##############################################################################
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###
### Running command:
###
### rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsubread_2.23.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rsubread.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rsubread.buildbin-libdir Rsubread_2.23.2.tar.gz'
>>>>>>>
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.23.2’
** 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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c HelperFunctions.c -o HelperFunctions.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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c R_wrapper.c -o R_wrapper.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c RsimReads.c -o RsimReads.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c SNPCalling.c -o SNPCalling.o
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;
^
6 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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c cell-counts.c -o cell-counts.o
cell-counts.c:3589:6: warning: format specifies type 'char *' but the argument has type 'void *' [-Wformat]
ADD_count_hash(str1->cellbc, str1->gene_no,1);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:3571:119: 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:3726:45: 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:3571:119: 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:4202:60: 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:4202:60: 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:4202:60: 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:4673:11: 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:4698:11: 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:4772:11: 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:4819:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
size_t frret = fread(&binlen, 1, 4, notmapped_fp);
^
cell-counts.c:4611:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
srInt_64 removed_umis = 0;
^
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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-bigtable.c -o core-bigtable.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-indel.c -o core-indel.o
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;
^
4 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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-interface-aligner.c -o core-interface-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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-junction.c -o core-junction.o
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;
^
9 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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core.c -o core.o
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;
^
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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detection-calls.c -o detection-calls.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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c flattenAnnotations.c -o flattenAnnotations.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c fullscan.c -o fullscan.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 2.23.2\"" -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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gen_rand_reads.c -o gen_rand_reads.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gene-algorithms.c -o gene-algorithms.o
gene-algorithms.c:795:6: warning: variable 'dynamic_delta' set but not used [-Wunused-but-set-variable]
int dynamic_delta = 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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gene-value-index.c -o gene-value-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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c hashtable.c -o 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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c index-builder.c -o index-builder.o
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;
^
4 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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c input-blc.c -o input-blc.o
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);
^
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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c input-files.c -o input-files.o
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;
^
9 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 2.23.2\"" -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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c long-hashtable.c -o long-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 2.23.2\"" -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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c mergeVCF.c -o mergeVCF.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 2.23.2\"" -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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c propmapped.c -o propmapped.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c qualityScores.c -o qualityScores.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c read-repair.c -o read-repair.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c readSummary.c -o readSummary.o
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;
^
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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c removeDupReads.c -o removeDupReads.o
removeDupReads.c:71:6: warning: variable 'chromosome_block_no' set but not used [-Wunused-but-set-variable]
int chromosome_block_no = 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 2.23.2\"" -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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sambam-file.c -o sambam-file.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c seek-zlib.c -o seek-zlib.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o
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){
^~
|
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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sublog.c -o sublog.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 2.23.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c tx-unique.c -o tx-unique.o
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 /Users/biocbuild/bbs-3.22-bioc/meat/Rsubread.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so
>>>>>>>
>>>>>>> Paths before fix:
Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so:
Rsubread.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so"
>>>>>>> Paths after fix:
Rsubread.buildbin-libdir/Rsubread/libs/Rsubread.so:
Rsubread.so (compatibility version 0.0.0, current version 0.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
