##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rsubread.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Rsubread_2.9.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Rsubread.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rsubread/DESCRIPTION' ... OK
* this is package 'Rsubread' version '2.9.4'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rsubread' can be installed ... WARNING
Found the following significant warnings:
  cell-counts.c:4351:3: warning: implicit declaration of function 'sleep'; did you mean '_sleep'? [-Wimplicit-function-declaration]
  cell-counts.c:4346:44: warning: '%06d' directive writing between 6 and 11 bytes into a region of size between 4 and 1003 [-Wformat-overflow=]
  cell-counts.c:1185:20: warning: '/temp-cellcounts-' directive writing 17 bytes into a region of size between 1 and 1000 [-Wformat-overflow=]
  cell-counts.c:3995:122: warning: array subscript 2 is above array bounds of 'int[1]' [-Warray-bounds]
See 'D:/biocbuild/bbs-3.15-bioc/meat/Rsubread.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 37.0Mb
  sub-directories of 1Mb or more:
    annot  31.1Mb
    qualf   3.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/Rsubread/libs/x64/Rsubread.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
align      27.81   8.12   36.09
propmapped 27.67   7.66   36.02
sublong    22.50   7.18   29.64
buildindex  7.42   4.16   11.80
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/Rsubread.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rsubread
###
##############################################################################
##############################################################################


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

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