULL, *RG=NULL, *testi; | ^~~~~ cell-counts.c: In function ‘cellCounts_add_covered_indels_in_table’: cell-counts.c:4005:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4005 | if(1) cellCounts_add_or_update_chroEvent_in_table(cct_context, sample_i, chroEvent_t_TYPE_INDEL , chro_name, chro_pos -1, rposv, inslen_negative, 0); // thread safe | ^~ cell-counts.c:4006:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4006 | if(nch=='D') chro_cursor += tmpi; | ^~ cell-counts.c:3987:13: warning: unused variable ‘retlen’ [-Wunused-variable] 3987 | int retlen = general_dynamic_align_moves_to_cigar(result_buffer, moved_len, result_cigar); | ^~~~~~ cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’: cell-counts.c:4102:45: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable] 4102 | int rgap = -1; | ^~~~ cell-counts.c:4167:37: warning: unused variable ‘is_update’ [-Wunused-variable] 4167 | int is_update = cellCounts_add_or_update_chroEvent_in_table(cct_context, sample_i, chroEvent_t_TYPE_JUNCTION, machro, mapos, tstpos, 0, 0);//mapos and tstpos are just borrowed variables. | ^~~~~~~~~ cell-counts.c:4155:37: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable] 4155 | int rgap = -1; | ^~~~ cell-counts.c:4142:37: warning: unused variable ‘manegative’ [-Wunused-variable] 4142 | int manegative = votetab -> masks[mai][maj]; | ^~~~~~~~~~ cell-counts.c:4054:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable] 4054 | int best_GTAG_negative = -1; | ^~~~~~~~~~~~~~~~~~ cell-counts.c:4051:29: warning: variable ‘best_misma_no’ set but not used [-Wunused-but-set-variable] 4051 | int best_misma_no = -1; | ^~~~~~~~~~~~~ cell-counts.c:4022:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable] 4022 | int i,j,reverse_text_offset, distinct_vote_number_i; | ^~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:4022:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable] 4022 | int i,j,reverse_text_offset, distinct_vote_number_i; | ^~~~~~~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_add_supported_unsupported_reads_from_cigar’: cell-counts.c:4265:37: warning: variable ‘on_chro_len’ set but not used [-Wunused-but-set-variable] 4265 | int on_chro_len = tmpi +1; | ^~~~~~~~~~~ cell-counts.c:4296:66: warning: variable ‘x2_not_matter’ set but not used [-Wunused-but-set-variable] 4296 | int is_the_last, x2_not_matter; | ^~~~~~~~~~~~~ cell-counts.c:4330:81: warning: array subscript has type ‘char’ [-Wchar-subscripts] 4330 | IVT_IntervalTreeNode * myroot = LR_roots[LRi]; | ^ cell-counts.c:4222:41: warning: unused variable ‘x3’ [-Wunused-variable] 4222 | int nch, tmpi=0, x1=0, b1off=0, x3; | ^~ cell-counts.c: In function ‘cellCounts_write_final_junctions’: cell-counts.c:7220:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable] 7220 | int unique_junctions = 0; | ^~~~~~~~~~~~~~~~ cell-counts.c:7199:20: warning: unused variable ‘ky_i2’ [-Wunused-variable] 7199 | int ky_i1, ky_i2; | ^~~~~ cell-counts.c:7199:13: warning: unused variable ‘ky_i1’ [-Wunused-variable] 7199 | int ky_i1, ky_i2; | ^~~~~ cell-counts.c:7197:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable] 7197 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail; | ^~~~~~~~~~~~~~ cell-counts.c:7163:13: warning: unused variable ‘infile_i’ [-Wunused-variable] 7163 | int infile_i, disk_is_full = 0, sample_i; | ^~~~~~~~ cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’: cell-counts.c:2375:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized] 2375 | if(search_start>0xffffff00) return; | ^ cell-counts.c:2364:30: note: ‘search_start’ was declared here 2364 | unsigned int search_start, search_end, search_block_id; | ^~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_write_final_other_events’: cell-counts.c:7130:40: warning: array subscript -999 is below array bounds of ‘HashTable *[65]’ [-Warray-bounds=] 7130 | ArrayList * small_large_keys = HashTableKeys(cct_context -> chroEvent_detail_table[sample_i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:324:27: note: while referencing ‘chroEvent_detail_table’ 324 | HashTable * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1]; | ^~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:7135:86: warning: array subscript -999 is below array bounds of ‘HashTable *[65]’ [-Warray-bounds=] 7135 | chroEvent_t * ed = HashTableGet(cct_context -> chroEvent_detail_table[sample_i] , ArrayListGet(small_large_keys,x1)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ cell-counts.c:324:27: note: while referencing ‘chroEvent_detail_table’ 324 | HashTable * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1]; | ^~~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-bigtable.c -o core-bigtable.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-indel.c -o core-indel.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-interface-aligner.c -o core-interface-aligner.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core-interface-subjunc.c -o core-interface-subjunc.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c core.c -o core.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c detectionCall.c -o detectionCall.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c detectionCallAnnotation.c -o detectionCallAnnotation.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c exon-algorithms.c -o exon-algorithms.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c exon-align-indel.c -o exon-align-indel.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c exon-align.c -o exon-align.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c flattenAnnotations.c -o flattenAnnotations.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c fullscan.c -o fullscan.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c fusion-align.c -o fusion-align.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c gen_rand_reads.c -o gen_rand_reads.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c gene-algorithms.c -o gene-algorithms.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c hashtable.c -o hashtable.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c index-builder.c -o index-builder.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c interval_merge.c -o interval_merge.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c long-hashtable.c -o long-hashtable.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c longread-mapping.c -o longread-mapping.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c mergeVCF.c -o mergeVCF.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c processExons.c -o processExons.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c propmapped.c -o propmapped.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c qualityScores.c -o qualityScores.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c read-repair.c -o read-repair.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c readSummary.c -o readSummary.o readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3900:58: warning: variable ‘assignment_target_number’ set but not used [-Wunused-but-set-variable] 3900 | srInt_64 assignment_target_number = tmp_voter_id; | ^~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘fc_thread_merge_results’: readSummary.c:3970:32: warning: unused variable ‘sample_i’ [-Wunused-variable] 3970 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ readSummary.c: In function ‘fc_write_final_junctions’: readSummary.c:5724:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable] 5724 | int unique_junctions = 0; | ^~~~~~~~~~~~~~~~ readSummary.c:5700:20: warning: unused variable ‘ky_i2’ [-Wunused-variable] 5700 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5700:13: warning: unused variable ‘ky_i1’ [-Wunused-variable] 5700 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5698:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable] 5698 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail; | ^~~~~~~~~~~~~~ readSummary.c: In function ‘readSummary’: readSummary.c:5971:52: warning: variable ‘scrna_total_BAM_no’ set but not used [-Wunused-but-set-variable] 5971 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; | ^~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3833:66: warning: ‘longest_overlap_score’ may be used uninitialized [-Wmaybe-uninitialized] 3833 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:3602:51: note: ‘longest_overlap_score’ was declared here 3602 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c removeDupReads.c -o removeDupReads.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sam2bed.c -o sam2bed.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sambam-file.c -o sambam-file.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c seek-zlib.c -o seek-zlib.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sorted-hashtable.c -o sorted-hashtable.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c sublog.c -o sublog.o gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.0\"" -g3 -fpic -g -O2 -Wall -Werror=format-security -c tx-unique.c -o tx-unique.o gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-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-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-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)