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This page was generated on 2021-09-20 12:05:23 -0400 (Mon, 20 Sep 2021).

INSTALL results for Rsubread on riesling1

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raw results

Package 1623/2029HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 2.7.3  (landing page)
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2021-09-19 14:50:04 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/Rsubread
git_branch: master
git_last_commit: d345cca
git_last_commit_date: 2021-09-10 01:05:57 -0400 (Fri, 10 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: Rsubread
Version: 2.7.3
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Rsubread_2.7.3.tar.gz && rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.7.3.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Rsubread_2.7.3.zip && rm Rsubread_2.7.3.tar.gz Rsubread_2.7.3.zip
StartedAt: 2021-09-19 16:26:00 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 16:29:07 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 187.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Rsubread_2.7.3.tar.gz && rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsubread.buildbin-libdir Rsubread_2.7.3.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Rsubread_2.7.3.zip && rm Rsubread_2.7.3.tar.gz Rsubread_2.7.3.zip
###
##############################################################################
##############################################################################


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100 10.4M  100 10.4M    0     0  16.4M      0 --:--:-- --:--:-- --:--:-- 16.4M

install for i386

* installing *source* package 'Rsubread' ...
** using staged installation
@@@@@ The operating system is Windows.
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c HelperFunctions.c -o HelperFunctions.o
In file included from HelperFunctions.c:56:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from HelperFunctions.c:59:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMbase-index.c -o LRMbase-index.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMchro-event.c -o LRMchro-event.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMfile-io.c -o LRMfile-io.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMhashtable.c -o LRMhashtable.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMhelper.c -o LRMhelper.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMseek-zlib.c -o LRMseek-zlib.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_wrapper.c -o R_wrapper.o
In file included from HelperFunctions.h:24,
                 from R_wrapper.c:35:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RsimReads.c -o RsimReads.o
In file included from RsimReads.c:21:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c SNPCalling.c -o SNPCalling.o
In file included from SNPCalling.c:33:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from SNPCalling.c:36:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c aligner.c -o aligner.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c atgcContent.c -o atgcContent.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c build-sam-index.c -o build-sam-index.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c cell-counts.c -o cell-counts.o
In file included from cell-counts.c:9:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from cell-counts.c:10:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
cell-counts.c: In function 'cellCounts_load_base_value_indexes':
cell-counts.c:714:26: warning: passing argument 1 of 'gvindex_load' from incompatible pointer type [-Wincompatible-pointer-types]
  rv = rv || gvindex_load(&cct_context -> value_index, tmp_fname);
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from sorted-hashtable.h:27,
                 from gene-algorithms.h:25,
                 from cell-counts.c:10:
gene-value-index.h:33:39: note: expected 'gene_value_index_t *' {aka 'struct <anonymous> *'} but argument is of type 'gene_value_index_t (*)[1]' {aka 'struct <anonymous> (*)[1]'}
 int gvindex_load(gene_value_index_t * index, const char filename []);
                  ~~~~~~~~~~~~~~~~~~~~~^~~~~
cell-counts.c: In function 'cellCounts_sort_feature_info':
cell-counts.c:1033:6: warning: unused variable 'curr_chro_number' [-Wunused-variable]
  int curr_chro_number = 0;
      ^~~~~~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_destroy_context':
cell-counts.c:1245:18: warning: passing argument 1 of 'gvindex_destory' from incompatible pointer type [-Wincompatible-pointer-types]
  gvindex_destory(&cct_context -> value_index);
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from sorted-hashtable.h:27,
                 from gene-algorithms.h:25,
                 from cell-counts.c:10:
gene-value-index.h:35:43: note: expected 'gene_value_index_t *' {aka 'struct <anonymous> *'} but argument is of type 'gene_value_index_t (*)[1]' {aka 'struct <anonymous> (*)[1]'}
