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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rsubread
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.23.4’
** using staged installation
@@@@@ The operating system is Darwin.
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMchro-event.c -o LRMchro-event.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMfile-io.c -o LRMfile-io.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMhashtable.c -o LRMhashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMhelper.c -o LRMhelper.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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:707:7: warning: variable 'window_no' set but not used [-Wunused-but-set-variable]
int window_no = 0;
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c aligner.c -o aligner.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c atgcContent.c -o atgcContent.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c build-sam-index.c -o build-sam-index.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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:1141:9: warning: unused variable 'params' [-Wunused-variable]
void * params [5];
^
cell-counts.c:1261:21: warning: variable 'last_start' set but not used [-Wunused-but-set-variable]
int last_end = -1, last_start = -1;
^
cell-counts.c:1477:23: warning: unused variable 'sample_i' [-Wunused-variable]
int xk1, edge_tab_i, sample_i;
^
cell-counts.c:2599:132: warning: unused variable 'testi' [-Wunused-variable]
char * sample_seq=NULL, *sample_qual=NULL, *BC_qual=NULL, *BC_seq=NULL, *UMI_seq=NULL, *UMI_qual=NULL, *lane_str=NULL, *RG=NULL, *testi;
^
cell-counts.c:2750:1: warning: non-void function does not return a value [-Wreturn-type]
}
^
cell-counts.c:3208:22: warning: unused variable 'x_candidate' [-Wunused-variable]
int x_3end, x_5end, x_candidate;
^
cell-counts.c:3350:2: 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:3464:194: warning: format specifies type 'int' but the argument has type 'long' [-Wformat]
if(0)if(strstr(thread_context -> realignment_event_read_name ,"R00000985779"))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:3419:7: warning: unused variable 'read_for_testing_len' [-Wunused-variable]
int read_for_testing_len = edge_region_end - edge_region_start +1;
^
cell-counts.c:3770:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
for(x1=0; nch=result_cigar[x1] ; x1++){
~~~^~~~~~~~~~~~~~~~~
cell-counts.c:3770:15: note: place parentheses around the assignment to silence this warning
for(x1=0; nch=result_cigar[x1] ; x1++){
^
( )
cell-counts.c:3770:15: note: use '==' to turn this assignment into an equality comparison
for(x1=0; nch=result_cigar[x1] ; x1++){
^
==
cell-counts.c:3881:10: warning: variable 'rgap' set but not used [-Wunused-but-set-variable]
int rgap = -1;
^
cell-counts.c:3911:5: 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:3921:9: warning: unused variable 'manegative' [-Wunused-variable]
int manegative = votetab -> masks[mai][maj];
^
cell-counts.c:3833:8: warning: variable 'best_GTAG_negative' set but not used [-Wunused-but-set-variable]
int best_GTAG_negative = -1;
^
cell-counts.c:3801:31: warning: unused variable 'distinct_vote_number_i' [-Wunused-variable]
int i,j,reverse_text_offset, distinct_vote_number_i;
^
cell-counts.c:3801:10: warning: unused variable 'reverse_text_offset' [-Wunused-variable]
int i,j,reverse_text_offset, distinct_vote_number_i;
^
cell-counts.c:3969:1: warning: non-void function does not return a value [-Wreturn-type]
}
^
cell-counts.c:4012:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(nch = cigar[x1++]){
~~~~^~~~~~~~~~~~~
cell-counts.c:4012:12: note: place parentheses around the assignment to silence this warning
while(nch = cigar[x1++]){
^
( )
cell-counts.c:4012:12: note: use '==' to turn this assignment into an equality comparison
while(nch = cigar[x1++]){
^
==
cell-counts.c:4074:24: warning: variable 'x2_not_matter' set but not used [-Wunused-but-set-variable]
int is_the_last, x2_not_matter;
^
cell-counts.c:4098:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
while(nch = cigar[x1++]){
~~~~^~~~~~~~~~~~~
cell-counts.c:4098:12: note: place parentheses around the assignment to silence this warning
while(nch = cigar[x1++]){
^
( )
cell-counts.c:4098:12: note: use '==' to turn this assignment into an equality comparison
while(nch = cigar[x1++]){
^
==
cell-counts.c:4108:46: warning: array subscript is of type 'char' [-Wchar-subscripts]
IVT_IntervalTreeNode * myroot = LR_roots[LRi];
^~~~
cell-counts.c:4133:107: 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:4133:121: 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:4142:115: 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:4142:129: 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:4000:34: warning: unused variable 'x3' [-Wunused-variable]
int nch, tmpi=0, x1=0, b1off=0, x3;
^
cell-counts.c:5176:6: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
ADD_count_hash(str1->cellbc, str1->gene_no,1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:5158:119: 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:5223:120: 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:5252:119: 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:5323:45: 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:5158:119: 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:6270:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
size_t frret = fread(§ion1_items,1, 8, input_fps[xk1]);
^
cell-counts.c:6295:11: 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:6369:11: 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:6416:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
size_t frret = fread(&binlen, 1, 4, notmapped_fp);
^
cell-counts.c:6208:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
srInt_64 removed_umis = 0;
^
cell-counts.c:6815:120: 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:6952:7: warning: unused variable 'unique_junctions' [-Wunused-variable]
int unique_junctions = 0;
^
cell-counts.c:6929:74: warning: unused variable 'gene_name_tail' [-Wunused-variable]
char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
^
cell-counts.c:6931:13: warning: unused variable 'ky_i2' [-Wunused-variable]
int ky_i1, ky_i2;
^
cell-counts.c:6931:6: warning: unused variable 'ky_i1' [-Wunused-variable]
int ky_i1, ky_i2;
^
cell-counts.c:6895:6: warning: unused variable 'infile_i' [-Wunused-variable]
int infile_i, disk_is_full = 0, sample_i;
^
46 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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:2592:8: warning: variable 'all_reads' set but not used [-Wunused-but-set-variable]
int all_reads = 0;
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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: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: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;
^
5 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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:1373:15: warning: variable 'linear_cursor' set but not used [-Wunused-but-set-variable]
unsigned int linear_cursor = linear;
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detectionCall.c -o detectionCall.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detectionCallAnnotation.c -o detectionCallAnnotation.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-algorithms.c -o exon-algorithms.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-align-indel.c -o exon-align-indel.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-align.c -o exon-align.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c fusion-align.c -o fusion-align.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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. ======"
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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. ======"
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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:2670:11: warning: variable 'all_orphants' set but not used [-Wunused-but-set-variable]
srInt_64 all_orphants = 0;
^
input-files.c:3244:6: warning: unused variable 'seq_len' [-Wunused-variable]
int seq_len = qual - seq - 1;
^
input-files.c:5289:16: warning: variable 'bam_signature' set but not used [-Wunused-but-set-variable]
unsigned int bam_signature;
^
4 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c interval_merge.c -o interval_merge.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c longread-mapping.c -o longread-mapping.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c processExons.c -o processExons.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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:5700:13: warning: unused variable 'ky_i2' [-Wunused-variable]
int ky_i1, ky_i2;
^
readSummary.c:5700:6: warning: unused variable 'ky_i1' [-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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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. ======"
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sam2bed.c -o sam2bed.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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. ======"
^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.23.4\"" -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 x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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)
