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###
### Running command:
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###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL Rsubread
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.23.2’
** 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/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c HelperFunctions.c -o HelperFunctions.o
In file included from HelperFunctions.c:56:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMbase-index.c -o LRMbase-index.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMchro-event.c -o LRMchro-event.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMfile-io.c -o LRMfile-io.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMhashtable.c -o LRMhashtable.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMhelper.c -o LRMhelper.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c R_wrapper.c -o R_wrapper.o
In file included from HelperFunctions.h:24,
                 from R_wrapper.c:35:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c RsimReads.c -o RsimReads.o
In file included from RsimReads.c:21:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c SNPCalling.c -o SNPCalling.o
In file included from SNPCalling.c:33:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c aligner.c -o aligner.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c atgcContent.c -o atgcContent.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c build-sam-index.c -o build-sam-index.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c cell-counts.c -o cell-counts.o
In file included from cell-counts.c:13:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
cell-counts.c: In function ‘cellCounts_junckey_sort_merge’:
cell-counts.c:352:88: warning: implicit declaration of function ‘junckey_sort_compare’ [-Wimplicit-function-declaration]
  352 |                 if((read_1_ptr == start+items1)||(read_2_ptr < start+items1+items2 &&  junckey_sort_compare(inptr, read_1_ptr, read_2_ptr) > 0 )) {
      |                                                                                        ^~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_args_context’:
cell-counts.c:808:26: warning: #warning "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======" [-Wcpp]
  808 |                         #warning "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======"
      |                          ^~~~~~~
cell-counts.c: In function ‘cellCounts_write_one_chroEvent’:
cell-counts.c:1126:47: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘int *’ [-Wformat=]
 1126 |                 fprintf(wfp,"%s\t%d\t%d\t%s\t%d\n", chro, pos1, pos2, ce -> from_truth?"ANNOTATED":"NEW", ce -> step2_supported_reads);
      |                                              ~^                                                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                               |                                                              |
      |                                               int                                                            int *
      |                                              %ls
cell-counts.c: In function ‘cellCounts_set_chroEvent_details’:
cell-counts.c:1151:93: warning: passing argument 2 of ‘HashTableGet’ makes pointer from integer without a cast [-Wint-conversion]
 1151 |         chroEvent_t * old_or_new_env = HashTableGet( cct_context -> chroEvent_detail_table, envkey);
      |                                                                                             ^~~~~~
      |                                                                                             |
      |                                                                                             srUInt_64 {aka long long unsigned int}
In file included from subread.h:35:
hashtable.h:231:61: note: expected ‘const void *’ but argument is of type ‘srUInt_64’ {aka ‘long long unsigned int’}
  231 | void * HashTableGet(const HashTable *hashTable, const void *key);
      |                                                 ~~~~~~~~~~~~^~~
cell-counts.c: In function ‘cellCounts_junction_in_table’:
cell-counts.c:1247:44: warning: passing argument 4 of ‘IVT_query_range’ from incompatible pointer type [-Wincompatible-pointer-types]
 1247 |         IVT_query_range( LR_roots[0], l,l, (IVT_IntervalTreeNode**)search_out, JUNCTION_MAX_COLOCATION, &coloc_num );
      |                                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                            |
      |                                            IVT_IntervalTreeNode **
In file included from cell-counts.c:15:
HelperFunctions.h:313:107: note: expected ‘IVT_Interval **’ but argument is of type ‘IVT_IntervalTreeNode **’
  313 | void IVT_query_range(IVT_IntervalTreeNode* root, srInt_64 edge_L_inc, srInt_64 edge_R_inc, IVT_Interval **outbuf, int outbuf_capa, int * items);
      |                                                                                            ~~~~~~~~~~~~~~~^~~~~~
cell-counts.c: In function ‘features_load_one_line’:
cell-counts.c:1366:95: warning: passing argument 3 of ‘HashTableSetDeallocationFunctions’ from incompatible pointer type [-Wincompatible-pointer-types]
 1366 |                 HashTableSetDeallocationFunctions(cct_context -> transcript_exon_table, free, ArrayListDestroy);
      |                                                                                               ^~~~~~~~~~~~~~~~
      |                                                                                               |
