##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rsubread_2.23.3.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rsubread.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.23.3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rsubread’ can be installed ... WARNING
Found the following significant warnings:
  ./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
  #warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
  cell-counts.c:721:2: warning: "====== SHOULD REMOVE '* 4' BELOW =========" [-W#warnings]
  #warning "====== SHOULD REMOVE '* 4' BELOW ========="
  cell-counts.c:724:2: warning: "====== SHOULD REMOVE '+ 4' BELOW =========" [-W#warnings]
  #warning "====== SHOULD REMOVE '+ 4' BELOW ========="
  cell-counts.c:816:5: warning: "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======" [-W#warnings]
                          #warning "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======"
  cell-counts.c:1134:93: warning: format specifies type 'int' but the argument has type 'int *' [-Wformat]
  cell-counts.c:3369:2: warning: "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn  =============" [-W#warnings]
  #warning "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn  ============="
  cell-counts.c:3483:194: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  cell-counts.c:3933:5: warning: "====  Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ====" [-W#warnings]
                          #warning "====  Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ===="
  cell-counts.c:4155:107: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
  cell-counts.c:4155:121: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  cell-counts.c:4164:115: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
  cell-counts.c:4164:129: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
  cell-counts.c:5158:6: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
  cell-counts.c:5205:120: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
  cell-counts.c:5234:119: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
  cell-counts.c:5305:45: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
  cell-counts.c:6797:120: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rsubread.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
  installed size is 36.8Mb
  sub-directories of 1Mb or more:
    annot  30.9Mb
    libs    1.1Mb
    qualf   3.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rsubread/libs/Rsubread.so’:
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
propmapped 48.975 77.633 127.770
align      47.438 76.785 125.361
sublong    11.813  1.762  13.503
buildindex  5.126  0.936   6.169
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rsubread.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.23.3’
** using staged installation
@@@@@ The operating system is Darwin.
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c HelperFunctions.c -o HelperFunctions.o
In file included from HelperFunctions.c:56:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMbase-index.c -o LRMbase-index.o
LRMbase-index.c:146:40: warning: variable 'all_mismatched' set but not used [-Wunused-but-set-variable]
        int read_chrsor = 0, all_matched = 0, all_mismatched = 0;
                                              ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMchro-event.c -o LRMchro-event.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMfile-io.c -o LRMfile-io.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMhashtable.c -o LRMhashtable.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMhelper.c -o LRMhelper.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMseek-zlib.c -o LRMseek-zlib.o
LRMseek-zlib.c:194:15: warning: variable 'this_chunk_size' set but not used [-Wunused-but-set-variable]
        unsigned int this_chunk_size = 0;
                     ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c R_wrapper.c -o R_wrapper.o
In file included from R_wrapper.c:35:
In file included from ./HelperFunctions.h:24:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c RsimReads.c -o RsimReads.o
In file included from RsimReads.c:21:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c SNPCalling.c -o SNPCalling.o
In file included from SNPCalling.c:33:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
SNPCalling.c:263:25: warning: variable 'OVERLAPPED_BASES' set but not used [-Wunused-but-set-variable]
        unsigned long long int OVERLAPPED_BASES=0;
                               ^
SNPCalling.c:264:25: warning: variable 'OVER_MISMA_BASES' set but not used [-Wunused-but-set-variable]
        unsigned long long int OVER_MISMA_BASES=0;
                               ^
SNPCalling.c:265:25: warning: variable 'ALL_BASES' set but not used [-Wunused-but-set-variable]
        unsigned long long int ALL_BASES=0;
                               ^
SNPCalling.c:571:26: warning: use of logical '||' with constant operand [-Wconstant-logical-operand]
                                if(all_result_needed || ( 0 &&  Known_SNP_here && p_middle < parameters -> cutoff_upper_bound ) ||  ( p_middle < p_cutoff && flanking_matched*20>(flanking_matched+ flanking_unmatched )*16)) 
                                                     ^  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SNPCalling.c:571:26: note: use '|' for a bitwise operation
                                if(all_result_needed || ( 0 &&  Known_SNP_here && p_middle < parameters -> cutoff_upper_bound ) ||  ( p_middle < p_cutoff && flanking_matched*20>(flanking_matched+ flanking_unmatched )*16)) 
                                                     ^~
                                                     |
