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This page was generated on 2022-01-21 11:06:36 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Rsubread on nebbiolo1


To the developers/maintainers of the Rsubread package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rsubread.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1659/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 2.9.1  (landing page)
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/Rsubread
git_branch: master
git_last_commit: 3f9f1ee
git_last_commit_date: 2021-12-16 17:33:52 -0500 (Thu, 16 Dec 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rsubread
Version: 2.9.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Rsubread_2.9.1.tar.gz
StartedAt: 2022-01-20 20:50:40 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 20:53:22 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 162.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: Rsubread.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Rsubread_2.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘2.9.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Rsubread’ can be installed ... WARNING
Found the following significant warnings:
  cell-counts.c:4429:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  cell-counts.c:4432:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  cell-counts.c:4433:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  cell-counts.c:4454:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  cell-counts.c:4456:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  cell-counts.c:4528:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  cell-counts.c:4530:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  cell-counts.c:4575:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  cell-counts.c:4578:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  cell-counts.c:3647:66: warning: array subscript 1 is above array bounds of ‘int[1]’ [-Warray-bounds]
  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:4007:73: warning: array subscript 1 is above array bounds of ‘int[1]’ [-Warray-bounds]
  cell-counts.c:3995:122: warning: array subscript 2 is above array bounds of ‘int[1]’ [-Warray-bounds]
  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=]
See ‘/home/biocbuild/bbs-3.15-bioc/meat/Rsubread.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 20.5Mb
  sub-directories of 1Mb or more:
    annot  14.1Mb
    libs    2.7Mb
    qualf   2.3Mb
* 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 ... NOTE
.extract.sample.table.cols: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
* 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 is not available
* 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
propmapped 24.896 15.272  40.466
align      23.682 15.419  39.371
sublong    21.403  7.446  28.890
buildindex  7.403  2.830  10.518
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/Rsubread.Rcheck/00check.log’
for details.



