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This page was generated on 2021-09-18 12:05:52 -0400 (Sat, 18 Sep 2021).

INSTALL results for Rsubread on nebbiolo2

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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: 2021-09-17 14:50:09 -0400 (Fri, 17 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Rsubread
StartedAt: 2021-09-17 16:02:02 -0400 (Fri, 17 Sep 2021)
EndedAt: 2021-09-17 16:02:39 -0400 (Fri, 17 Sep 2021)
EllapsedTime: 36.8 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Linux.
** libs
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c LRMbase-index.c -o LRMbase-index.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c LRMchro-event.c -o LRMchro-event.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c LRMfile-io.c -o LRMfile-io.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c LRMhashtable.c -o LRMhashtable.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c LRMhelper.c -o LRMhelper.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c aligner.c -o aligner.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c atgcContent.c -o atgcContent.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c build-sam-index.c -o build-sam-index.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
cell-counts.c: In function ‘cellCounts_close_sample_SamBam_writers’:
cell-counts.c:586:7: warning: passing argument 1 of ‘free’ discards ‘volatile’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  586 |  free(gz_lock);
      |       ^~~~~~~
In file included from cell-counts.c:4:
/usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘volatile pthread_spinlock_t *’ {aka ‘volatile int *’}
  565 | extern void free (void *__ptr) __THROW;
      |                   ~~~~~~^~~~~
cell-counts.c: In function ‘cellCounts_sample_SamBam_writers_new_files’:
cell-counts.c:666:13: warning: assignment discards ‘volatile’ qualifier from pointer target type [-Wdiscarded-qualifiers]
  666 |    wtrptr[5]=gzfp_lock;
      |             ^
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]
  714 |  rv = rv || gvindex_load(&cct_context -> value_index, tmp_fname);
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                          |
      |                          gene_value_index_t (*)[1] {aka struct <anonymous> (*)[1]}
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]’}
   33 | 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]
 1033 |  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]
 1245 |  gvindex_destory(&cct_context -> value_index);
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                  |
      |                  gene_value_index_t (*)[1] {aka struct <anonymous> (*)[1]}
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]’}
   35 | 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]
 1399 |  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]
 1762 |  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]
 1738 |  int x1=0;
      |      ^~
cell-counts.c: In function ‘cellCounts_vote_and_add_count’:
cell-counts.c:1847:9: warning: assignment discards ‘volatile’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 1847 |   pps[5]=&cct_context -> fastq_unassigned_lock;
      |         ^
cell-counts.c:1804:6: warning: unused variable ‘fields’ [-Wunused-variable]
 1804 |  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]
 1906 |   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]
 1945 |  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]
 2120 |   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]
 2123 |   if(offsets[sri]!=0x77){
      |             ^
cell-counts.c:2124:26: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2124 |    *read_pos_move=offsets[sri];
      |                          ^
cell-counts.c:2132:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2132 |   if(offsets[sri]!=0x77){
      |             ^
cell-counts.c:2133:11: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2133 |    offsets[sri] -= (*read_pos_move);
      |           ^
cell-counts.c:2136:25: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2136 |     offset_cur = offsets[sri];
      |                         ^
cell-counts.c:2138:29: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2138 |    high_conf_index = offsets[sri];
      |                             ^
cell-counts.c:2140:27: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2140 |   if(offset_cur != offsets[sri] && subread0>0){
      |                           ^
cell-counts.c:2141:10: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2141 |    alnrec[toli]= subread0;
      |          ^
cell-counts.c:2145:24: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2145 |    offset_cur = offsets[sri];
      |                        ^
cell-counts.c:2153:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2153 |   if(offsets[sri]==0x77) subread0 =-1;
      |             ^
cell-counts.c:2156:11: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2156 |     alnrec[toli]= subread0;
      |           ^
cell-counts.c:2167:21: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2167 |   for(toli=0; alnrec[toli]; toli+=3){
      |                     ^
cell-counts.c:2168:51: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2168 |    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]
 2309 |   unsigned int meet_end = abs_pos + first_correct_base + indel_offset;
      |                ^~~~~~~~
cell-counts.c:2377:3: warning: #warning "============ IMPROVE THIS FORMULA AS Subread ==========" [-Wcpp]
 2377 |  #warning "============ IMPROVE THIS FORMULA AS Subread =========="
      |   ^~~~~~~
cell-counts.c:2279:6: warning: unused variable ‘indels_in_highconf’ [-Wunused-variable]
 2279 |  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]
 2404 |  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]
 2536 |   #warning "======== IGNORED SOME NEW CANDIDATE LOCATIONS BY (1) =================="
      |    ^~~~~~~
cell-counts.c:2530:7: warning: unused variable ‘subread_number_P1’ [-Wunused-variable]
 2530 |   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]
 2642 |  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]
 2641 |  unsigned int low_index_border = cct_context -> value_index -> start_base_offset;
      |               ^~~~~~~~~~~~~~~~
cell-counts.c:2629:30: warning: unused variable ‘thread_context’ [-Wunused-variable]
 2629 |  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]
 2627 |  int sqr_interval=10000;
      |      ^~~~~~~~~~~~
cell-counts.c:2621:6: warning: unused variable ‘xk1’ [-Wunused-variable]
 2621 |  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]