SNPCalling.c:697:114: warning: use of logical '||' with constant operand [-Wconstant-logical-operand]
        if(parameters -> fisher_exact_testlen || parameters -> test_two_strands || parameters->neighbour_abundance_test || 1)
                                                                                                                        ^  ~
SNPCalling.c:697:114: note: use '|' for a bitwise operation
        if(parameters -> fisher_exact_testlen || parameters -> test_two_strands || parameters->neighbour_abundance_test || 1)
                                                                                                                        ^~
                                                                                                                        |
SNPCalling.c:707:7: warning: variable 'window_no' set but not used [-Wunused-but-set-variable]
                int window_no = 0;
                    ^
7 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c aligner.c -o aligner.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c atgcContent.c -o atgcContent.o
atgcContent.c:72:7: warning: variable 'line_num' set but not used [-Wunused-but-set-variable]
  int line_num = 0;
      ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c build-sam-index.c -o build-sam-index.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c cell-counts.c -o cell-counts.o
In file included from cell-counts.c:13:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
cell-counts.c:721:2: warning: "====== SHOULD REMOVE '* 4' BELOW =========" [-W#warnings]
#warning "====== SHOULD REMOVE '* 4' BELOW ========="
 ^
cell-counts.c:724:2: warning: "====== SHOULD REMOVE '+ 4' BELOW =========" [-W#warnings]
#warning "====== SHOULD REMOVE '+ 4' BELOW ========="
 ^
cell-counts.c:816:5: warning: "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======" [-W#warnings]
                        #warning "====== Yang Liao added '+20' for better junction calling -- think about it in final release??? ======"
                         ^
cell-counts.c:1134:93: warning: format specifies type 'int' but the argument has type 'int *' [-Wformat]
                fprintf(wfp,"%s\t%d\t%d\t%s\t%d\n", chro, pos1, pos2, ce -> from_truth?"ANNOTATED":"NEW", ce -> step2_supported_reads);
                                             ~~                                                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:1267:21: warning: variable 'last_start' set but not used [-Wunused-but-set-variable]
        int last_end = -1, last_start = -1;
                           ^
cell-counts.c:2769:1: warning: non-void function does not return a value [-Wreturn-type]
}
^
cell-counts.c:3227:22: warning: unused variable 'x_candidate' [-Wunused-variable]
        int x_3end, x_5end, x_candidate;
                            ^
cell-counts.c:3369:2: warning: "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn  =============" [-W#warnings]
#warning "========= THIS IS FOR TESTING EFFICIENCY; NOT NEEDED IN RELASED VERSIOn  ============="
 ^
cell-counts.c:3483:194: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
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);
                                                                                                                          ~~                                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                                                                          %ld
cell-counts.c:3438:7: warning: unused variable 'read_for_testing_len' [-Wunused-variable]
                int read_for_testing_len = edge_region_end - edge_region_start +1;
                    ^
cell-counts.c:3788:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
        for(x1=0; nch=result_cigar[x1] ; x1++){
                  ~~~^~~~~~~~~~~~~~~~~
cell-counts.c:3788:15: note: place parentheses around the assignment to silence this warning
        for(x1=0; nch=result_cigar[x1] ; x1++){
                     ^
                  (                   )
cell-counts.c:3788:15: note: use '==' to turn this assignment into an equality comparison
        for(x1=0; nch=result_cigar[x1] ; x1++){
                     ^
                     ==
cell-counts.c:3903:10: warning: variable 'rgap' set but not used [-Wunused-but-set-variable]
                                        int rgap = -1;
                                            ^
cell-counts.c:3933:5: warning: "====  Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ====" [-W#warnings]
                        #warning "====  Think: could a read contribute multiple junctions? could a major half contribute multiple junctions? ===="
                         ^
cell-counts.c:3943:9: warning: unused variable 'manegative' [-Wunused-variable]
                                int manegative = votetab -> masks[mai][maj];
                                    ^
cell-counts.c:3855:8: warning: variable 'best_GTAG_negative' set but not used [-Wunused-but-set-variable]
                        int best_GTAG_negative = -1;
                            ^
cell-counts.c:3823:10: warning: unused variable 'reverse_text_offset' [-Wunused-variable]
        int i,j,reverse_text_offset, distinct_vote_number_i;
                ^
cell-counts.c:3823:31: warning: unused variable 'distinct_vote_number_i' [-Wunused-variable]
        int i,j,reverse_text_offset, distinct_vote_number_i;
                                     ^
cell-counts.c:3991:1: warning: non-void function does not return a value [-Wreturn-type]
}
^
cell-counts.c:4034:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
        while(nch = cigar[x1++]){
              ~~~~^~~~~~~~~~~~~
cell-counts.c:4034:12: note: place parentheses around the assignment to silence this warning
