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This page was generated on 2025-08-09 12:06 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1821/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 2.23.3  (landing page)
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/Rsubread
git_branch: devel
git_last_commit: 7de7817
git_last_commit_date: 2025-07-30 02:02:59 -0400 (Wed, 30 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


INSTALL results for Rsubread on nebbiolo2

To the developers/maintainers of the Rsubread package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsubread.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Rsubread
Version: 2.23.3
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Rsubread
StartedAt: 2025-08-08 15:03:50 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 15:04:32 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 42.1 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.23.3’
** 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-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMbase-index.c -o LRMbase-index.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMchro-event.c -o LRMchro-event.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMfile-io.c -o LRMfile-io.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMhashtable.c -o LRMhashtable.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMhelper.c -o LRMhelper.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c aligner.c -o aligner.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c atgcContent.c -o atgcContent.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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_args_context’:
cell-counts.c:721:2: warning: #warning "====== SHOULD REMOVE '* 4' BELOW =========" [-Wcpp]
  721 | #warning "====== SHOULD REMOVE '* 4' BELOW ========="
      |  ^~~~~~~
cell-counts.c:724:2: warning: #warning "====== SHOULD REMOVE '+ 4' BELOW =========" [-Wcpp]
  724 | #warning "====== SHOULD REMOVE '+ 4' BELOW ========="
      |  ^~~~~~~
cell-counts.c:816:26: warning: #warning "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======" [-Wcpp]
  816 |                         #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:1134:47: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘int *’ [-Wformat=]
 1134 |                 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_copy_txn_to_juncs’:
cell-counts.c:1287:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 1287 | if(!ignore_GTF) cellCounts_add_or_update_chroEvent_in_table(cct_context, chroEvent_t_TYPE_EXON, chname_strand , start, end, 0, 1);
      | ^~
cell-counts.c:1289:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 1289 |                 if(last_end>0){
      |                 ^~
cell-counts.c:1267:28: warning: variable ‘last_start’ set but not used [-Wunused-but-set-variable]
 1267 |         int last_end = -1, last_start = -1;
      |                            ^~~~~~~~~~
cell-counts.c: In function ‘cellCounts_end_build_candidature_from_stacks’:
cell-counts.c:3227:29: warning: unused variable ‘x_candidate’ [-Wunused-variable]
 3227 |         int x_3end, x_5end, x_candidate;
      |                             ^~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_build_junction_read_finalise_current_stack’:
cell-counts.c:3369:2: warning: #warning "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn  =============" [-Wcpp]
 3369 | #warning "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn  ============="
      |  ^~~~~~~
cell-counts.c: In function ‘cellCounts_tree_iterative_search’:
cell-counts.c:3483:124: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=]
 3483 | if(0)if(strstr(thread_context -> realignment_event_read_name ,"R00000895964"))fprintf(stderr,"REMOTE_TEST TYPE %d LEN %d (%d) REMOTE_loc_read = %d  TO3=%d  %s\n", envdtl -> event_type, inslen, (void*)envdtl -> length - NULL, remote_first_matching_base_read, to3end, thread_context -> realignment_event_read_name);
      |                                                                                                                           ~^
      |                                                                                                                            |
      |                                                                                                                            int
      |                                                                                                                           %ld
cell-counts.c:3438:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable]
 3438 |                 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:3788:19: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 3788 |         for(x1=0; nch=result_cigar[x1] ; x1++){
      |                   ^~~
cell-counts.c:3802:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
 3802 | 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:3803:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
 3803 |                                 if(nch=='D') chro_cursor += tmpi;
      |                                 ^~
cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’:
cell-counts.c:3903:45: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable]
 3903 |                                         int rgap = -1;
      |                                             ^~~~
cell-counts.c:3933:26: warning: #warning "====  Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ====" [-Wcpp]
 3933 |                         #warning "====  Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ===="
      |                          ^~~~~~~
cell-counts.c:3943:37: warning: unused variable ‘manegative’ [-Wunused-variable]
 3943 |                                 int manegative = votetab -> masks[mai][maj];
      |                                     ^~~~~~~~~~
cell-counts.c:3855:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable]
 3855 |                         int best_GTAG_negative = -1;
      |                             ^~~~~~~~~~~~~~~~~~
cell-counts.c:3823:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable]
 3823 |         int i,j,reverse_text_offset, distinct_vote_number_i;
      |                                      ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:3823:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable]
 3823 |         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:4034:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 4034 |         while(nch = cigar[x1++]){
      |               ^~~
cell-counts.c:4096:66: warning: variable ‘x2_not_matter’ set but not used [-Wunused-but-set-variable]
 4096 |                                                 int is_the_last, x2_not_matter;
      |                                                                  ^~~~~~~~~~~~~
cell-counts.c:4120:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 4120 |         while(nch = cigar[x1++]){
      |               ^~~
cell-counts.c:4130:81: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 4130 |                                         IVT_IntervalTreeNode * myroot = LR_roots[LRi];
