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###
### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/R CMD INSTALL Rsubread
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.27.1’
** using staged installation
@@@@@ The operating system is Linux.
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c BAM-to-junctions-extract.c -o BAM-to-junctions-extract.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c HelperFunctions.c -o HelperFunctions.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMbase-index.c -o LRMbase-index.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMchro-event.c -o LRMchro-event.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMfile-io.c -o LRMfile-io.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMhashtable.c -o LRMhashtable.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMhelper.c -o LRMhelper.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c R_wrapper.c -o R_wrapper.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c RsimReads.c -o RsimReads.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c SNPCalling.c -o SNPCalling.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c aligner.c -o aligner.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c atgcContent.c -o atgcContent.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -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-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -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:1185:16: warning: unused variable ‘params’ [-Wunused-variable]
 1185 |         void * params [5];
      |                ^~~~~~
cell-counts.c: In function ‘cellCounts_add_or_update_chroEvent_in_table’:
cell-counts.c:1268:23: warning: variable ‘new_details’ set but not used [-Wunused-but-set-variable]
 1268 |         chroEvent_t * new_details = NULL;
      |                       ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_copy_txn_to_juncs’:
cell-counts.c:1321:28: warning: variable ‘last_start’ set but not used [-Wunused-but-set-variable]
 1321 |         int last_end = -1, last_start = -1;
      |                            ^~~~~~~~~~
cell-counts.c: In function ‘cellCounts_register_junc_feature’:
cell-counts.c:1527:30: warning: unused variable ‘sample_i’ [-Wunused-variable]
 1527 |         int xk1, edge_tab_i, sample_i;
      |                              ^~~~~~~~
cell-counts.c: In function ‘cellCounts_get_cellbarcode_no’:
cell-counts.c:2488:21: warning: unused variable ‘cbclen’ [-Wunused-variable]
 2488 |                 int cbclen = strstr(cbc,"|")-cbc, bc2_end=0, bc1_end=0, bc1_start=0, xx3, bc1=-1, bc2=-1;
      |                     ^~~~~~
cell-counts.c: In function ‘cellCounts_write_read_in_batch_bin’:
cell-counts.c:2923:139: warning: unused variable ‘testi’ [-Wunused-variable]
 2923 |         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:3422:37: warning: unused variable ‘thread_context’ [-Wunused-variable]
 3422 |         cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
      |                                     ^~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_softclip_candidate’:
cell-counts.c:3470:37: warning: unused variable ‘thread_context’ [-Wunused-variable]
 3470 |         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:3534:29: warning: unused variable ‘cigar_rlen’ [-Wunused-variable]
 3534 |                         int cigar_rlen = cellCounts_reduce_Cigar(cigar_being_built,final_cigar,&sum_ins);
      |                             ^~~~~~~~~~
cell-counts.c:3488:29: warning: unused variable ‘x_candidate’ [-Wunused-variable]
 3488 |         int x_3end, x_5end, x_candidate;
      |                             ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_tree_iterative_search’:
cell-counts.c:3716:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable]
 3716 |                 int read_for_testing_len = edge_region_end - edge_region_start +1;
      |                     ^~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_explain_one_alignment’:
cell-counts.c:3805:139: warning: unused variable ‘testi’ [-Wunused-variable]
 3805 |         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:4053:13: warning: unused variable ‘retlen’ [-Wunused-variable]
 4053 |         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:4212:37: warning: unused variable ‘is_update’ [-Wunused-variable]
 4212 |                                 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:4200:37: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable]
 4200 |                                 int rgap = -1;
      |                                     ^~~~
cell-counts.c:4187:37: warning: unused variable ‘manegative’ [-Wunused-variable]
 4187 |                                 int manegative = votetab -> masks[mai][maj];
      |                                     ^~~~~~~~~~
cell-counts.c:4108:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable]
 4108 |                         int best_GTAG_negative = -1;
      |                             ^~~~~~~~~~~~~~~~~~
cell-counts.c:4105:29: warning: variable ‘best_misma_no’ set but not used [-Wunused-but-set-variable]
 4105 |                         int best_misma_no = -1;
      |                             ^~~~~~~~~~~~~
cell-counts.c:4080:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable]
 4080 |         int i,j,reverse_text_offset, distinct_vote_number_i;
      |                                      ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4080:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable]
 4080 |         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:4306:37: warning: variable ‘on_chro_len’ set but not used [-Wunused-but-set-variable]
 4306 |                                 int on_chro_len = tmpi +1;
      |                                     ^~~~~~~~~~~
cell-counts.c:4336:66: warning: variable ‘x2_not_matter’ set but not used [-Wunused-but-set-variable]
 4336 |                                                 int is_the_last, x2_not_matter;
      |                                                                  ^~~~~~~~~~~~~
cell-counts.c:4369:81: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 4369 |                                         IVT_IntervalTreeNode * myroot = LR_roots[LRi];
      |                                                                                 ^
cell-counts.c:4262:41: warning: unused variable ‘x3’ [-Wunused-variable]
 4262 |         int nch, tmpi=0, x1=0, b1off=0, x3;
      |                                         ^~
cell-counts.c: In function ‘cellCounts_do_one_batch’:
cell-counts.c:6074:48: warning: unused variable ‘cigar_bin_ptr’ [-Wunused-variable]