        while(nch = cigar[x1++]){
                  ^
              (                )
cell-counts.c:4034:12: note: use '==' to turn this assignment into an equality comparison
        while(nch = cigar[x1++]){
                  ^
                  ==
cell-counts.c:4096:24: warning: variable 'x2_not_matter' set but not used [-Wunused-but-set-variable]
                                                int is_the_last, x2_not_matter;
                                                                 ^
cell-counts.c:4120:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
        while(nch = cigar[x1++]){
              ~~~~^~~~~~~~~~~~~
cell-counts.c:4120:12: note: place parentheses around the assignment to silence this warning
        while(nch = cigar[x1++]){
                  ^
              (                )
cell-counts.c:4120:12: note: use '==' to turn this assignment into an equality comparison
        while(nch = cigar[x1++]){
                  ^
                  ==
cell-counts.c:4130:46: warning: array subscript is of type 'char' [-Wchar-subscripts]
                                        IVT_IntervalTreeNode * myroot = LR_roots[LRi];
                                                                                ^~~~
cell-counts.c:4155:107: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
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");
                                                                ~~                                        ^~~~~~~~~~~~
                                                                %lld
cell-counts.c:4155:121: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
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");
                                                                     ~~                                                 ^~~~~~~~~~~~~~~~~
                                                                     %ld
cell-counts.c:4164:115: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
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");
                                                                   ~~                                             ^~~~~~~~~~~~
                                                                   %lld
cell-counts.c:4164:129: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
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");
                                                                        ~~                                                      ^~~~~~~~~~~~~~~~~
                                                                        %ld
cell-counts.c:4022:34: warning: unused variable 'x3' [-Wunused-variable]
        int nch, tmpi=0, x1=0, b1off=0, x3;
                                        ^
cell-counts.c:5158:6: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
                                        ADD_count_hash(str1->cellbc, str1->gene_no,1);
                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:5140:119: note: expanded from macro 'ADD_count_hash'
        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]);\
                                                                                             ~~                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:5205:120: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
                                                                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 ]);
                                                                                                                                                  ~~                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:5234:119: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
                                                        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 ]);
                                                                                                                                          ~~                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:5305:45: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
                        else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1);
                                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:5140:119: note: expanded from macro 'ADD_count_hash'
        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]);\
                                                                                             ~~                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:5781:60: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
                                if(outblocki < finished_job -> task -> inbin_number -1 && CELLCOUNTS_BAMBLOCK_COMP_NUMBER>1)nextoffset = finished_job -> task -> inbin_batch_start_offsets[outblocki +1];
                                                                                       ^  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:5781:60: note: use '&' for a bitwise operation
                                if(outblocki < finished_job -> task -> inbin_number -1 && CELLCOUNTS_BAMBLOCK_COMP_NUMBER>1)nextoffset = finished_job -> task -> inbin_batch_start_offsets[outblocki +1];
                                                                                       ^~
                                                                                       &
cell-counts.c:5781:60: note: remove constant to silence this warning
                                if(outblocki < finished_job -> task -> inbin_number -1 && CELLCOUNTS_BAMBLOCK_COMP_NUMBER>1)nextoffset = finished_job -> task -> inbin_batch_start_offsets[outblocki +1];
