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###
### Running command:
###
### rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsubread_2.25.2.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_2.25.2.tar.gz'
>>>>>>>
* installing *source* package ‘Rsubread’ ...
** this is package ‘Rsubread’ version ‘2.25.2’
** using staged installation
@@@@@ The operating system is Darwin.
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c HelperFunctions.c -o HelperFunctions.o
HelperFunctions.c:2991:16: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
2991 | M[k] = NEG_INF;
| ^~~~~~~
HelperFunctions.c:2939:23: note: expanded from macro 'NEG_INF'
2939 | #define NEG_INF (-1LL << 60)
| ~~~~ ^
HelperFunctions.c:2992:17: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
2992 | Ix[k] = NEG_INF;
| ^~~~~~~
HelperFunctions.c:2939:23: note: expanded from macro 'NEG_INF'
2939 | #define NEG_INF (-1LL << 60)
| ~~~~ ^
HelperFunctions.c:2993:17: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
2993 | Iy[k] = NEG_INF;
| ^~~~~~~
HelperFunctions.c:2939:23: note: expanded from macro 'NEG_INF'
2939 | #define NEG_INF (-1LL << 60)
| ~~~~ ^
3 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
146 | int read_chrsor = 0, all_matched = 0, all_mismatched = 0;
| ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMchro-event.c -o LRMchro-event.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMfile-io.c -o LRMfile-io.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMhashtable.c -o LRMhashtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMhelper.c -o LRMhelper.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
194 | unsigned int this_chunk_size = 0;
| ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c R_wrapper.c -o R_wrapper.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c RsimReads.c -o RsimReads.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
263 | unsigned long long int OVERLAPPED_BASES=0;
| ^
SNPCalling.c:264:25: warning: variable 'OVER_MISMA_BASES' set but not used [-Wunused-but-set-variable]
264 | unsigned long long int OVER_MISMA_BASES=0;
| ^
SNPCalling.c:265:25: warning: variable 'ALL_BASES' set but not used [-Wunused-but-set-variable]
265 | unsigned long long int ALL_BASES=0;
| ^
SNPCalling.c:707:7: warning: variable 'window_no' set but not used [-Wunused-but-set-variable]
707 | int window_no = 0;
| ^
4 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c aligner.c -o aligner.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
72 | int line_num = 0;
| ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c build-sam-index.c -o build-sam-index.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c cell-counts.c -o cell-counts.o
cell-counts.c:1180:9: warning: unused variable 'params' [-Wunused-variable]
1180 | void * params [5];
| ^~~~~~
cell-counts.c:1263:16: warning: variable 'new_details' set but not used [-Wunused-but-set-variable]
1263 | chroEvent_t * new_details = NULL;
| ^
cell-counts.c:1317:21: warning: variable 'last_start' set but not used [-Wunused-but-set-variable]
1317 | int last_end = -1, last_start = -1;
| ^
cell-counts.c:1523:23: warning: unused variable 'sample_i' [-Wunused-variable]
1523 | int xk1, edge_tab_i, sample_i;
| ^~~~~~~~
cell-counts.c:2823:132: warning: unused variable 'testi' [-Wunused-variable]
2823 | 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:3394:30: warning: unused variable 'thread_context' [-Wunused-variable]
3394 | cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
| ^~~~~~~~~~~~~~
cell-counts.c:3530:2: warning: "======= THIS IS FOR DEBUGGING CRASH ('__DEBUG_NO_LOOK') =======" [-W#warnings]
3530 | #warning "======= THIS IS FOR DEBUGGING CRASH ('__DEBUG_NO_LOOK') ======="
| ^
cell-counts.c:3520:8: warning: unused variable 'cigar_rlen' [-Wunused-variable]
3520 | int cigar_rlen = cellCounts_reduce_Cigar(cigar_end5,final_cigar,&sum_ins);
| ^~~~~~~~~~
cell-counts.c:3470:22: warning: unused variable 'x_candidate' [-Wunused-variable]
3470 | int x_3end, x_5end, x_candidate;
| ^~~~~~~~~~~
cell-counts.c:3723:7: warning: unused variable 'read_for_testing_len' [-Wunused-variable]
