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###
### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rsubread
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c HelperFunctions.c -o HelperFunctions.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c LRMbase-index.c -o LRMbase-index.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c LRMchro-event.c -o LRMchro-event.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c LRMfile-io.c -o LRMfile-io.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c LRMhashtable.c -o LRMhashtable.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c LRMhelper.c -o LRMhelper.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c LRMseek-zlib.c -o LRMseek-zlib.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c R_wrapper.c -o R_wrapper.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RsimReads.c -o RsimReads.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c SNPCalling.c -o SNPCalling.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c aligner.c -o aligner.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c atgcContent.c -o atgcContent.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c build-sam-index.c -o build-sam-index.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cell-counts.c -o cell-counts.o
cell-counts.c: In function 'cellCounts_sort_feature_info':
cell-counts.c:1042:6: warning: unused variable 'curr_chro_number' [-Wunused-variable]
  int curr_chro_number = 0;
      ^~~~~~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_parallel_gzip_writer_add_read_fqs_scRNA':
cell-counts.c:1752:6: warning: unused variable 'x1' [-Wunused-variable]
  int x1=0;
      ^~
cell-counts.c: In function 'cellCounts_vote_and_add_count':
cell-counts.c:1818:6: warning: unused variable 'fields' [-Wunused-variable]
  int fields = cellCounts_scan_read_name_str(cct_context, NULL, read_name, &sample_seq, &sample_qual, &BC_seq, &BC_qual, &UMI_seq, &UMI_qual, &lane_str, &RG, &rname_trimmed_len);
      ^~~~~~
cell-counts.c: In function 'cellCounts_prepare_context_for_align':
cell-counts.c:1970:30: warning: unused variable 'thread_context' [-Wunused-variable]
  cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
                              ^~~~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_fetch_next_read_pair':
cell-counts.c:2067:6: warning: unused variable 'lockret2' [-Wunused-variable]
  int lockret2=cellCounts_lock_release(&cct_context -> input_dataset_lock);
      ^~~~~~~~
cell-counts.c:2053:6: warning: unused variable 'lockret1' [-Wunused-variable]
  int lockret1=cellCounts_lock_occupy(&cct_context -> input_dataset_lock);
      ^~~~~~~~
cell-counts.c: In function 'cellCounts_indel_recorder_copy':
cell-counts.c:2156:17: warning: array subscript has type 'char' [-Wchar-subscripts]
   for(sri=votrec[toli]; sri<=votrec[toli+1]; sri++) offsets[sri -1] = votrec[toli+2];
                 ^
cell-counts.c:2159:13: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offsets[sri]!=0x77){
             ^
cell-counts.c:2160:26: warning: array subscript has type 'char' [-Wchar-subscripts]
    *read_pos_move=offsets[sri];
                          ^
cell-counts.c:2168:13: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offsets[sri]!=0x77){
             ^
cell-counts.c:2169:11: warning: array subscript has type 'char' [-Wchar-subscripts]
    offsets[sri] -= (*read_pos_move);
           ^
cell-counts.c:2172:25: warning: array subscript has type 'char' [-Wchar-subscripts]
     offset_cur = offsets[sri];
                         ^
cell-counts.c:2174:29: warning: array subscript has type 'char' [-Wchar-subscripts]
    high_conf_index = offsets[sri];
                             ^
cell-counts.c:2176:27: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offset_cur != offsets[sri] && subread0>0){
                           ^
cell-counts.c:2177:10: warning: array subscript has type 'char' [-Wchar-subscripts]
    alnrec[toli]= subread0;
          ^
cell-counts.c:2181:24: warning: array subscript has type 'char' [-Wchar-subscripts]
    offset_cur = offsets[sri];
                        ^
cell-counts.c:2189:13: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offsets[sri]==0x77) subread0 =-1;
             ^
cell-counts.c:2192:11: warning: array subscript has type 'char' [-Wchar-subscripts]
     alnrec[toli]= subread0;
           ^
cell-counts.c:2203:21: warning: array subscript has type 'char' [-Wchar-subscripts]
   for(toli=0; alnrec[toli]; toli+=3){
                     ^
cell-counts.c:2204:51: warning: array subscript has type 'char' [-Wchar-subscripts]
    SUBREADprintf("  %d ~ %d : indels=%d\n", alnrec[toli], alnrec[toli+1], alnrec[toli+2]);
                                                   ^
cell-counts.c: In function 'cellCounts_explain_one_read':
cell-counts.c:2345:16: warning: unused variable 'meet_end' [-Wunused-variable]
   unsigned int meet_end = abs_pos + first_correct_base + indel_offset;
                ^~~~~~~~
cell-counts.c:2315:6: warning: unused variable 'indels_in_highconf' [-Wunused-variable]
  int indels_in_highconf = cellCounts_indel_recorder_copy(indel_offsets, votetab -> indel_recorder[vote_i][vote_j], tolimax, all_subreads, &read_pos_move, read_name, abs_pos);
      ^~~~~~~~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_select_and_write_alignments':
cell-counts.c:2437:18: warning: unused variable 'topbuf' [-Wunused-variable]
  topK_buffer_t * topbuf = &thread_context->topKbuff;
                  ^~~~~~
cell-counts.c: In function 'cellCounts_process_copy_ptrs_to_votes':
cell-counts.c:2600:7: warning: unused variable 'subread_number_P1' [-Wunused-variable]