                                                                                      ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:6252:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                        size_t frret = fread(&section1_items,1, 8, input_fps[xk1]);
                               ^
cell-counts.c:6277:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                        size_t frret = fread(last_rbin_buffer[xk1]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[xk1]);
                               ^
cell-counts.c:6351:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                        size_t frret = fread(last_rbin_buffer[selected_fp_no]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[selected_fp_no]);
                               ^
cell-counts.c:6398:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
                size_t frret = fread(&binlen, 1, 4, notmapped_fp);
                       ^
cell-counts.c:6190:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
        srInt_64 removed_umis = 0;
                 ^
cell-counts.c:6797:120: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
if(0)if( gene_name_list -> numOfElements )fprintf(stderr,"SUBADD_DIST of %lld, %s\n", gene_name_list -> numOfElements, gene_name_list -> elementList[0]);
                                                                               ~~                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:6921:7: warning: unused variable 'unique_junctions' [-Wunused-variable]
                int unique_junctions = 0;
                    ^
cell-counts.c:6869:6: warning: unused variable 'infile_i' [-Wunused-variable]
        int infile_i, disk_is_full = 0;
            ^
cell-counts.c:6900:74: warning: unused variable 'gene_name_tail' [-Wunused-variable]
        char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
                                                                                ^
cell-counts.c:6902:6: warning: unused variable 'ky_i1' [-Wunused-variable]
        int ky_i1, ky_i2;
            ^
cell-counts.c:6902:13: warning: unused variable 'ky_i2' [-Wunused-variable]
        int ky_i1, ky_i2;
                   ^
44 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-bigtable.c -o core-bigtable.o
In file included from core-bigtable.c:12:
In file included from ./core.h:46:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-indel.c -o core-indel.o
In file included from core-indel.c:28:
In file included from ./HelperFunctions.h:24:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
core-indel.c:455:32: warning: variable 'all_junctions' set but not used [-Wunused-but-set-variable]
        int to_be_removed_number = 0, all_junctions = 0;
                                      ^
core-indel.c:2592:8: warning: variable 'all_reads' set but not used [-Wunused-but-set-variable]
                        int all_reads = 0;
                            ^
core-indel.c:4060:11: warning: variable 'all_indels_in_window' set but not used [-Wunused-but-set-variable]
                                                int all_indels_in_window = 0;
                                                    ^
core-indel.c:3695:6: warning: variable 'global_read_no' set but not used [-Wunused-but-set-variable]
        int global_read_no = 0;
            ^
5 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-interface-aligner.c -o core-interface-aligner.o
In file included from core-interface-aligner.c:7:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-interface-subjunc.c -o core-interface-subjunc.o
In file included from core-interface-subjunc.c:7:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core-junction.c -o core-junction.o
In file included from core-junction.c:25:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
core-junction.c:568:24: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
        }else if(is_same_best && 0){
                              ^  ~
core-junction.c:568:24: note: use '&' for a bitwise operation
        }else if(is_same_best && 0){
                              ^~
                              &
core-junction.c:568:24: note: remove constant to silence this warning
        }else if(is_same_best && 0){
                             ~^~~~
core-junction.c:3166:6: warning: variable 'total_perfect_matched_sections' set but not used [-Wunused-but-set-variable]
        int total_perfect_matched_sections = 0;
            ^
core-junction.c:4154:6: warning: variable 'no_sup_juncs' set but not used [-Wunused-but-set-variable]
        int no_sup_juncs = 0;
            ^
core-junction.c:4155:6: warning: variable 'all_juncs' set but not used [-Wunused-but-set-variable]
        int all_juncs = 0;
            ^
core-junction.c:4286:6: warning: variable 'no_sup_juncs' set but not used [-Wunused-but-set-variable]
        int no_sup_juncs = 0, disk_is_full = 0;
            ^
core-junction.c:4386:38: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
        if ( (rl <= EXON_LONG_READ_LENGTH ) && (!EXON_EXTENDING_SCAN)) return;
                                            ^  ~~~~~~~~~~~~~~~~~~~~~~
core-junction.c:4386:38: note: use '&' for a bitwise operation
        if ( (rl <= EXON_LONG_READ_LENGTH ) && (!EXON_EXTENDING_SCAN)) return;
                                            ^~
                                            &
core-junction.c:4386:38: note: remove constant to silence this warning
        if ( (rl <= EXON_LONG_READ_LENGTH ) && (!EXON_EXTENDING_SCAN)) return;
                                           ~^~~~~~~~~~~~~~~~~~~~~~~~~
core-junction.c:4764:8: warning: variable 'coverage_len' set but not used [-Wunused-but-set-variable]
                        int coverage_len = max_end - max_start + vote->coverage_end[i][j] - vote->coverage_start[i][j];