 void gvindex_destory(gene_value_index_t * index);
                      ~~~~~~~~~~~~~~~~~~~~~^~~~~
cell-counts.c: In function 'cellCounts_calculate_pos_weight':
cell-counts.c:1399:8: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  while(nch = *(cigar++)){
        ^~~
cell-counts.c: In function 'cellCounts_parallel_gzip_writer_add_read_fqs_scRNA':
cell-counts.c:1762:2: warning: implicit declaration of function 'parallel_gzip_writer_add_text_qual'; did you mean 'parallel_gzip_writer_add_text'? [-Wimplicit-function-declaration]
  parallel_gzip_writer_add_text_qual(outR1fp,R1qual, R1len,thread_no);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  parallel_gzip_writer_add_text
cell-counts.c:1738:6: warning: unused variable 'x1' [-Wunused-variable]
  int x1=0;
      ^~
cell-counts.c: In function 'cellCounts_vote_and_add_count':
cell-counts.c:1804:6: 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_write_read_in_batch_bin':
cell-counts.c:1906:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   for(nchi=0; nch= thread_context -> reporting_cigars[reporting_index][nchi]; nchi++){
               ^~~
cell-counts.c: In function 'cellCounts_prepare_context_for_align':
cell-counts.c:1945:30: 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_indel_recorder_copy':
cell-counts.c:2120:17: 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:2123:13: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offsets[sri]!=0x77){
             ^
cell-counts.c:2124:26: warning: array subscript has type 'char' [-Wchar-subscripts]
    *read_pos_move=offsets[sri];
                          ^
cell-counts.c:2132:13: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offsets[sri]!=0x77){
             ^
cell-counts.c:2133:11: warning: array subscript has type 'char' [-Wchar-subscripts]
    offsets[sri] -= (*read_pos_move);
           ^
cell-counts.c:2136:25: warning: array subscript has type 'char' [-Wchar-subscripts]
     offset_cur = offsets[sri];
                         ^
cell-counts.c:2138:29: warning: array subscript has type 'char' [-Wchar-subscripts]
    high_conf_index = offsets[sri];
                             ^
cell-counts.c:2140:27: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offset_cur != offsets[sri] && subread0>0){
                           ^
cell-counts.c:2141:10: warning: array subscript has type 'char' [-Wchar-subscripts]
    alnrec[toli]= subread0;
          ^
cell-counts.c:2145:24: warning: array subscript has type 'char' [-Wchar-subscripts]
    offset_cur = offsets[sri];
                        ^
cell-counts.c:2153:13: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offsets[sri]==0x77) subread0 =-1;
             ^
cell-counts.c:2156:11: warning: array subscript has type 'char' [-Wchar-subscripts]
     alnrec[toli]= subread0;
           ^
cell-counts.c:2167:21: warning: array subscript has type 'char' [-Wchar-subscripts]
   for(toli=0; alnrec[toli]; toli+=3){
                     ^
cell-counts.c:2168:51: 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:2309:16: warning: unused variable 'meet_end' [-Wunused-variable]
   unsigned int meet_end = abs_pos + first_correct_base + indel_offset;
                ^~~~~~~~
cell-counts.c:2377:3: warning: #warning "============ IMPROVE THIS FORMULA AS Subread ==========" [-Wcpp]
  #warning "============ IMPROVE THIS FORMULA AS Subread =========="
   ^~~~~~~
cell-counts.c:2279:6: 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:2404:18: 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:2536:4: warning: #warning "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) ==================" [-Wcpp]
   #warning "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) =================="
    ^~~~~~~
cell-counts.c:2530:7: 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:2642:15: 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:2641:15: warning: unused variable 'low_index_border' [-Wunused-variable]
  unsigned int low_index_border = cct_context -> value_index -> start_base_offset;
               ^~~~~~~~~~~~~~~~
cell-counts.c:2629:30: warning: unused variable 'thread_context' [-Wunused-variable]
  cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
                              ^~~~~~~~~~~~~~
cell-counts.c:2627:6: warning: unused variable 'sqr_interval' [-Wunused-variable]
  int sqr_interval=10000;
      ^~~~~~~~~~~~
cell-counts.c:2621:6: warning: unused variable 'xk1' [-Wunused-variable]
  int xk1;
      ^~~
cell-counts.c: In function 'cellCounts_merge_batches_worker':
cell-counts.c:3285:35: 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_merged_45K_to_90K_sum_WRT':
cell-counts.c:3735:14: 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:3734:14: 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:3770:14: 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:3979:3: warning: implicit declaration of function 'sleep'; did you mean '_sleep'? [-Wimplicit-function-declaration]
   sleep(2);
   ^~~~~