      |                                                                                               void (*)(ArrayList *)
hashtable.h:491:47: note: expected ‘void (*)(void *)’ but argument is of type ‘void (*)(ArrayList *)’
  491 |                                        void (*valueDeallocator)(void *value));
      |                                        ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_register_junc_feature’:
cell-counts.c:1533:16: warning: ‘return’ with a value, in function returning void [-Wreturn-type]
 1533 |         return 0;
      |                ^
cell-counts.c:1453:6: note: declared here
 1453 | void cellCounts_register_junc_feature(cellcounts_global_t * cct_context, char * feature_name, char * transcript_id, char * chro, unsigned int start, unsigned int stop, int is_negative){
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_release_context_from_align’:
cell-counts.c:2739:54: warning: passing argument 1 of ‘destroy_typical_dynamic_align’ from incompatible pointer type [-Wincompatible-pointer-types]
 2739 |         destroy_typical_dynamic_align(thread_context -> dynamic_align_buffers, MAX_SCRNA_READ_LENGTH);
      |                                       ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
      |                                                      |
      |                                                      char ***
HelperFunctions.h:284:45: note: expected ‘void ***’ but argument is of type ‘char ***’
  284 | void destroy_typical_dynamic_align(void *** buffers,int max_read_length);
      |                                    ~~~~~~~~~^~~~~~~
cell-counts.c: In function ‘cellCounts_prepare_context_for_align’:
cell-counts.c:2743:51: warning: passing argument 1 of ‘init_typical_dynamic_align’ from incompatible pointer type [-Wincompatible-pointer-types]
 2743 |         init_typical_dynamic_align(thread_context -> dynamic_align_buffers, thread_context -> dynamic_align_penalties, MAX_SCRNA_READ_LENGTH);
      |                                    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
      |                                                   |
      |                                                   char ***
HelperFunctions.h:283:42: note: expected ‘void ***’ but argument is of type ‘char ***’
  283 | void init_typical_dynamic_align(void *** buffers, int * penalties, int max_read_length);
      |                                 ~~~~~~~~~^~~~~~~
cell-counts.c: In function ‘cellCounts_end_build_candidature_from_stacks’:
cell-counts.c:3196:29: warning: unused variable ‘x_candidate’ [-Wunused-variable]
 3196 |         int x_3end, x_5end, x_candidate;
      |                             ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_build_junction_read_finalise_current_stack’:
cell-counts.c:3315:2: warning: #warning "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn  =============" [-Wcpp]
 3315 | #warning "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn  ============="
      |  ^~~~~~~
cell-counts.c: In function ‘cellCounts_build_junction_read_one_end’:
cell-counts.c:3384:45: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
 3384 | if(0)fprintf(stderr,"GAP_IN_EVENT %d Dist: %d    locs %d ~ %d  gaplen %d\n",x1, abs(evb -> start - this_end_last_correct_maiping_chro), evb -> attr +1-NULL, evb -> start+1, abs( evb -> attr-NULL - evb -> start  ));
      |                                            ~^
      |                                             |
      |                                             int
      |                                            %lld
cell-counts.c:3384:56: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=]
 3384 | if(0)fprintf(stderr,"GAP_IN_EVENT %d Dist: %d    locs %d ~ %d  gaplen %d\n",x1, abs(evb -> start - this_end_last_correct_maiping_chro), evb -> attr +1-NULL, evb -> start+1, abs( evb -> attr-NULL - evb -> start  ));
      |                                                       ~^
      |                                                        |
      |                                                        int
      |                                                       %ld
cell-counts.c:3384:61: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
 3384 | if(0)fprintf(stderr,"GAP_IN_EVENT %d Dist: %d    locs %d ~ %d  gaplen %d\n",x1, abs(evb -> start - this_end_last_correct_maiping_chro), evb -> attr +1-NULL, evb -> start+1, abs( evb -> attr-NULL - evb -> start  ));
      |                                                            ~^                                                                                                ~~~~~~~~~~~~~~
      |                                                             |                                                                                                            |
      |                                                             int                                                                                                          srInt_64 {aka long long int}
      |                                                            %lld
cell-counts.c:3384:72: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long long int’ [-Wformat=]
 3384 | if(0)fprintf(stderr,"GAP_IN_EVENT %d Dist: %d    locs %d ~ %d  gaplen %d\n",x1, abs(evb -> start - this_end_last_correct_maiping_chro), evb -> attr +1-NULL, evb -> start+1, abs( evb -> attr-NULL - evb -> start  ));
      |                                                                       ~^
      |                                                                        |
      |                                                                        int