                            ^
core-junction.c:5728:13: warning: variable 'small_dist' set but not used [-Wunused-but-set-variable]
                long long small_dist = event_body -> event_small_side, large_dist = event_body -> event_large_side;
                          ^
core-junction.c:5728:58: warning: variable 'large_dist' set but not used [-Wunused-but-set-variable]
                long long small_dist = event_body -> event_small_side, large_dist = event_body -> event_large_side;
                                                                       ^
10 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c core.c -o core.o
In file included from core.c:45:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
core.c:184:79: warning: variable 'real_lenwidth' set but not used [-Wunused-but-set-variable]
                int is_R_code,x1,content_len = strlen(content), state, txt_len, is_cut = 0, real_lenwidth;
                                                                                            ^
core.c:1373:15: warning: variable 'linear_cursor' set but not used [-Wunused-but-set-variable]
        unsigned int linear_cursor = linear;
                     ^
3 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detection-calls.c -o detection-calls.o
In file included from detection-calls.c:8:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detectionCall.c -o detectionCall.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
detectionCallAnnotation.c:154:6: warning: variable 'binnum' set but not used [-Wunused-but-set-variable]
        int binnum = 0;
            ^
detectionCallAnnotation.c:184:6: warning: variable 'linenum' set but not used [-Wunused-but-set-variable]
        int linenum;
            ^
detectionCallAnnotation.c:274:6: warning: variable 'linenum' set but not used [-Wunused-but-set-variable]
        int linenum;
            ^
3 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-algorithms.c -o exon-algorithms.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-align-indel.c -o exon-align-indel.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c exon-align.c -o exon-align.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c flattenAnnotations.c -o flattenAnnotations.o
In file included from flattenAnnotations.c:41:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c fullscan.c -o fullscan.o
In file included from fullscan.c:26:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c fusion-align.c -o fusion-align.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gen_rand_reads.c -o gen_rand_reads.o
In file included from gen_rand_reads.c:26:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gene-algorithms.c -o gene-algorithms.o
In file included from gene-algorithms.c:36:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
gene-algorithms.c:795:6: warning: variable 'dynamic_delta' set but not used [-Wunused-but-set-variable]
        int dynamic_delta = 0;
            ^
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c gene-value-index.c -o gene-value-index.o
In file included from gene-value-index.c:25:
In file included from ./gene-value-index.h:24:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c hashtable.c -o hashtable.o
In file included from hashtable.c:18:
In file included from ./core.h:46:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c index-builder.c -o index-builder.o
In file included from index-builder.c:31:
In file included from ./gene-value-index.h:24:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
index-builder.c:157:16: warning: variable 'all_skips' set but not used [-Wunused-but-set-variable]
                int skips=0, all_skips = 0;
                             ^
index-builder.c:543:10: warning: variable 'read_len' set but not used [-Wunused-but-set-variable]
                int i, read_len = 0;
                       ^
index-builder.c:545:16: warning: variable 'all_skips' set but not used [-Wunused-but-set-variable]
                int skips=0, all_skips = 0;
                             ^
index-builder.c:490:23: warning: variable 'read_no' set but not used [-Wunused-but-set-variable]
        unsigned int offset, read_no;
                             ^
5 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c input-blc.c -o input-blc.o
In file included from input-blc.c:8:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
input-blc.c:580:17: warning: unused variable 'npos' [-Wunused-variable]
                                                long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
                                                          ^
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c input-files.c -o input-files.o
In file included from input-files.c:35:
In file included from ./input-files.h:23:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
input-files.c:2478:17: warning: use of logical '||' with constant operand [-Wconstant-logical-operand]
        if(ret == Z_OK || 1){
                       ^  ~
input-files.c:2478:17: note: use '|' for a bitwise operation
        if(ret == Z_OK || 1){
                       ^~
                       |
input-files.c:2670:11: warning: variable 'all_orphants' set but not used [-Wunused-but-set-variable]
        srInt_64 all_orphants = 0;
                 ^
input-files.c:2794:6: warning: variable 'current_blocks' set but not used [-Wunused-but-set-variable]
        int current_blocks = 0;
            ^
input-files.c:3244:6: warning: unused variable 'seq_len' [-Wunused-variable]
        int seq_len = qual - seq - 1;
            ^
input-files.c:4953:49: warning: variable 'block_no' set but not used [-Wunused-but-set-variable]