   _sleep
cell-counts.c: In function 'cellCounts_run_in_thread':
cell-counts.c:1940:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
cell-counts.c: In function 'cellCounts_do_cellbc_batches':
cell-counts.c:4265:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
cell-counts.c: In function 'delete_file_thread':
cell-counts.c:3974:44: 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:3974:24: 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:3974:5: 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:1176:20: 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:1176:17: 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:1176:3: 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:1446:7: 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:3610:69: warning: array subscript 1 is above array bounds of 'int[1]' [-Warray-bounds]
   int nextoffset = finished_job -> task -> inbin_batch_start_offsets[1];
                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
cell-counts.c:3616:122: 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/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-bigtable.c -o core-bigtable.o
In file included from core.h:46,
                 from core-bigtable.c:12:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from core-bigtable.h:7,
                 from core-bigtable.c:13:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-indel.c -o core-indel.o
In file included from HelperFunctions.h:24,
                 from core-indel.c:28:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-value-index.h:25,
                 from core-indel.c:29:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-interface-aligner.c -o core-interface-aligner.o
In file included from core-interface-aligner.c:7:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-interface-subjunc.c -o core-interface-subjunc.o
In file included from core-interface-subjunc.c:7:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-junction.c -o core-junction.o
In file included from core-junction.c:25:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-value-index.h:25,
                 from core-junction.c:27:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core.c -o core.o
In file included from core.c:45:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from core.c:50:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c detection-calls.c -o detection-calls.o
In file included from detection-calls.c:8:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from detection-calls.c:12:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c detectionCall.c -o detectionCall.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exon-algorithms.c -o exon-algorithms.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exon-align-indel.c -o exon-align-indel.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exon-align.c -o exon-align.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flattenAnnotations.c -o flattenAnnotations.o
In file included from flattenAnnotations.c:41:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from flattenAnnotations.c:44:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fullscan.c -o fullscan.o
In file included from fullscan.c:26:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-value-index.h:25,
                 from fullscan.c:27:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fusion-align.c -o fusion-align.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gen_rand_reads.c -o gen_rand_reads.o
In file included from gen_rand_reads.c:26:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from gen_rand_reads.c:31:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gene-algorithms.c -o gene-algorithms.o
In file included from gene-algorithms.c:36:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from gene-algorithms.c:38:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gene-value-index.c -o gene-value-index.o
In file included from gene-value-index.h:24,
                 from gene-value-index.c:25:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-value-index.h:25,
                 from gene-value-index.c:25:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hashtable.c -o hashtable.o
In file included from core.h:46,
                 from hashtable.c:18:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c index-builder.c -o index-builder.o
In file included from gene-value-index.h:24,
                 from index-builder.c:31:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-value-index.h:25,
                 from index-builder.c:31:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c input-blc.c -o input-blc.o
In file included from input-blc.c:7:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from input-blc.c:10:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
input-blc.c: In function 'cacheBCL_qualTest_BAMmode':