Installation output

Rsubread.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL Rsubread
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ The operating system is Linux.
** libs
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c HelperFunctions.c -o HelperFunctions.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c LRMbase-index.c -o LRMbase-index.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c LRMchro-event.c -o LRMchro-event.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c LRMfile-io.c -o LRMfile-io.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c LRMhashtable.c -o LRMhashtable.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c LRMhelper.c -o LRMhelper.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c LRMseek-zlib.c -o LRMseek-zlib.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c R_wrapper.c -o R_wrapper.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c RsimReads.c -o RsimReads.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c SNPCalling.c -o SNPCalling.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c aligner.c -o aligner.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c atgcContent.c -o atgcContent.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c build-sam-index.c -o build-sam-index.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -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]
 1042 |  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]
 1752 |  int x1=0;
      |      ^~
cell-counts.c: In function ‘cellCounts_vote_and_add_count’:
cell-counts.c:1818:6: warning: unused variable ‘fields’ [-Wunused-variable]
 1818 |  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]
 1970 |  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]
 2067 |  int lockret2=cellCounts_lock_release(&cct_context -> input_dataset_lock);
      |      ^~~~~~~~
cell-counts.c:2053:6: warning: unused variable ‘lockret1’ [-Wunused-variable]
 2053 |  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]
 2156 |   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]
 2159 |   if(offsets[sri]!=0x77){
      |             ^
cell-counts.c:2160:26: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2160 |    *read_pos_move=offsets[sri];
      |                          ^
cell-counts.c:2168:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2168 |   if(offsets[sri]!=0x77){
      |             ^
cell-counts.c:2169:11: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2169 |    offsets[sri] -= (*read_pos_move);
      |           ^
cell-counts.c:2172:25: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2172 |     offset_cur = offsets[sri];
      |                         ^
cell-counts.c:2174:29: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2174 |    high_conf_index = offsets[sri];
      |                             ^
cell-counts.c:2176:27: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2176 |   if(offset_cur != offsets[sri] && subread0>0){
      |                           ^
cell-counts.c:2177:10: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2177 |    alnrec[toli]= subread0;
      |          ^
cell-counts.c:2181:24: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2181 |    offset_cur = offsets[sri];
      |                        ^
cell-counts.c:2189:13: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2189 |   if(offsets[sri]==0x77) subread0 =-1;
      |             ^
cell-counts.c:2192:11: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2192 |     alnrec[toli]= subread0;
      |           ^
cell-counts.c:2203:21: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2203 |   for(toli=0; alnrec[toli]; toli+=3){
      |                     ^
cell-counts.c:2204:51: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2204 |    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]
 2345 |   unsigned int meet_end = abs_pos + first_correct_base + indel_offset;
      |                ^~~~~~~~
cell-counts.c:2315:6: warning: unused variable ‘indels_in_highconf’ [-Wunused-variable]
 2315 |  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]
 2437 |  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]
 2600 |   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]
 2722 |   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]
 2881 |  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]
 2880 |  unsigned int low_index_border = cct_context -> value_index -> start_base_offset;
      |               ^~~~~~~~~~~~~~~~
cell-counts.c:2868:30: warning: unused variable ‘thread_context’ [-Wunused-variable]
 2868 |  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]
 2866 |  int sqr_interval=10000;
      |      ^~~~~~~~~~~~
cell-counts.c:2860:6: warning: unused variable ‘xk1’ [-Wunused-variable]
 2860 |  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]
 3028 |     int building_rbin_offset = 0, read_text_rev_offset =0;
      |         ^~~~~~~~~~~~~~~~~~~~
cell-counts.c:2988:15: warning: unused variable ‘high_index_border’ [-Wunused-variable]
 2988 |  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]
 2987 |  unsigned int low_index_border = cct_context -> value_index -> start_base_offset;
      |               ^~~~~~~~~~~~~~~~
cell-counts.c:2971:6: warning: unused variable ‘sqr_interval’ [-Wunused-variable]
 2971 |  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]
 3651 |    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]
 3989 |   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]
 4114 |  HashTable * sorted_order_p1_to_i_p1_tab = vp2[1];
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4113:14: warning: unused variable ‘loaded_features’ [-Wunused-variable]
 4113 |  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]
 4149 |  HashTable * sorted_order_p1_to_i_p1_tab = tv2[1];
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_do_cellbc_batches’:
cell-counts.c:4429:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4429 |    fread(&section1_items,1, 8, input_fps[xk1]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4432:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4432 |     fread(&cellbcP0_geneno0B,1,8,input_fps[xk1]);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4433:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4433 |     fread(&umis,1,8,input_fps[xk1]);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4454:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4454 |    fread(last_rbin_buffer[xk1]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[xk1]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4456:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4456 |    fread(last_rbin_buffer[xk1] + 16+ 8*genes+ cct_context -> UMI_length + 4, 1, binlen, input_fps[xk1]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4528:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4528 |    fread(last_rbin_buffer[selected_fp_no]+16, 1, 8*genes+ cct_context -> UMI_length + 4, input_fps[selected_fp_no]);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4530:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4530 |    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:4575:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4575 |   fread(&binlen, 1, 4, notmapped_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c:4578:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 4578 |   fread(tofill -> inbin + tofill -> inbin_len, 1, binlen, notmapped_fp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_merge_batches_worker’:
cell-counts.c:3647:66: warning: array subscript 1 is above array bounds of ‘int[1]’ [-Warray-bounds]
 3647 |    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:1185:20: warning: ‘/temp-cellcounts-’ directive writing 17 bytes into a region of size between 1 and 1000 [-Wformat-overflow=]
 1185 |   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, 150]
 1185 |   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:1456:7: warning: ‘search_start’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 1456 |   int search_start, search_end, search_block_id;
      |       ^~~~~~~~~~~~
cell-counts.c: In function ‘cellCounts_save_BAM_result’:
cell-counts.c:4007:73: warning: array subscript 1 is above array bounds of ‘int[1]’ [-Warray-bounds]
 4007 |    else inblock_size = finished_job -> task -> inbin_batch_start_offsets[outblocki +1] -  finished_job -> task -> inbin_batch_start_offsets[outblocki];
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cell-counts.c:3995:122: warning: array subscript 2 is above array bounds of ‘int[1]’ [-Warray-bounds]
 3995 |     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:4346:44: warning: ‘%06d’ directive writing between 6 and 11 bytes into a region of size between 4 and 1003 [-Wformat-overflow=]
 4346 |     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, 150]
 4346 |     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-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c core-bigtable.c -o core-bigtable.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c core-indel.c -o core-indel.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c core-interface-aligner.c -o core-interface-aligner.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c core-interface-subjunc.c -o core-interface-subjunc.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c core-junction.c -o core-junction.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c core.c -o core.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c detection-calls.c -o detection-calls.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c detectionCall.c -o detectionCall.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c detectionCallAnnotation.c -o detectionCallAnnotation.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c exon-algorithms.c -o exon-algorithms.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c exon-align-indel.c -o exon-align-indel.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c exon-align.c -o exon-align.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c flattenAnnotations.c -o flattenAnnotations.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c fullscan.c -o fullscan.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c fusion-align.c -o fusion-align.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c gen_rand_reads.c -o gen_rand_reads.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c gene-algorithms.c -o gene-algorithms.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c gene-value-index.c -o gene-value-index.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c hashtable.c -o hashtable.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c index-builder.c -o index-builder.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -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]
 1006 |   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]
 1006 |   char *cell_barcode = NULL, *sample_barcode=NULL, *lane_str=NULL;
      |                               ^~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c input-files.c -o input-files.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c interval_merge.c -o interval_merge.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c long-hashtable.c -o long-hashtable.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c longread-mapping.c -o longread-mapping.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c mergeVCF.c -o mergeVCF.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c processExons.c -o processExons.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c propmapped.c -o propmapped.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c qualityScores.c -o qualityScores.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c read-repair.c -o read-repair.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c readSummary.c -o readSummary.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c removeDupReads.c -o removeDupReads.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c sam2bed.c -o sam2bed.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -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]
 2379 |  int old_chro_no = -1, last_written_BAI_chro = -1;
      |                        ^~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c seek-zlib.c -o seek-zlib.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c sorted-hashtable.c -o sorted-hashtable.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c sublog.c -o sublog.o
gcc -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.9.1\""  -fpic  -g -O2  -Wall -c tx-unique.c -o tx-unique.o
gcc -shared -L/home/biocbuild/bbs-3.15-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-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-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
** 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)

Tests output


Example timings

Rsubread.Rcheck/Rsubread-Ex.timings

nameusersystemelapsed
align23.68215.41939.371
buildindex 7.403 2.83010.518
featureCounts0.0010.0000.001
findCommonVariants0.0000.0000.001
getInBuiltAnnotation0.3070.0780.390
promoterRegions0.9530.0290.988
propmapped24.89615.27240.466
qualityScores0.0430.0080.052
simReads0.0000.0000.001
sublong21.403 7.44628.890