      |                                                                       %lld
cell-counts.c:3390:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable]
 3390 |                 int read_for_testing_len = edge_region_end - edge_region_start +1;
      |                     ^~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_add_covered_indels_in_table’:
cell-counts.c:3717:17: warning: passing argument 7 of ‘general_dynamic_align’ from incompatible pointer type [-Wincompatible-pointer-types]
 3717 |                 dpbuf, dpplt, cellCounts_add_covered_indels_in_table_getval, cct_context);
      |                 ^~~~~
      |                 |
      |                 char ***
HelperFunctions.h:281:12: note: expected ‘void ***’ but argument is of type ‘char ***’
  281 |   void *** buffers, int * penalties, char (* get_index_base_value) (unsigned int pos, void * context), void * general_context);
      |   ~~~~~~~~~^~~~~~~
cell-counts.c:3722:19: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 3722 |         for(x1=0; nch=result_cigar[x1] ; x1++){
      |                   ^~~
cell-counts.c:3736:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 3736 | if(1)                           cellCounts_add_or_update_chroEvent_in_table(cct_context, chroEvent_t_TYPE_INDEL , chro_name, chro_pos -1, rposv, inslen_negative, 0); // thread safe
      | ^~
cell-counts.c:3737:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 3737 |                                 if(nch=='D') chro_cursor += tmpi;
      |                                 ^~
cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’:
cell-counts.c:3837:45: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable]
 3837 |                                         int rgap = -1;
      |                                             ^~~~
cell-counts.c:3867:26: warning: #warning "====  Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ====" [-Wcpp]
 3867 |                         #warning "====  Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ===="
      |                          ^~~~~~~
cell-counts.c:3877:37: warning: unused variable ‘manegative’ [-Wunused-variable]
 3877 |                                 int manegative = votetab -> masks[mai][maj];
      |                                     ^~~~~~~~~~
cell-counts.c:3789:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable]
 3789 |                         int best_GTAG_negative = -1;
      |                             ^~~~~~~~~~~~~~~~~~
cell-counts.c:3757:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable]
 3757 |         int i,j,reverse_text_offset, distinct_vote_number_i;
      |                                      ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:3757:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable]
 3757 |         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:3937:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 3937 |         while(nch = cigar[x1++]){
      |               ^~~
cell-counts.c:3967:81: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 3967 |                                         IVT_IntervalTreeNode * myroot = LR_roots[LRi];
      |                                                                                 ^
cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_cell’:
cell-counts.c:4963:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
 4963 |         fprintf( cct_context -> read_assignment_detail_fp,  "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc),  str1 -> umi, cct_context ->gene_name_array[gn]);\
      |                                                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                                       |
      |                                                                                                                       void *
cell-counts.c:4981:41: note: in expansion of macro ‘ADD_count_hash’
 4981 |                                         ADD_count_hash(str1->cellbc, str1->gene_no,1);
      |                                         ^~~~~~~~~~~~~~
cell-counts.c:4963:95: note: format string is defined here
 4963 |         fprintf( cct_context -> read_assignment_detail_fp,  "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc),  str1 -> umi, cct_context ->gene_name_array[gn]);\
      |                                                                                              ~^
      |                                                                                               |
      |                                                                                               char *
      |                                                                                              %p
cell-counts.c:5028:148: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
 5028 |                                                                 fprintf( cct_context -> read_assignment_detail_fp,  "FIX_UMI_SIMILAR\tSAMPLE%03d\t%s\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, acc_str -> cellbc),  try_str -> umi, acc_str -> umi, cct_context ->gene_name_array[ acc_str -> gene_no ]);
      |                                                                                                                                                   ~^                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                                                                    |                           |
      |                                                                                                                                                    char *                      void *