3723 | int read_for_testing_len = edge_region_end - edge_region_start +1;
| ^~~~~~~~~~~~~~~~~~~~
cell-counts.c:3829:132: warning: unused variable 'testi' [-Wunused-variable]
3829 | 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:4092:6: warning: unused variable 'retlen' [-Wunused-variable]
4092 | int retlen = general_dynamic_align_moves_to_cigar(result_buffer, moved_len, result_cigar);
| ^~~~~~
cell-counts.c:4205:10: warning: variable 'rgap' set but not used [-Wunused-but-set-variable]
4205 | int rgap = -1;
| ^
cell-counts.c:4245:9: warning: unused variable 'manegative' [-Wunused-variable]
4245 | int manegative = votetab -> masks[mai][maj];
| ^~~~~~~~~~
cell-counts.c:4157:8: warning: variable 'best_GTAG_negative' set but not used [-Wunused-but-set-variable]
4157 | int best_GTAG_negative = -1;
| ^
cell-counts.c:4127:10: warning: unused variable 'reverse_text_offset' [-Wunused-variable]
4127 | int i,j,reverse_text_offset, distinct_vote_number_i;
| ^~~~~~~~~~~~~~~~~~~
cell-counts.c:4127:31: warning: unused variable 'distinct_vote_number_i' [-Wunused-variable]
4127 | int i,j,reverse_text_offset, distinct_vote_number_i;
| ^~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4373:9: warning: variable 'on_chro_len' set but not used [-Wunused-but-set-variable]
4373 | int on_chro_len = tmpi +1;
| ^
cell-counts.c:4404:24: warning: variable 'x2_not_matter' set but not used [-Wunused-but-set-variable]
4404 | int is_the_last, x2_not_matter;
| ^
cell-counts.c:4438:46: warning: array subscript is of type 'char' [-Wchar-subscripts]
4438 | IVT_IntervalTreeNode * myroot = LR_roots[LRi];
| ^~~~
cell-counts.c:4328:34: warning: unused variable 'x3' [-Wunused-variable]
4328 | int nch, tmpi=0, x1=0, b1off=0, x3;
| ^~
cell-counts.c:5079:6: warning: variable 'preads' set but not used [-Wunused-but-set-variable]
5079 | int preads=0;
| ^
cell-counts.c:5536:4: warning: "===== DISABLED TABLE_BASED BATCHING !!! =====" [-W#warnings]
5536 | #warning "===== DISABLED TABLE_BASED BATCHING !!! ====="
| ^
cell-counts.c:5677:171: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
5677 | fprintf(stderr,"STEP_%d_FINN_X1: %.10s gene_no=%016lld supReads=%d start=%d,%d CELL_BC=%d CHANGED=%d\n", is_UMI_step2+1, str1->umi, str1 -> gene_no, str1->supp_reads,x1, sec_start, str1->cellbc, is_umi_changed);
| ~~ ^~
| %lld
cell-counts.c:5677:175: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
5677 | fprintf(stderr,"STEP_%d_FINN_X1: %.10s gene_no=%016lld supReads=%d start=%d,%d CELL_BC=%d CHANGED=%d\n", is_UMI_step2+1, str1->umi, str1 -> gene_no, str1->supp_reads,x1, sec_start, str1->cellbc, is_umi_changed);
| ~~ ^~~~~~~~~
| %lld
cell-counts.c:5676:29: warning: unused variable 'str2' [-Wunused-variable]
5676 | struct cell_gene_umi_supp * str2 = ArrayListGet(structs, sec_start +1);
| ^~~~
cell-counts.c:6513:112: warning: format specifies type 'int' but the argument has type 'srInt_64' (aka 'long long') [-Wformat]
6513 | fprintf(stderr,"%dth resample: BOOT_30TH: %lld UMI / %lld cells. Top UMIs (original/resampled) %lld %lld \n", x1, UMIs_30th_div10, list_cellBCs_sorted_by_UMIs -> numOfElements, ori_umis , top_umis);
| ~~ ^~
| %lld
cell-counts.c:6729:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
6729 | size_t frret = fread(§ion1_items,1, 8, input_fps[xk1]);
| ^
cell-counts.c:6754:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
6754 | size_t frret = fread(last_rbin_buffer[xk1]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[xk1]);
| ^
cell-counts.c:6828:11: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
6828 | 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:6875:10: warning: variable 'frret' set but not used [-Wunused-but-set-variable]
6875 | size_t frret = fread(&binlen, 1, 4, notmapped_fp);
| ^
cell-counts.c:6667:11: warning: variable 'removed_umis' set but not used [-Wunused-but-set-variable]
6667 | srInt_64 removed_umis = 0;
| ^
cell-counts.c:7411:7: warning: unused variable 'unique_junctions' [-Wunused-variable]
7411 | int unique_junctions = 0;
| ^~~~~~~~~~~~~~~~