input-blc.c:1007:53: 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:1007:31: warning: variable 'sample_barcode' set but not used [-Wunused-but-set-variable]
   char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
                               ^~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c input-files.c -o input-files.o
In file included from input-files.h:23,
                 from input-files.c:35:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from input-files.c:41:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
input-files.c: In function 'SAM_nosort_run_once':
input-files.c:5338:23: warning: argument 1 value '4294967295' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
   char * header_txt = malloc(max(1000000,pairer->BAM_l_text));
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from input-files.c:24:
C:/rtools40/mingw32/i686-w64-mingw32/include/stdlib.h:457:17: note: in a call to allocation function 'malloc' declared here
   void *__cdecl malloc(size_t _Size);
                 ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c interval_merge.c -o interval_merge.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c long-hashtable.c -o long-hashtable.o
In file included from core.h:46,
                 from long-hashtable.c:31:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
long-hashtable.c: In function 'lnhash_create':
long-hashtable.c:46:46: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '8589934592' to '0' [-Woverflow]
   the_table -> key_repeated_numbers = malloc(sizeof(short) * 0x100000000llu);
                                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c longread-mapping.c -o longread-mapping.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mergeVCF.c -o mergeVCF.o
In file included from mergeVCF.c:7:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from mergeVCF.c:10:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c processExons.c -o processExons.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c propmapped.c -o propmapped.o
In file included from propmapped.c:34:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from propmapped.c:39:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c qualityScores.c -o qualityScores.o
In file included from qualityScores.c:27:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c read-repair.c -o read-repair.o
In file included from read-repair.c:6:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c readSummary.c -o readSummary.o
In file included from readSummary.c:41:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from readSummary.c:44:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
readSummary.c: In function 'scRNA_find_gene_to_umi_mark_deletee':
readSummary.c:5761:43: warning: right shift count >= width of type [-Wshift-count-overflow]
     int cellno = ( key_bc_umi_p1-NULL-1 ) >> 32;
                                           ^~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c removeDupReads.c -o removeDupReads.o
In file included from removeDupReads.c:27:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sam2bed.c -o sam2bed.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sambam-file.c -o sambam-file.o
In file included from sambam-file.c:33:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from sambam-file.c:36:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
sambam-file.c:1930: warning: "MAX_ALLOWED_GAP_IN_BAI_CHUNK" redefined
 #define MAX_ALLOWED_GAP_IN_BAI_CHUNK 5 // the number of blocks, not the file positions.
 
In file included from core.h:47,
                 from sambam-file.c:34:
sambam-file.h:258: note: this is the location of the previous definition
 #define MAX_ALLOWED_GAP_IN_BAI_CHUNK 10  // 10 blocks
 
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/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c seek-zlib.c -o seek-zlib.o
In file included from core.h:46,
                 from seek-zlib.c:2:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from seek-zlib.c:5:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sorted-hashtable.c -o sorted-hashtable.o
In file included from sorted-hashtable.h:25,
                 from sorted-hashtable.c:20:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from sorted-hashtable.c:20:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sublog.c -o sublog.o
In file included from sublog.c:26:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c tx-unique.c -o tx-unique.o
In file included from tx-unique.h:4,
                 from tx-unique.c:6:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
C:/rtools40/mingw32/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/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/Rsubread.buildbin-libdir/00LOCK-Rsubread/00new/Rsubread/libs/i386
** 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
   'Rsubread.Rnw' 
** 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

install for x64

* installing *source* package 'Rsubread' ...
@@@@@ The operating system is Windows.