 3285 |    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]
 3735 |  HashTable * sorted_order_p1_to_i_p1_tab = vp2[1];
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:3734:14: warning: unused variable ‘loaded_features’ [-Wunused-variable]
 3734 |  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]
 3770 |  HashTable * sorted_order_p1_to_i_p1_tab = tv2[1];
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_run_in_thread’:
cell-counts.c:1940:1: warning: control reaches end of non-void function [-Wreturn-type]
 1940 | }
      | ^
cell-counts.c: In function ‘cellCounts_do_cellbc_batches’:
cell-counts.c:4052:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4052 |    fread(&section1_items,1, 8, input_fps[xk1]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4055:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4055 |     fread(&cellbcP0_geneno0B,1,8,input_fps[xk1]);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4056:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4056 |     fread(&umis,1,8,input_fps[xk1]);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4077:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4077 |    fread(last_rbin_buffer[xk1]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[xk1]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4079:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4079 |    fread(last_rbin_buffer[xk1] + 16+ 8*genes+ cct_context -> UMI_length + 4, 1, binlen, input_fps[xk1]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4151:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4151 |    fread(last_rbin_buffer[selected_fp_no]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[selected_fp_no]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4153:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4153 |    fread(last_rbin_buffer[selected_fp_no] + 16+ 8*genes+ cct_context -> UMI_length + 4, 1, binlen, input_fps[selected_fp_no]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4198:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4198 |   fread(&binlen, 1, 4, notmapped_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4201:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4201 |   fread(tofill -> inbin + tofill -> inbin_len, 1, binlen, notmapped_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4265:1: warning: control reaches end of non-void function [-Wreturn-type]
 4265 | }
      | ^
cell-counts.c: In function ‘cellCounts_merge_batches_worker’:
cell-counts.c:3281:66: warning: array subscript 1 is above array bounds of ‘int[1]’ [-Warray-bounds]
 3281 |    else inblock_size= current_input  -> inbin_batch_start_offsets[current_blk +1] - current_input -> inbin_batch_start_offsets[current_blk ];
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
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=]
 1176 |   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, 150]
 1176 |   sprintf(fname,"%s/temp-cellcounts-%06d-%03d.tmpbin",cct_context->temp_file_dir,getpid(), x1);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from cell-counts.c:2:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 35 and 1039 bytes into a destination of size 1000
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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]
 1446 |   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]
 3610 |   int nextoffset = finished_job -> task -> inbin_batch_start_offsets[1];
      |                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
cell-counts.c:3628:73: warning: array subscript 1 is above array bounds of ‘int[1]’ [-Warray-bounds]
 3628 |    else inblock_size = finished_job -> task -> inbin_batch_start_offsets[outblocki +1] -  finished_job -> task -> inbin_batch_start_offsets[outblocki];
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cell-counts.c:3616:122: warning: array subscript 2 is above array bounds of ‘int[1]’ [-Warray-bounds]
 3616 |     if(outblocki < finished_job -> task -> inbin_number -1)nextoffset = finished_job -> task -> inbin_batch_start_offsets[outblocki +1];
      |                                                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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=]
 3974 |     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, 150]
 3974 |     sprintf(tmp_fname, "%s/temp-cellcounts-%06d-%03d.tmpbin", cct_context -> temp_file_dir, getpid(), x1);
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from cell-counts.c:2:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 35 and 1039 bytes into a destination of size 1020
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c detectionCall.c -o detectionCall.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c exon-align-indel.c -o exon-align-indel.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c exon-align.c -o exon-align.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c fusion-align.c -o fusion-align.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #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]
 1007 |   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]
 1007 |   char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
      |                               ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c interval_merge.c -o interval_merge.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c longread-mapping.c -o longread-mapping.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c processExons.c -o processExons.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -c sam2bed.c -o sam2bed.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
sambam-file.c:1930: warning: "MAX_ALLOWED_GAP_IN_BAI_CHUNK" redefined
 1930 | #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
  258 | #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]
 2379 |  int old_chro_no = -1, last_written_BAI_chro = -1;;
      |                        ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #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]
   31 | #warning "REMOVE '- 69' NEXT LINE "
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.7.3\""  -fpic  -g -O2  -Wall -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]
  205 | #warning "============ ADD '-21' from next line  ================"
      |  ^~~~~~~
subread.h:207:2: warning: #warning "============ ADD '-13' from next line  ================" [-Wcpp]
  207 | #warning "============ ADD '-13' from next line  ================"
      |  ^~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-Rsubread/00new/Rsubread/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Rsubread.Rnw’ 
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rsubread)