cell-counts.c:7354:6: warning: unused variable 'infile_i' [-Wunused-variable]
7354 | int infile_i, disk_is_full = 0, sample_i;
| ^~~~~~~~
cell-counts.c:7388:74: warning: unused variable 'gene_name_tail' [-Wunused-variable]
7388 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
| ^~~~~~~~~~~~~~
cell-counts.c:7390:6: warning: unused variable 'ky_i1' [-Wunused-variable]
7390 | int ky_i1, ky_i2;
| ^~~~~
cell-counts.c:7390:13: warning: unused variable 'ky_i2' [-Wunused-variable]
7390 | int ky_i1, ky_i2;
| ^~~~~
37 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-bigtable.c -o core-bigtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
455 | 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]
2592 | int all_reads = 0;
| ^
core-indel.c:4060:11: warning: variable 'all_indels_in_window' set but not used [-Wunused-but-set-variable]
4060 | int all_indels_in_window = 0;
| ^
core-indel.c:3695:6: warning: variable 'global_read_no' set but not used [-Wunused-but-set-variable]
3695 | int global_read_no = 0;
| ^
4 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-interface-aligner.c -o core-interface-aligner.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c core-junction.c -o core-junction.o
core-junction.c:3166:6: warning: variable 'total_perfect_matched_sections' set but not used [-Wunused-but-set-variable]
3166 | int total_perfect_matched_sections = 0;
| ^
core-junction.c:4154:6: warning: variable 'no_sup_juncs' set but not used [-Wunused-but-set-variable]
4154 | int no_sup_juncs = 0;
| ^
core-junction.c:4155:6: warning: variable 'all_juncs' set but not used [-Wunused-but-set-variable]
4155 | int all_juncs = 0;
| ^
core-junction.c:4286:6: warning: variable 'no_sup_juncs' set but not used [-Wunused-but-set-variable]
4286 | int no_sup_juncs = 0, disk_is_full = 0;
| ^
core-junction.c:4764:8: warning: variable 'coverage_len' set but not used [-Wunused-but-set-variable]
4764 | 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]
5728 | 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]
5728 | long long small_dist = event_body -> event_small_side, large_dist = event_body -> event_large_side;
| ^
7 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
184 | 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]
1373 | unsigned int linear_cursor = linear;
| ^
2 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detection-calls.c -o detection-calls.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c detectionCall.c -o detectionCall.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
154 | int binnum = 0;
| ^
detectionCallAnnotation.c:184:6: warning: variable 'linenum' set but not used [-Wunused-but-set-variable]
184 | int linenum;
| ^
detectionCallAnnotation.c:274:6: warning: variable 'linenum' set but not used [-Wunused-but-set-variable]
274 | int linenum;
| ^
3 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-algorithms.c -o exon-algorithms.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-align-indel.c -o exon-align-indel.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c exon-align.c -o exon-align.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c flattenAnnotations.c -o flattenAnnotations.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c fullscan.c -o fullscan.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c fusion-align.c -o fusion-align.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gen_rand_reads.c -o gen_rand_reads.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
795 | int dynamic_delta = 0;
| ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c gene-value-index.c -o gene-value-index.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c hashtable.c -o hashtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
157 | int skips=0, all_skips = 0;
| ^
index-builder.c:543:10: warning: variable 'read_len' set but not used [-Wunused-but-set-variable]
543 | int i, read_len = 0;
| ^
index-builder.c:545:16: warning: variable 'all_skips' set but not used [-Wunused-but-set-variable]
545 | int skips=0, all_skips = 0;
| ^
index-builder.c:490:23: warning: variable 'read_no' set but not used [-Wunused-but-set-variable]