   int subread_number_P1 = 1+((myno >= applied_subreads_per_strand)?myno - applied_subreads_per_strand:myno);
       ^~~~~~~~~~~~~~~~~
cell-counts.c: In function 'simpleMode_cellCounts_process_copy_ptrs_to_votes':
cell-counts.c:2722:7: warning: unused variable 'subread_number_P1' [-Wunused-variable]
   int subread_number_P1 = 1+((myno >= applied_subreads_per_strand)?myno - applied_subreads_per_strand:myno);
       ^~~~~~~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_do_voting':
cell-counts.c:2881:15: warning: unused variable 'high_index_border' [-Wunused-variable]
  unsigned int high_index_border = cct_context -> value_index -> start_base_offset + cct_context -> value_index -> length;
               ^~~~~~~~~~~~~~~~~
cell-counts.c:2880:15: warning: unused variable 'low_index_border' [-Wunused-variable]
  unsigned int low_index_border = cct_context -> value_index -> start_base_offset;
               ^~~~~~~~~~~~~~~~
cell-counts.c:2868:30: warning: unused variable 'thread_context' [-Wunused-variable]
  cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
                              ^~~~~~~~~~~~~~
cell-counts.c:2866:6: warning: unused variable 'sqr_interval' [-Wunused-variable]
  int sqr_interval=10000;
      ^~~~~~~~~~~~
cell-counts.c:2860:6: warning: unused variable 'xk1' [-Wunused-variable]
  int xk1;
      ^~~
cell-counts.c: In function 'simpleMode_cellCounts_do_voting':
cell-counts.c:3028:9: warning: variable 'building_rbin_offset' set but not used [-Wunused-but-set-variable]
     int building_rbin_offset = 0, read_text_rev_offset =0;
         ^~~~~~~~~~~~~~~~~~~~
cell-counts.c:2988:15: warning: unused variable 'high_index_border' [-Wunused-variable]
  unsigned int high_index_border = cct_context -> value_index -> start_base_offset + cct_context -> value_index -> length;
               ^~~~~~~~~~~~~~~~~
cell-counts.c:2987:15: warning: unused variable 'low_index_border' [-Wunused-variable]
  unsigned int low_index_border = cct_context -> value_index -> start_base_offset;
               ^~~~~~~~~~~~~~~~
cell-counts.c:2971:6: warning: unused variable 'sqr_interval' [-Wunused-variable]
  int sqr_interval=10000;
      ^~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_merge_batches_worker':
cell-counts.c:3651:35: warning: pointer targets in assignment from 'char *' to 'Bytef *' {aka 'unsigned char *'} differ in signedness [-Wpointer-sign]
    my_current_job -> strm.next_in = inbin_blk ;
                                   ^
cell-counts.c: In function 'cellCounts_save_BAM_result':
cell-counts.c:3989:89: warning: statement with no effect [-Wunused-value]
   if(CELLCOUNTS_BAMBLOCK_COMP_NUMBER>1)finished_job -> task -> inbin_batch_start_offsets[1];
                                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
cell-counts.c: In function 'cellCounts_merged_45K_to_90K_sum_WRT':
cell-counts.c:4114:14: warning: unused variable 'sorted_order_p1_to_i_p1_tab' [-Wunused-variable]
  HashTable * sorted_order_p1_to_i_p1_tab = vp2[1];
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4113:14: warning: unused variable 'loaded_features' [-Wunused-variable]
  ArrayList * loaded_features = vp2[0];
              ^~~~~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_merged_write_nozero_geneids_WRT':
cell-counts.c:4149:14: warning: unused variable 'sorted_order_p1_to_i_p1_tab' [-Wunused-variable]
  HashTable * sorted_order_p1_to_i_p1_tab = tv2[1];
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function 'delete_file_thread':
cell-counts.c:4351:3: warning: implicit declaration of function 'sleep'; did you mean '_sleep'? [-Wimplicit-function-declaration]
   sleep(2);
   ^~~~~
   _sleep
cell-counts.c:4346:44: warning: '%06d' directive writing between 6 and 11 bytes into a region of size between 4 and 1003 [-Wformat-overflow=]
     sprintf(tmp_fname, "%s/temp-cellcounts-%06d-%03d.tmpbin", cct_context -> temp_file_dir, getpid(), x1);
                                            ^~~~
cell-counts.c:4346:24: note: directive argument in the range [0, 151]
     sprintf(tmp_fname, "%s/temp-cellcounts-%06d-%03d.tmpbin", cct_context -> temp_file_dir, getpid(), x1);
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4346:5: note: 'sprintf' output between 35 and 1039 bytes into a destination of size 1020
     sprintf(tmp_fname, "%s/temp-cellcounts-%06d-%03d.tmpbin", cct_context -> temp_file_dir, getpid(), x1);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_open_cellbc_batches':
cell-counts.c:1185:20: warning: '/temp-cellcounts-' directive writing 17 bytes into a region of size between 1 and 1000 [-Wformat-overflow=]
   sprintf(fname,"%s/temp-cellcounts-%06d-%03d.tmpbin",cct_context->temp_file_dir,getpid(), x1);
                    ^~~~~~~~~~~~~~~~~
cell-counts.c:1185:17: note: directive argument in the range [0, 151]
   sprintf(fname,"%s/temp-cellcounts-%06d-%03d.tmpbin",cct_context->temp_file_dir,getpid(), x1);
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:1185:3: note: 'sprintf' output between 35 and 1039 bytes into a destination of size 1000
   sprintf(fname,"%s/temp-cellcounts-%06d-%03d.tmpbin",cct_context->temp_file_dir,getpid(), x1);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_find_hits_for_mapped_section':
cell-counts.c:1456:7: warning: 'search_start' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int search_start, search_end, search_block_id;
       ^~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_save_BAM_result':
cell-counts.c:3995:122: warning: array subscript 2 is above array bounds of 'int[1]' [-Warray-bounds]