        int seq_len = 0, name_len = 0, cigar_opts = 0, block_no=0;
                                                       ^
input-files.c:4954:11: warning: variable 'reads' set but not used [-Wunused-but-set-variable]
        srInt_64 reads =0;
                 ^
input-files.c:5289:16: warning: variable 'bam_signature' set but not used [-Wunused-but-set-variable]
                unsigned int bam_signature;
                             ^
input-files.c:5599:7: warning: variable 'reads' set but not used [-Wunused-but-set-variable]
                int reads = 0;
                    ^
input-files.c:5828:12: warning: variable 'finished_second_reads' set but not used [-Wunused-but-set-variable]
                srInt_64 finished_second_reads = 0;
                         ^
10 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c interval_merge.c -o interval_merge.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c long-hashtable.c -o long-hashtable.o
In file included from long-hashtable.c:31:
In file included from ./core.h:46:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c longread-mapping.c -o longread-mapping.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c mergeVCF.c -o mergeVCF.o
In file included from mergeVCF.c:7:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c processExons.c -o processExons.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c propmapped.c -o propmapped.o
In file included from propmapped.c:34:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c qualityScores.c -o qualityScores.o
In file included from qualityScores.c:27:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c read-repair.c -o read-repair.o
In file included from read-repair.c:6:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c readSummary.c -o readSummary.o
In file included from readSummary.c:41:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
readSummary.c:3900:16: warning: variable 'assignment_target_number' set but not used [-Wunused-but-set-variable]
                                                srInt_64 assignment_target_number = tmp_voter_id;
                                                         ^
readSummary.c:3970:25: warning: unused variable 'sample_i' [-Wunused-variable]
        int xk1, xk2, ret = 0, sample_i;
                               ^
readSummary.c:5724:7: warning: unused variable 'unique_junctions' [-Wunused-variable]
                int unique_junctions = 0;
                    ^
readSummary.c:5698:74: warning: unused variable 'gene_name_tail' [-Wunused-variable]
        char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
                                                                                ^
readSummary.c:5700:6: warning: unused variable 'ky_i1' [-Wunused-variable]
        int ky_i1, ky_i2;
            ^
readSummary.c:5700:13: warning: unused variable 'ky_i2' [-Wunused-variable]
        int ky_i1, ky_i2;
                   ^
readSummary.c:5971:45: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable]
        int  isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
                                                   ^
8 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c removeDupReads.c -o removeDupReads.o
In file included from removeDupReads.c:27:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
removeDupReads.c:71:6: warning: variable 'chromosome_block_no' set but not used [-Wunused-but-set-variable]
        int chromosome_block_no = 0;
            ^
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sam2bed.c -o sam2bed.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sambam-file.c -o sambam-file.o
In file included from sambam-file.c:33:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c seek-zlib.c -o seek-zlib.o
In file included from seek-zlib.c:2:
In file included from ./core.h:46:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
In file included from sorted-hashtable.c:20:
In file included from ./sorted-hashtable.h:25:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
sorted-hashtable.c:1396:31: warning: use of logical '||' with constant operand [-Wconstant-logical-operand]
        if(0)if(sizeof( size_t ) != 8|| sizeof(long int ) != 8|| sizeof(int ) != 4){
                                     ^  ~~~~~~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1396:31: note: use '|' for a bitwise operation
        if(0)if(sizeof( size_t ) != 8|| sizeof(long int ) != 8|| sizeof(int ) != 4){
                                     ^~
                                     |
sorted-hashtable.c:1396:56: warning: use of logical '||' with constant operand [-Wconstant-logical-operand]
        if(0)if(sizeof( size_t ) != 8|| sizeof(long int ) != 8|| sizeof(int ) != 4){
                                                              ^  ~~~~~~~~~~~~~~~~~
sorted-hashtable.c:1396:56: note: use '|' for a bitwise operation
        if(0)if(sizeof( size_t ) != 8|| sizeof(long int ) != 8|| sizeof(int ) != 4){
                                                              ^~
                                                              |
3 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c sublog.c -o sublog.o
In file included from sublog.c:26:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 2.23.3\""  -fPIC  -falign-functions=64 -Wall -g -O2  -c tx-unique.c -o tx-unique.o
In file included from tx-unique.c:6:
In file included from ./tx-unique.h:4:
./subread.h:502:2: warning: "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======" [-W#warnings]
#warning "====== Yang Liao added '+300' for debugging junc-detection. Not needed in release. ======"
 ^
1 warning generated.
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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)