      |                                                                                                                                                   %p
cell-counts.c:5057:140: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
 5057 |                                                         fprintf( cct_context -> read_assignment_detail_fp,  "FIX_UMI_SIMILAR\tSAMPLE%03d\t%s\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, acc_str -> cellbc),  try_str -> umi, acc_str -> umi, cct_context ->gene_name_array[ acc_str -> gene_no ]);
      |                                                                                                                                           ~^                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                                                            |                           |
      |                                                                                                                                            char *                      void *
      |                                                                                                                                           %p
cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_step’:
cell-counts.c:4963:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
 4963 |         fprintf( cct_context -> read_assignment_detail_fp,  "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc),  str1 -> umi, cct_context ->gene_name_array[gn]);\
      |                                                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                                       |
      |                                                                                                                       void *
cell-counts.c:5128:66: note: in expansion of macro ‘ADD_count_hash’
 5128 |                         else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1);
      |                                                                  ^~~~~~~~~~~~~~
cell-counts.c:4963:95: note: format string is defined here
 4963 |         fprintf( cct_context -> read_assignment_detail_fp,  "UMI_FINALLY_ASSIGN\tSAMPLE%03d\t%s\t%s\t%s\n",sample_no, ArrayListGet(cct_context -> cell_barcodes_array, bc),  str1 -> umi, cct_context ->gene_name_array[gn]);\
      |                                                                                              ~^
      |                                                                                               |
      |                                                                                               char *
      |                                                                                              %p
cell-counts.c: In function ‘cellCounts_find_nearest_gene_dist’:
cell-counts.c:6620:81: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
 6620 | if(0)if( gene_name_list -> numOfElements )fprintf(stderr,"SUBADD_DIST of %lld, %s\n", gene_name_list -> numOfElements, gene_name_list -> elementList[0]);
      |                                                                                ~^                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                 |                                                                   |
      |                                                                                 char *                                                              void *
      |                                                                                %p
cell-counts.c: In function ‘cellCounts_write_final_junctions’:
cell-counts.c:6740:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable]
 6740 |                 int unique_junctions = 0;
      |                     ^~~~~~~~~~~~~~~~
cell-counts.c:6721:20: warning: unused variable ‘ky_i2’ [-Wunused-variable]
 6721 |         int ky_i1, ky_i2;
      |                    ^~~~~
cell-counts.c:6721:13: warning: unused variable ‘ky_i1’ [-Wunused-variable]
 6721 |         int ky_i1, ky_i2;
      |             ^~~~~
cell-counts.c:6719:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable]
 6719 |         char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
      |                                                                                 ^~~~~~~~~~~~~~
cell-counts.c:6688:13: warning: unused variable ‘infile_i’ [-Wunused-variable]
 6688 |         int infile_i, disk_is_full = 0;
      |             ^~~~~~~~
cell-counts.c: In function ‘features_load_one_line’:
cell-counts.c:1451:1: warning: control reaches end of non-void function [-Wreturn-type]
 1451 | }
      | ^
cell-counts.c: In function ‘cellCounts_release_context_from_align’:
cell-counts.c:2740:1: warning: control reaches end of non-void function [-Wreturn-type]
 2740 | }
      | ^
cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’:
cell-counts.c:3925:1: warning: control reaches end of non-void function [-Wreturn-type]
 3925 | }
      | ^
cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’:
cell-counts.c:2202:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized]
 2202 |                 if(search_start>0xffffff00) return;
      |                   ^
cell-counts.c:2191:30: note: ‘search_start’ was declared here
 2191 |                 unsigned int search_start, search_end, search_block_id;
      |                              ^~~~~~~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core-bigtable.c -o core-bigtable.o
In file included from core.h:46,
                 from core-bigtable.c:12:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core-indel.c -o core-indel.o
In file included from HelperFunctions.h:24,