     if(outblocki < finished_job -> task -> inbin_number -1)nextoffset = finished_job -> task -> inbin_batch_start_offsets[outblocki +1];
                                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c core-bigtable.c -o core-bigtable.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c core-indel.c -o core-indel.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c core-interface-aligner.c -o core-interface-aligner.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c core-interface-subjunc.c -o core-interface-subjunc.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c core-junction.c -o core-junction.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c core.c -o core.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c detection-calls.c -o detection-calls.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c detectionCall.c -o detectionCall.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c exon-algorithms.c -o exon-algorithms.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c exon-align-indel.c -o exon-align-indel.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c exon-align.c -o exon-align.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c flattenAnnotations.c -o flattenAnnotations.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fullscan.c -o fullscan.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c fusion-align.c -o fusion-align.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c gen_rand_reads.c -o gen_rand_reads.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c gene-algorithms.c -o gene-algorithms.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c gene-value-index.c -o gene-value-index.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c hashtable.c -o hashtable.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c index-builder.c -o index-builder.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c input-blc.c -o input-blc.o
input-blc.c: In function 'cacheBCL_qualTest_BAMmode':
input-blc.c:1006:53: warning: variable 'lane_str' set but not used [-Wunused-but-set-variable]
   char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
                                                     ^~~~~~~~
input-blc.c:1006:31: warning: variable 'sample_barcode' set but not used [-Wunused-but-set-variable]
   char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
                               ^~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c input-files.c -o input-files.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c interval_merge.c -o interval_merge.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c long-hashtable.c -o long-hashtable.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c longread-mapping.c -o longread-mapping.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c mergeVCF.c -o mergeVCF.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c processExons.c -o processExons.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c propmapped.c -o propmapped.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c qualityScores.c -o qualityScores.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c read-repair.c -o read-repair.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c readSummary.c -o readSummary.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c removeDupReads.c -o removeDupReads.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sam2bed.c -o sam2bed.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sambam-file.c -o sambam-file.o
sambam-file.c: In function 'SamBam_writer_sort_bins_to_BAM':
sambam-file.c:2379:24: warning: variable 'last_written_BAI_chro' set but not used [-Wunused-but-set-variable]
  int old_chro_no = -1, last_written_BAI_chro = -1;
                        ^~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c seek-zlib.c -o seek-zlib.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sorted-hashtable.c -o sorted-hashtable.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sublog.c -o sublog.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.4\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c tx-unique.c -o tx-unique.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Rsubread.dll tmp.def HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Rsubread/00new/Rsubread/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rsubread'
    finding HTML links ... done
    RsubreadUsersGuide                      html  
    align                                   html  
    atgcContent                             html  
    buildindex                              html  
    cellCounts                              html  
    detectionCall                           html  
    detectionCallAnnotation                 html  
    exactSNP                                html  
    featureCounts                           html  
    findCommonVariants                      html  
    flattenGTF                              html  
    getInBuiltAnnotation                    html  
    processExons                            html  
    promoterRegions                         html  
    propmapped                              html  
    qualityScores                           html  
    removeDupReads                          html  
    repair                                  html  
    sam2bed                                 html  
    simReads                                html  
    sublong                                 html  
    txUnique                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rsubread)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'HDTD' is missing or broken
 done