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c HelperFunctions.c -o HelperFunctions.o
In file included from HelperFunctions.c:56:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from HelperFunctions.c:59:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMbase-index.c -o LRMbase-index.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMchro-event.c -o LRMchro-event.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMfile-io.c -o LRMfile-io.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMhashtable.c -o LRMhashtable.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMhelper.c -o LRMhelper.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMseek-zlib.c -o LRMseek-zlib.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_wrapper.c -o R_wrapper.o
In file included from HelperFunctions.h:24,
                 from R_wrapper.c:35:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RsimReads.c -o RsimReads.o
In file included from RsimReads.c:21:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c SNPCalling.c -o SNPCalling.o
In file included from SNPCalling.c:33:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from SNPCalling.c:36:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c aligner.c -o aligner.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c atgcContent.c -o atgcContent.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c build-sam-index.c -o build-sam-index.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c cell-counts.c -o cell-counts.o
In file included from cell-counts.c:9:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from cell-counts.c:10:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
cell-counts.c: In function 'cellCounts_load_base_value_indexes':
cell-counts.c:714:26: warning: passing argument 1 of 'gvindex_load' from incompatible pointer type [-Wincompatible-pointer-types]
  rv = rv || gvindex_load(&cct_context -> value_index, tmp_fname);
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from sorted-hashtable.h:27,
                 from gene-algorithms.h:25,
                 from cell-counts.c:10:
gene-value-index.h:33:39: note: expected 'gene_value_index_t *' {aka 'struct <anonymous> *'} but argument is of type 'gene_value_index_t (*)[1]' {aka 'struct <anonymous> (*)[1]'}
 int gvindex_load(gene_value_index_t * index, const char filename []);
                  ~~~~~~~~~~~~~~~~~~~~~^~~~~
cell-counts.c: In function 'cellCounts_sort_feature_info':
cell-counts.c:1033:6: warning: unused variable 'curr_chro_number' [-Wunused-variable]
  int curr_chro_number = 0;
      ^~~~~~~~~~~~~~~~
cell-counts.c: In function 'cellCounts_destroy_context':
cell-counts.c:1245:18: warning: passing argument 1 of 'gvindex_destory' from incompatible pointer type [-Wincompatible-pointer-types]
  gvindex_destory(&cct_context -> value_index);
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from sorted-hashtable.h:27,
                 from gene-algorithms.h:25,
                 from cell-counts.c:10:
gene-value-index.h:35:43: note: expected 'gene_value_index_t *' {aka 'struct <anonymous> *'} but argument is of type 'gene_value_index_t (*)[1]' {aka 'struct <anonymous> (*)[1]'}
 void gvindex_destory(gene_value_index_t * index);
                      ~~~~~~~~~~~~~~~~~~~~~^~~~~
cell-counts.c: In function 'cellCounts_calculate_pos_weight':
cell-counts.c:1399:8: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  while(nch = *(cigar++)){
        ^~~
cell-counts.c: In function 'cellCounts_parallel_gzip_writer_add_read_fqs_scRNA':
cell-counts.c:1762:2: warning: implicit declaration of function 'parallel_gzip_writer_add_text_qual'; did you mean 'parallel_gzip_writer_add_text'? [-Wimplicit-function-declaration]
  parallel_gzip_writer_add_text_qual(outR1fp,R1qual, R1len,thread_no);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  parallel_gzip_writer_add_text
cell-counts.c:1738:6: warning: unused variable 'x1' [-Wunused-variable]
  int x1=0;
      ^~
cell-counts.c: In function 'cellCounts_vote_and_add_count':
cell-counts.c:1804:6: 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_write_read_in_batch_bin':
cell-counts.c:1906:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   for(nchi=0; nch= thread_context -> reporting_cigars[reporting_index][nchi]; nchi++){
               ^~~
cell-counts.c: In function 'cellCounts_prepare_context_for_align':
cell-counts.c:1945:30: 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_indel_recorder_copy':
cell-counts.c:2120:17: 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:2123:13: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offsets[sri]!=0x77){
             ^
cell-counts.c:2124:26: warning: array subscript has type 'char' [-Wchar-subscripts]
    *read_pos_move=offsets[sri];
                          ^
cell-counts.c:2132:13: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offsets[sri]!=0x77){
             ^
cell-counts.c:2133:11: warning: array subscript has type 'char' [-Wchar-subscripts]
    offsets[sri] -= (*read_pos_move);
           ^
cell-counts.c:2136:25: warning: array subscript has type 'char' [-Wchar-subscripts]
     offset_cur = offsets[sri];
                         ^
cell-counts.c:2138:29: warning: array subscript has type 'char' [-Wchar-subscripts]
    high_conf_index = offsets[sri];
                             ^
cell-counts.c:2140:27: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offset_cur != offsets[sri] && subread0>0){
                           ^
cell-counts.c:2141:10: warning: array subscript has type 'char' [-Wchar-subscripts]
    alnrec[toli]= subread0;
          ^
cell-counts.c:2145:24: warning: array subscript has type 'char' [-Wchar-subscripts]
    offset_cur = offsets[sri];