                 from core-indel.c:28:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core-interface-aligner.c -o core-interface-aligner.o
In file included from core-interface-aligner.c:7:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core-interface-subjunc.c -o core-interface-subjunc.o
In file included from core-interface-subjunc.c:7:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core-junction.c -o core-junction.o
In file included from core-junction.c:25:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
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/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core.c -o core.o
In file included from core.c:45:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c detection-calls.c -o detection-calls.o
In file included from detection-calls.c:8:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
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/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c detectionCall.c -o detectionCall.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c exon-algorithms.c -o exon-algorithms.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c exon-align-indel.c -o exon-align-indel.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c exon-align.c -o exon-align.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c flattenAnnotations.c -o flattenAnnotations.o
In file included from flattenAnnotations.c:41:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c fullscan.c -o fullscan.o
In file included from fullscan.c:26:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c fusion-align.c -o fusion-align.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c gen_rand_reads.c -o gen_rand_reads.o
In file included from gen_rand_reads.c:26:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c gene-algorithms.c -o gene-algorithms.o
In file included from gene-algorithms.c:36:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c gene-value-index.c -o gene-value-index.o
In file included from gene-value-index.h:24,
                 from gene-value-index.c:25:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
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 ))
      |                                 ^~
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/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c hashtable.c -o hashtable.o
In file included from core.h:46,
                 from hashtable.c:18:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c index-builder.c -o index-builder.o
In file included from gene-value-index.h:24,
                 from index-builder.c:31:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c input-blc.c -o input-blc.o
In file included from input-blc.c:8:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
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/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c input-files.c -o input-files.o
In file included from input-files.h:23,
                 from input-files.c:35:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
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/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c interval_merge.c -o interval_merge.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c long-hashtable.c -o long-hashtable.o
In file included from core.h:46,
                 from long-hashtable.c:31:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c longread-mapping.c -o longread-mapping.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c mergeVCF.c -o mergeVCF.o
In file included from mergeVCF.c:7:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c processExons.c -o processExons.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c propmapped.c -o propmapped.o
In file included from propmapped.c:34:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c qualityScores.c -o qualityScores.o
In file included from qualityScores.c:27:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c read-repair.c -o read-repair.o
In file included from read-repair.c:6:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c readSummary.c -o readSummary.o
In file included from readSummary.c:41:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
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/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c removeDupReads.c -o removeDupReads.o
In file included from removeDupReads.c:27:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c sam2bed.c -o sam2bed.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c sambam-file.c -o sambam-file.o
In file included from sambam-file.c:33:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c seek-zlib.c -o seek-zlib.o
In file included from core.h:46,
                 from seek-zlib.c:2:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c sorted-hashtable.c -o sorted-hashtable.o
In file included from sorted-hashtable.h:25,
                 from sorted-hashtable.c:20:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c sublog.c -o sublog.o
In file included from sublog.c:26:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.22-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.2\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c tx-unique.c -o tx-unique.o
In file included from tx-unique.h:4,
                 from tx-unique.c:6:
subread.h:502:2: warning: #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-Wcpp]
  502 | #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
      |  ^~~~~~~
gcc -std=gnu2x -shared -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
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/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)