490 | unsigned int offset, read_no;
| ^
4 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c input-blc.c -o input-blc.o
input-blc.c:585:17: warning: unused variable 'npos' [-Wunused-variable]
585 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET);
| ^~~~
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c input-files.c -o input-files.o
input-files.c:2670:11: warning: variable 'all_orphants' set but not used [-Wunused-but-set-variable]
2670 | srInt_64 all_orphants = 0;
| ^
input-files.c:2794:6: warning: variable 'current_blocks' set but not used [-Wunused-but-set-variable]
2794 | int current_blocks = 0;
| ^
input-files.c:3244:6: warning: unused variable 'seq_len' [-Wunused-variable]
3244 | int seq_len = qual - seq - 1;
| ^~~~~~~
input-files.c:4953:49: warning: variable 'block_no' set but not used [-Wunused-but-set-variable]
4953 | 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]
4954 | srInt_64 reads =0;
| ^
input-files.c:5289:16: warning: variable 'bam_signature' set but not used [-Wunused-but-set-variable]
5289 | unsigned int bam_signature;
| ^
input-files.c:5599:7: warning: variable 'reads' set but not used [-Wunused-but-set-variable]
5599 | int reads = 0;
| ^
input-files.c:5828:12: warning: variable 'finished_second_reads' set but not used [-Wunused-but-set-variable]
5828 | srInt_64 finished_second_reads = 0;
| ^
8 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c interval_merge.c -o interval_merge.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c long-hashtable.c -o long-hashtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c longread-mapping.c -o longread-mapping.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c mergeVCF.c -o mergeVCF.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c processExons.c -o processExons.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c propmapped.c -o propmapped.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c qualityScores.c -o qualityScores.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c read-repair.c -o read-repair.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
3900 | srInt_64 assignment_target_number = tmp_voter_id;
| ^
readSummary.c:3970:25: warning: unused variable 'sample_i' [-Wunused-variable]
3970 | int xk1, xk2, ret = 0, sample_i;
| ^~~~~~~~
readSummary.c:5724:7: warning: unused variable 'unique_junctions' [-Wunused-variable]
5724 | int unique_junctions = 0;
| ^~~~~~~~~~~~~~~~
readSummary.c:5698:74: warning: unused variable 'gene_name_tail' [-Wunused-variable]
5698 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail;
| ^~~~~~~~~~~~~~
readSummary.c:5700:6: warning: unused variable 'ky_i1' [-Wunused-variable]
5700 | int ky_i1, ky_i2;
| ^~~~~
readSummary.c:5700:13: warning: unused variable 'ky_i2' [-Wunused-variable]
5700 | int ky_i1, ky_i2;
| ^~~~~
readSummary.c:5971:45: warning: variable 'scrna_total_BAM_no' set but not used [-Wunused-but-set-variable]
5971 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no;
| ^
7 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -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]
71 | int chromosome_block_no = 0;
| ^
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sam2bed.c -o sam2bed.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sambam-file.c -o sambam-file.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c seek-zlib.c -o seek-zlib.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c softclip-test.c -o softclip-test.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sorted-hashtable.c -o sorted-hashtable.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c sublog.c -o sublog.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DMAKE_FOR_EXON -D MACOS -D SUBREAD_VERSION="\"Rsubread 2.25.2\"" -fPIC -falign-functions=64 -Wall -g -O2 -c tx-unique.c -o tx-unique.o
clang -arch arm64 -std=gnu23 -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 softclip-test.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-3.23-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 1356.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!