                        ^
cell-counts.c:2153:13: warning: array subscript has type 'char' [-Wchar-subscripts]
   if(offsets[sri]==0x77) subread0 =-1;
             ^
cell-counts.c:2156:11: warning: array subscript has type 'char' [-Wchar-subscripts]
     alnrec[toli]= subread0;
           ^
cell-counts.c:2167:21: warning: array subscript has type 'char' [-Wchar-subscripts]
   for(toli=0; alnrec[toli]; toli+=3){
                     ^
cell-counts.c:2168:51: 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:2309:16: warning: unused variable 'meet_end' [-Wunused-variable]
   unsigned int meet_end = abs_pos + first_correct_base + indel_offset;
                ^~~~~~~~
cell-counts.c:2377:3: warning: #warning "============ IMPROVE THIS FORMULA AS Subread ==========" [-Wcpp]
  #warning "============ IMPROVE THIS FORMULA AS Subread =========="
   ^~~~~~~
cell-counts.c:2279:6: 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:2404:18: 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:2536:4: warning: #warning "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) ==================" [-Wcpp]
   #warning "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) =================="
    ^~~~~~~
cell-counts.c:2530:7: 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:2642:15: 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:2641:15: warning: unused variable 'low_index_border' [-Wunused-variable]
  unsigned int low_index_border = cct_context -> value_index -> start_base_offset;
               ^~~~~~~~~~~~~~~~
cell-counts.c:2629:30: warning: unused variable 'thread_context' [-Wunused-variable]
  cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no;
                              ^~~~~~~~~~~~~~
cell-counts.c:2627:6: warning: unused variable 'sqr_interval' [-Wunused-variable]
  int sqr_interval=10000;
      ^~~~~~~~~~~~
cell-counts.c:2621:6: warning: unused variable 'xk1' [-Wunused-variable]
  int xk1;
      ^~~
cell-counts.c: In function 'cellCounts_merge_batches_worker':
cell-counts.c:3285:35: 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_merged_45K_to_90K_sum_WRT':
cell-counts.c:3735:14: 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:3734:14: 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:3770:14: 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:3979:3: warning: implicit declaration of function 'sleep'; did you mean '_sleep'? [-Wimplicit-function-declaration]
   sleep(2);
   ^~~~~
   _sleep
cell-counts.c: In function 'cellCounts_run_in_thread':
cell-counts.c:1940:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
cell-counts.c: In function 'cellCounts_do_cellbc_batches':
cell-counts.c:4265:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
cell-counts.c: In function 'delete_file_thread':
cell-counts.c:3974:44: 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:3974:24: 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:3974:5: 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:1176:20: 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:1176:17: 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:1176:3: 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:1446:7: 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:3610:69: warning: array subscript 1 is above array bounds of 'int[1]' [-Warray-bounds]
   int nextoffset = finished_job -> task -> inbin_batch_start_offsets[1];
                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
cell-counts.c:3616:122: 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-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-bigtable.c -o core-bigtable.o
In file included from core.h:46,
                 from core-bigtable.c:12:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from core-bigtable.h:7,
                 from core-bigtable.c:13:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-indel.c -o core-indel.o
In file included from HelperFunctions.h:24,
                 from core-indel.c:28:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-value-index.h:25,
                 from core-indel.c:29:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-interface-aligner.c -o core-interface-aligner.o
In file included from core-interface-aligner.c:7:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-interface-subjunc.c -o core-interface-subjunc.o
In file included from core-interface-subjunc.c:7:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core-junction.c -o core-junction.o
In file included from core-junction.c:25:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-value-index.h:25,
                 from core-junction.c:27:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c core.c -o core.o
In file included from core.c:45:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from core.c:50:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c detection-calls.c -o detection-calls.o
In file included from detection-calls.c:8:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from detection-calls.c:12:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c detectionCall.c -o detectionCall.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exon-algorithms.c -o exon-algorithms.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exon-align-indel.c -o exon-align-indel.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c exon-align.c -o exon-align.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c flattenAnnotations.c -o flattenAnnotations.o
In file included from flattenAnnotations.c:41:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from flattenAnnotations.c:44:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fullscan.c -o fullscan.o
In file included from fullscan.c:26:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-value-index.h:25,