      |                                                                                 ^
cell-counts.c:4155:66: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
 4155 | if(0)fprintf(stderr,"SUPP_NON   query-cov %d ~ %d   non-env-cov %d ~ %d   %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , is_the_last?"SKIPPED":"ADDED");
      |                                                                 ~^                                        ~~~~~~~~~~~~
      |                                                                  |                                            |
      |                                                                  int                                          srInt_64 {aka long long int}
      |                                                                 %lld
cell-counts.c:4155:71: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=]
 4155 | if(0)fprintf(stderr,"SUPP_NON   query-cov %d ~ %d   non-env-cov %d ~ %d   %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , is_the_last?"SKIPPED":"ADDED");
      |                                                                      ~^
      |                                                                       |
      |                                                                       int
      |                                                                      %ld
cell-counts.c:4164:69: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘srInt_64’ {aka ‘long long int’} [-Wformat=]
 4164 | if(0)fprintf(stderr,"SUPP_X2TEST   query-cov %d ~ %d   non-env-cov %d ~ %d  X2 %d %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , x2, (is_the_last && is_same_x2)?"SKIPPED":"ADDED");
      |                                                                    ~^                                             ~~~~~~~~~~~~
      |                                                                     |                                                 |
      |                                                                     int                                               srInt_64 {aka long long int}
      |                                                                    %lld
cell-counts.c:4164:74: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘long int’ [-Wformat=]
 4164 | if(0)fprintf(stderr,"SUPP_X2TEST   query-cov %d ~ %d   non-env-cov %d ~ %d  X2 %d %s\n", Mstart_base, Mlast_base, evb -> start, evb -> attr -NULL , x2, (is_the_last && is_same_x2)?"SKIPPED":"ADDED");
      |                                                                         ~^
      |                                                                          |
      |                                                                          int
      |                                                                         %ld
cell-counts.c:4022:41: warning: unused variable ‘x3’ [-Wunused-variable]
 4022 |         int nch, tmpi=0, x1=0, b1off=0, x3;
      |                                         ^~
cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_cell’:
cell-counts.c:5140:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
 5140 |         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:5158:41: note: in expansion of macro ‘ADD_count_hash’
 5158 |                                         ADD_count_hash(str1->cellbc, str1->gene_no,1);
      |                                         ^~~~~~~~~~~~~~
cell-counts.c:5140:95: note: format string is defined here
 5140 |         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:5205:148: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
 5205 |                                                                 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:5234:140: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
 5234 |                                                         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:5140:61: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
 5140 |         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:5305:66: note: in expansion of macro ‘ADD_count_hash’
 5305 |                         else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1);
      |                                                                  ^~~~~~~~~~~~~~
cell-counts.c:5140:95: note: format string is defined here
 5140 |         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:6797:81: warning: format ‘%s’ expects argument of type ‘char *’, but argument 4 has type ‘void *’ [-Wformat=]
 6797 | 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:6921:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable]
 6921 |                 int unique_junctions = 0;
      |                     ^~~~~~~~~~~~~~~~
cell-counts.c:6902:20: warning: unused variable ‘ky_i2’ [-Wunused-variable]
 6902 |         int ky_i1, ky_i2;
      |                    ^~~~~
cell-counts.c:6902:13: warning: unused variable ‘ky_i1’ [-Wunused-variable]
 6902 |         int ky_i1, ky_i2;
      |             ^~~~~
cell-counts.c:6900:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable]
 6900 |         char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
      |                                                                                 ^~~~~~~~~~~~~~
cell-counts.c:6869:13: warning: unused variable ‘infile_i’ [-Wunused-variable]
 6869 |         int infile_i, disk_is_full = 0;
      |             ^~~~~~~~
cell-counts.c: In function ‘cellCounts_release_context_from_align’:
cell-counts.c:2769:1: warning: control reaches end of non-void function [-Wreturn-type]
 2769 | }
      | ^
cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’:
cell-counts.c:3991:1: warning: control reaches end of non-void function [-Wreturn-type]
 3991 | }
      | ^
cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’:
cell-counts.c:2231:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized]
 2231 |                 if(search_start>0xffffff00) return;
      |                   ^
cell-counts.c:2220:30: note: ‘search_start’ was declared here
 2220 |                 unsigned int search_start, search_end, search_block_id;
      |                              ^~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c detectionCall.c -o detectionCall.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c exon-algorithms.c -o exon-algorithms.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c exon-align.c -o exon-align.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c fusion-align.c -o fusion-align.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c interval_merge.c -o interval_merge.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c longread-mapping.c -o longread-mapping.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c processExons.c -o processExons.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -g3  -fpic  -g -O2  -Wall -Werror=format-security -c sam2bed.c -o sam2bed.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include   -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.23.3\"" -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/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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)