 6074 |                                 unsigned int * cigar_bin_ptr = ( unsigned int * )(rbinptr +36 + l_read_name);
      |                                                ^~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_finalise_per_junction_cell_table’:
cell-counts.c:6953:15: warning: unused variable ‘temp_dir’ [-Wunused-variable]
 6953 |         char *temp_dir = cct_context -> temp_file_dir;
      |               ^~~~~~~~
cell-counts.c:6952:13: warning: unused variable ‘thread_no’ [-Wunused-variable]
 6952 |         int thread_no, sample_i;
      |             ^~~~~~~~~
cell-counts.c: In function ‘cellCounts_write_final_junctions’:
cell-counts.c:7422:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable]
 7422 |                 int unique_junctions = 0;
      |                     ^~~~~~~~~~~~~~~~
cell-counts.c:7401:20: warning: unused variable ‘ky_i2’ [-Wunused-variable]
 7401 |         int ky_i1, ky_i2;
      |                    ^~~~~
cell-counts.c:7401:13: warning: unused variable ‘ky_i1’ [-Wunused-variable]
 7401 |         int ky_i1, ky_i2;
      |             ^~~~~
cell-counts.c:7399:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable]
 7399 |         char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
      |                                                                                 ^~~~~~~~~~~~~~
cell-counts.c:7365:13: warning: unused variable ‘infile_i’ [-Wunused-variable]
 7365 |         int infile_i, disk_is_full = 0, sample_i;
      |             ^~~~~~~~
cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’:
cell-counts.c:2388:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized]
 2388 |                 if(search_start>0xffffff00) return;
      |                   ^
cell-counts.c:2377:30: note: ‘search_start’ was declared here
 2377 |                 unsigned int search_start, search_end, search_block_id;
      |                              ^~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_do_one_batch’:
cell-counts.c:6070:89: warning: ‘is_homopolymer_or_N_this_UR’ may be used uninitialized [-Wmaybe-uninitialized]
 6070 |                         if(cct_context->do_cell_level_junction_detection && umi[0]!='-' && !is_homopolymer_or_N_this_UR){
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:6043:29: note: ‘is_homopolymer_or_N_this_UR’ was declared here
 6043 |                         int is_homopolymer_or_N_this_UR;
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core-bigtable.c -o core-bigtable.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core-indel.c -o core-indel.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core-interface-aligner.c -o core-interface-aligner.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -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/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c core.c -o core.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -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/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c detectionCall.c -o detectionCall.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c exon-algorithms.c -o exon-algorithms.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -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-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c exon-align.c -o exon-align.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c flattenAnnotations.c -o flattenAnnotations.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c fullscan.c -o fullscan.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c fusion-align.c -o fusion-align.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c gen_rand_reads.c -o gen_rand_reads.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c gene-algorithms.c -o gene-algorithms.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -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/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c hashtable.c -o hashtable.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c index-builder.c -o index-builder.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -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:585:59: warning: unused variable ‘npos’ [-Wunused-variable]
  585 |                                                 long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
      |                                                           ^~~~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -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/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c interval_merge.c -o interval_merge.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c long-hashtable.c -o long-hashtable.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c longread-mapping.c -o longread-mapping.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c mergeVCF.c -o mergeVCF.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c processExons.c -o processExons.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c propmapped.c -o propmapped.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c qualityScores.c -o qualityScores.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c read-repair.c -o read-repair.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -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/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c removeDupReads.c -o removeDupReads.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c sam2bed.c -o sam2bed.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c sambam-file.c -o sambam-file.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c seek-zlib.c -o seek-zlib.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c softclip-test.c -o softclip-test.o
softclip-test.c: In function ‘calculate_soft_clipping’:
softclip-test.c:43:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
   43 |         if(is_mismatch) free(is_mismatch); if(is_insertion) free(is_insertion);
      |         ^~
softclip-test.c:43:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
   43 |         if(is_mismatch) free(is_mismatch); if(is_insertion) free(is_insertion);
      |                                            ^~
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c sorted-hashtable.c -o sorted-hashtable.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c sublog.c -o sublog.o
gcc -std=gnu2x -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.27.1\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c tx-unique.c -o tx-unique.o
gcc -std=gnu2x -shared -L/usr/local/lib -o Rsubread.so BAM-to-junctions-extract.o 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 softclip-test.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.24-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)