                 from fullscan.c:27:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c fusion-align.c -o fusion-align.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gen_rand_reads.c -o gen_rand_reads.o
In file included from gen_rand_reads.c:26:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from gen_rand_reads.c:31:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gene-algorithms.c -o gene-algorithms.o
In file included from gene-algorithms.c:36:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from gene-algorithms.c:38:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gene-value-index.c -o gene-value-index.o
In file included from gene-value-index.h:24,
                 from gene-value-index.c:25:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-value-index.h:25,
                 from gene-value-index.c:25:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c hashtable.c -o hashtable.o
In file included from core.h:46,
                 from hashtable.c:18:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c index-builder.c -o index-builder.o
In file included from gene-value-index.h:24,
                 from index-builder.c:31:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-value-index.h:25,
                 from index-builder.c:31:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c input-blc.c -o input-blc.o
In file included from input-blc.c:7:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from input-blc.c:10:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
input-blc.c: In function 'cacheBCL_qualTest_BAMmode':
input-blc.c:1007:53: 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:1007:31: 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-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c input-files.c -o input-files.o
In file included from input-files.h:23,
                 from input-files.c:35:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from input-files.c:41:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c interval_merge.c -o interval_merge.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c long-hashtable.c -o long-hashtable.o
In file included from core.h:46,
                 from long-hashtable.c:31:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c longread-mapping.c -o longread-mapping.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mergeVCF.c -o mergeVCF.o
In file included from mergeVCF.c:7:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from mergeVCF.c:10:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c processExons.c -o processExons.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c propmapped.c -o propmapped.o
In file included from propmapped.c:34:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from propmapped.c:39:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c qualityScores.c -o qualityScores.o
In file included from qualityScores.c:27:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c read-repair.c -o read-repair.o
In file included from read-repair.c:6:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c readSummary.c -o readSummary.o
In file included from readSummary.c:41:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from readSummary.c:44:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c removeDupReads.c -o removeDupReads.o
In file included from removeDupReads.c:27:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sam2bed.c -o sam2bed.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sambam-file.c -o sambam-file.o
In file included from sambam-file.c:33:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from sambam-file.c:36:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
sambam-file.c:1930: warning: "MAX_ALLOWED_GAP_IN_BAI_CHUNK" redefined
 #define MAX_ALLOWED_GAP_IN_BAI_CHUNK 5 // the number of blocks, not the file positions.
 
In file included from core.h:47,
                 from sambam-file.c:34:
sambam-file.h:258: note: this is the location of the previous definition
 #define MAX_ALLOWED_GAP_IN_BAI_CHUNK 10  // 10 blocks
 
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-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c seek-zlib.c -o seek-zlib.o
In file included from core.h:46,
                 from seek-zlib.c:2:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from gene-algorithms.h:25,
                 from seek-zlib.c:5:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sorted-hashtable.c -o sorted-hashtable.o
In file included from sorted-hashtable.h:25,
                 from sorted-hashtable.c:20:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
In file included from sorted-hashtable.c:20:
sorted-hashtable.h:31:2: warning: #warning "REMOVE '- 69' NEXT LINE " [-Wcpp]
 #warning "REMOVE '- 69' NEXT LINE "
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sublog.c -o sublog.o
In file included from sublog.c:26:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\"" -D_FILE_OFFSET_BITS=64    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c tx-unique.c -o tx-unique.o
In file included from tx-unique.h:4,
                 from tx-unique.c:6:
subread.h:205:2: warning: #warning "============ ADD '-21' from next line  ================" [-Wcpp]
 #warning "============ ADD '-21' from next line  ================"
  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
 #warning "============ ADD '-13' from next line  ================"
  ^~~~~~~
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-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsubread' as Rsubread_2.7.3.zip
* DONE (Rsubread)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'Rsubread' successfully unpacked and MD5 sums checked